chrom1 start1 end1 chrom2 start2 end2 name type split span gene1 gene2 comment chr10 26219090 26219092 chrX 139017963 139017973 TCGA-KK-A8IK BND 17 21 GAD2 FGF13 chr10 44379703 44379707 chrX 616477 616481 TCGA-KK-A8IK BND 10 26 CXCL12 * chr14 82279343 82279343 chrX 11935249 11935249 TCGA-KK-A8IK BND 15 35 * * chr2 202715337 202715346 chrX 80215135 80215147 TCGA-KK-A8IK BND 22 17 FAM117B * chr3 107980964 107980965 chrX 139017963 139017973 TCGA-KK-A8IK BND 19 45 * FGF13 chrX 368696 368698 chrX 369943 369945 TCGA-KK-A8IK INV 50 14 PPP2R3B PPP2R3B chrX 616265 616265 chrX 617020 617020 TCGA-KK-A8IK INV 38 41 * * chrX 66236038 66236038 chrX 66257020 66257020 TCGA-KK-A8IK DEL 3 38 HEPH HEPH chrX 66851442 66851443 chrX 66958018 66958019 TCGA-KK-A8IK DUP 28 47 * * chrX 81588737 81588742 chrX 81588737 81588742 TCGA-KK-A8IK INS 33 4 * * chrX 87788930 87788933 chrX 87789052 87789052 TCGA-KK-A8IK DEL 9 5 * * chr10 74951334 74951347 chrX 53909245 53909258 TCGA-CH-5737 BND 13 40 KAT6B * chr10 92823451 92823453 chrX 33431228 33431230 TCGA-CH-5737 BND 10 16 * * chr11 5880367 5881041 chrX 148895691 148896153 TCGA-CH-5737 BND 11 6 TRIM5 AFF2 chr15 47014474 47014474 chrX 96962350 96962350 TCGA-CH-5737 BND 13 39 * DIAPH2 chr19 12012257 12012258 chrX 66573835 66573836 TCGA-CH-5737 BND 36 2 ZNF433-AS1 * chr2 53878474 53878482 chrX 88715165 88715173 TCGA-CH-5737 BND 49 44 PSME4 * chr5 163583886 163583886 chrX 40211110 40211110 TCGA-CH-5737 BND 37 13 * * chrX 100537140 100537563 chrX 100537988 100538261 TCGA-CH-5737 DEL 1 31 * * chrX 103494011 103494011 chrX 103494309 103494309 TCGA-CH-5737 DEL 3 41 * * chrX 114100471 114100473 chrX 114100794 114100794 TCGA-CH-5737 DEL 30 23 * * chrX 118515953 118515954 chrX 118516176 118516176 TCGA-CH-5737 DEL 36 38 DOCK11 DOCK11 chrX 123546511 123546511 chrX 123546602 123546602 TCGA-CH-5737 DEL 26 34 * * chrX 135387181 135387181 chrX 144259230 144259240 TCGA-CH-5737 INV 18 8 * * chrX 143002883 143002885 chrX 143003276 143003276 TCGA-CH-5737 DEL 33 29 * * chrX 144259230 144259240 chrX 144259230 144259240 TCGA-CH-5737 INS 43 22 * * chrX 144259230 144259240 chrX 144262222 144262222 TCGA-CH-5737 DEL 6 31 * * chrX 149294732 149294732 chrX 149296345 149296345 TCGA-CH-5737 DEL 25 46 * * chrX 23299089 23299089 chrX 23299376 23299376 TCGA-CH-5737 DEL 7 34 * * chrX 46423878 46423880 chrX 46424118 46424118 TCGA-CH-5737 DEL 19 47 * * chrX 65670878 65670878 chrX 65671179 65671179 TCGA-CH-5737 DEL 30 5 MSN MSN chrX 81932199 81932199 chrX 81932251 81932251 TCGA-CH-5737 DEL 9 30 * * chr4 68261053 68261683 chrX 73624374 73624815 TCGA-G9-6333 BND 6 22 * CHIC1 chrX 129431459 129431459 chrX 129431559 129431559 TCGA-G9-6333 DEL 8 46 * * chrX 24693873 24693873 chrX 24693934 24693934 TCGA-G9-6333 DEL 4 34 POLA1 POLA1 chrX 3996445 3996445 chrX 3996557 3996557 TCGA-G9-6333 DEL 5 12 * * chrX 52460639 52461099 chrX 52586948 52587688 TCGA-G9-6333 DEL 49 37 * * chrX 53073920 53073920 chrX 53074213 53074213 TCGA-G9-6333 DEL 37 19 GPR173 GPR173 chrX 57393723 57393724 chrX 67900259 67900260 TCGA-G9-6333 DUP 40 32 FAAH2 * chr11 19618726 19619187 chrX 82104296 82104604 TCGA-EJ-5531 BND 14 17 NAV2 * chr13 71028718 71029049 chrX 78215873 78216264 TCGA-EJ-5531 BND 23 25 LINC00348 * chr16 3915503 3915506 chrX 77430962 77430965 TCGA-EJ-5531 BND 7 31 * * chr16 3916185 3916188 chrX 77430701 77430704 TCGA-EJ-5531 BND 1 14 * * chr16 57858924 57858924 chrX 19885833 19885833 TCGA-EJ-5531 BND 5 4 KIFC3 SH3KBP1 chr16 66832283 66832284 chrX 48934051 48934052 TCGA-EJ-5531 BND 32 20 NAE1 OTUD5 chr1 37155725 37155729 chrX 11783587 11783591 TCGA-EJ-5531 BND 45 22 * * chr22 36267478 36267481 chrX 154522409 154522412 TCGA-EJ-5531 BND 50 38 APOL1 * chr2 14502974 14502975 chrX 79986754 79986755 TCGA-EJ-5531 BND 31 18 * * chr5 126267205 126267206 chrX 87392063 87392064 TCGA-EJ-5531 BND 2 44 AC116362.1 * chr5 25161129 25161131 chrX 86111163 86111165 TCGA-EJ-5531 BND 44 25 LINC02228 * chr6 56098034 56098034 chrX 83878431 83878431 TCGA-EJ-5531 BND 28 42 COL21A1 CYLC1 chr6 83145154 83145154 chrX 87024848 87024848 TCGA-EJ-5531 BND 48 5 DOP1A * chr9 88845223 88845223 chrX 53722535 53722535 TCGA-EJ-5531 BND 2 21 * * chrX 117494884 117494885 chrX 117519576 117519577 TCGA-EJ-5531 DEL 47 40 * * chrX 117652748 117652751 chrX 118344489 118344492 TCGA-EJ-5531 DEL 22 47 * * chrX 140531584 140531584 chrX 140566850 140566850 TCGA-EJ-5531 INV 16 1 * * chrX 140544217 140544217 chrX 141747795 141747795 TCGA-EJ-5531 INV 47 20 * * chrX 140578410 140578410 chrX 141809970 141809970 TCGA-EJ-5531 INV 44 15 * * chrX 153186747 153186751 chrX 153190683 153190687 TCGA-EJ-5531 INV 48 31 * * chrX 154506296 154506298 chrX 154552976 154552978 TCGA-EJ-5531 DUP 9 1 FAM3A IKBKG chrX 249414 249453 chrX 249475 249475 TCGA-EJ-5531 DEL 45 41 * * chrX 38357273 38357274 chrX 38357776 38357776 TCGA-EJ-5531 DEL 44 23 AF241726.1 AF241726.1 chrX 47999011 47999011 chrX 47999491 47999491 TCGA-EJ-5531 DEL 34 25 ZNF81 ZNF81 chrX 62764201 62764201 chrX 62764859 62764859 TCGA-EJ-5531 DEL 49 48 * * chrX 64602178 64602178 chrX 64603336 64603336 TCGA-EJ-5531 DEL 33 20 * * chrX 66736019 66736019 chrX 66944550 66944550 TCGA-EJ-5531 DUP 16 15 * * chrX 66837803 66837803 chrX 66939545 66939555 TCGA-EJ-5531 DUP 10 21 * * chrX 66864436 66864437 chrX 69277005 69277006 TCGA-EJ-5531 DUP 48 5 * * chrX 72165490 72165492 chrX 72166362 72166364 TCGA-EJ-5531 INV 8 37 * * chrX 77256531 77256932 chrX 131466741 131467469 TCGA-EJ-5531 INV 2 47 * IGSF1 chrX 90773100 90773832 chrY 4355376 4355735 TCGA-EJ-5531 BND 21 44 * * chrX 91473964 91473965 chrX 94225501 94225502 TCGA-EJ-5531 INV 30 8 * * chrX 93158701 93158701 chrX 94523963 94523963 TCGA-EJ-5531 INV 18 26 * * chrX 94542167 94542167 chrX 94542291 94542291 TCGA-EJ-5531 DEL 35 27 * * chr10 87868176 87868178 chrX 1077161 1077163 TCGA-EJ-7330 BND 21 28 PTEN * chr11 133016321 133016321 chrX 57036162 57036162 TCGA-EJ-7330 BND 22 26 OPCML * chr11 133030944 133030945 chrX 69390631 69390632 TCGA-EJ-7330 BND 6 12 OPCML * chr11 133344319 133344319 chrX 66885562 66885562 TCGA-EJ-7330 BND 30 50 OPCML * chr12 78220633 78220636 chrX 67736925 67736928 TCGA-EJ-7330 BND 23 12 * * chr15 55303854 55303854 chrX 42285701 42285701 TCGA-EJ-7330 BND 17 34 RAB27A AL023875.1 chr1 54917208 54917209 chrX 87941978 87941979 TCGA-EJ-7330 BND 38 15 * * chr1 54917677 54917677 chrX 87939837 87939837 TCGA-EJ-7330 BND 18 46 * * chr1 80501766 80501769 chrX 67232097 67232100 TCGA-EJ-7330 BND 29 24 * * chr2 77438281 77438285 chrX 11713696 11713700 TCGA-EJ-7330 BND 20 21 LRRTM4 AC004554.1 chr3 82347711 82347724 chrX 11714310 11714322 TCGA-EJ-7330 BND 13 9 LINC02008 AC004554.1 chr3 82347711 82347724 chrX 11714577 11714586 TCGA-EJ-7330 BND 35 33 LINC02008 AC004554.1 chr4 117669650 117669663 chrX 122528487 122528500 TCGA-EJ-7330 BND 17 31 LINC01378 * chr4 19078853 19078855 chrX 87512959 87512961 TCGA-EJ-7330 BND 2 1 * * chrX 100016737 100016738 chrX 114942001 114942002 TCGA-EJ-7330 DEL 34 38 * * chrX 138521831 138521845 chrX 138521831 138521845 TCGA-EJ-7330 INS 2 36 * * chrX 21270614 21270630 chrX 21270614 21270630 TCGA-EJ-7330 INS 2 30 AL807742.1 AL807742.1 chrX 22398264 22398271 chrX 22398264 22398271 TCGA-EJ-7330 INS 10 10 PTCHD1-AS PTCHD1-AS chrX 29598163 29598163 chrX 29651430 29651430 TCGA-EJ-7330 DEL 23 36 IL1RAPL1 IL1RAPL1 chrX 30689819 30689822 chrX 30689933 30689933 TCGA-EJ-7330 DEL 42 26 GK GK chrX 31741443 31741445 chrX 31826045 31826047 TCGA-EJ-7330 DEL 16 29 DMD DMD chrX 35346242 35346242 chrX 35346538 35346538 TCGA-EJ-7330 DEL 13 22 * * chrX 56634984 56634988 chrX 56635378 56635382 TCGA-EJ-7330 INV 11 18 * * chrX 57040074 57040076 chrX 66886347 66886349 TCGA-EJ-7330 DUP 36 21 * * chrX 57040417 57040418 chrX 69387495 69387496 TCGA-EJ-7330 INV 38 23 * * chrX 66158189 66158193 chrX 66161692 66161696 TCGA-EJ-7330 INV 13 41 * HEPH chrX 66209391 66209396 chrX 66210857 66210862 TCGA-EJ-7330 INV 17 38 HEPH HEPH chrX 66393875 66393875 chrX 66477652 66477652 TCGA-EJ-7330 DUP 18 4 * * chrX 66461266 66461269 chrX 70819920 70819923 TCGA-EJ-7330 DEL 4 1 * TEX11 chrX 66813436 66813437 chrX 66824037 66824038 TCGA-EJ-7330 INV 27 6 * * chrX 66815318 66815320 chrX 66920224 66920226 TCGA-EJ-7330 DUP 33 20 * * chrX 66861170 66861172 chrX 66863259 66863261 TCGA-EJ-7330 INV 38 30 * * chrX 67232097 67232100 chrX 67860148 67860148 TCGA-EJ-7330 INV 40 48 * * chrX 7004058 7004059 chrX 7117322 7117323 TCGA-EJ-7330 DEL 40 8 * PUDP chrX 70672680 70672683 chrX 70815036 70815039 TCGA-EJ-7330 DEL 38 42 TEX11 TEX11 chrX 73601248 73601250 chrX 73601337 73601337 TCGA-EJ-7330 DEL 4 39 CHIC1 CHIC1 chrX 7805431 7805433 chrX 11713472 11713476 TCGA-EJ-7330 DEL 6 39 * AC004554.1 chrX 903846 903849 chrX 912438 912441 TCGA-EJ-7330 INV 44 36 * * chr13 33987554 33987556 chrX 66886717 66886719 TCGA-XK-AAJ3 BND 27 41 * * chr14 45045638 45045638 chrX 23780126 23780126 TCGA-XK-AAJ3 BND 45 3 TOGARAM1 AC131011.1 chr22 12702922 12702944 chrX 44139809 44139831 TCGA-XK-AAJ3 BND 25 46 * * chrX 100537042 100537566 chrX 100537972 100538258 TCGA-XK-AAJ3 DEL 16 17 * * chrX 66819046 66819048 chrX 66924381 66924383 TCGA-XK-AAJ3 DUP 11 21 * * chrX 66874553 66874557 chrX 66939545 66939555 TCGA-XK-AAJ3 DUP 28 42 * * chrX 66886717 66886719 chrX 66927988 66927990 TCGA-XK-AAJ3 DUP 38 38 * * chrX 77739086 77739087 chrX 77761831 77761832 TCGA-XK-AAJ3 DEL 38 34 ATRX ATRX chr11 49154731 49154732 chrX 22489401 22489402 TCGA-EJ-5510 BND 38 37 FOLH1 PTCHD1-AS chr11 49158472 49158476 chrX 23687582 23687586 TCGA-EJ-5510 BND 16 1 FOLH1 * chr12 106209781 106210214 chrX 141252034 141252411 TCGA-EJ-5510 BND 42 32 * * chr14 97918878 97919318 chrX 11714534 11714896 TCGA-EJ-5510 BND 15 40 * AC004554.1 chr14 97919189 97919189 chrX 11714373 11714423 TCGA-EJ-5510 BND 16 15 * AC004554.1 chr16 59201888 59202357 chrX 11714072 11714437 TCGA-EJ-5510 BND 15 12 * AC004554.1 chr16 59202092 59202549 chrX 11714505 11714895 TCGA-EJ-5510 BND 9 3 * AC004554.1 chr16 59202257 59202260 chrX 11714258 11714261 TCGA-EJ-5510 BND 32 34 * AC004554.1 chrX 137979491 137979492 chrX 139471580 139471581 TCGA-EJ-5510 DEL 38 9 Z96074.1 * chrX 137992282 137992282 chrX 142880681 142880681 TCGA-EJ-5510 DUP 49 20 * * chrX 138069297 138069298 chrX 142887701 142887702 TCGA-EJ-5510 DEL 22 9 * * chrX 148300971 148301016 chrX 148348125 148348170 TCGA-EJ-5510 DUP 26 25 * * chrX 20189831 20189832 chrX 23697040 23697041 TCGA-EJ-5510 DEL 20 10 RPS6KA3 * chrX 2197061 2197064 chrX 48672810 48672813 TCGA-EJ-5510 INV 48 29 * * chrX 38028824 38028827 chrX 54151674 54151677 TCGA-EJ-5510 INV 28 48 AF241726.1 FAM120C chrX 38481221 38481222 chrX 54179131 54179132 TCGA-EJ-5510 INV 15 29 AF241726.1 FAM120C chrX 38481954 38481956 chrX 57922447 57922449 TCGA-EJ-5510 INV 40 37 AF241726.1 * chrX 66794596 66794596 chrX 67033515 67033515 TCGA-EJ-5510 DUP 25 48 * * chrX 84091226 84091226 chrX 87650404 87650404 TCGA-EJ-5510 DEL 20 46 RPS6KA6 KLHL4 chrX 84125119 84125119 chrX 86097151 86097151 TCGA-EJ-5510 DUP 34 31 RPS6KA6 * chrX 84577959 84577959 chrX 87973450 87973450 TCGA-EJ-5510 INV 3 34 * * chrX 85104140 85104140 chrX 85545027 85545027 TCGA-EJ-5510 INV 35 30 SATL1 * chrX 85190532 85190533 chrX 85193470 85193471 TCGA-EJ-5510 DEL 15 12 SATL1 SATL1 chrX 85241193 85241193 chrX 86182336 86182336 TCGA-EJ-5510 DEL 48 25 SATL1 DACH2 chrX 85258970 85258970 chrX 86125235 86125235 TCGA-EJ-5510 INV 15 27 ZNF711 * chrX 85544963 85544963 chrX 87767125 87767125 TCGA-EJ-5510 DEL 35 28 * * chrX 85616476 85616476 chrX 86171171 86171171 TCGA-EJ-5510 INV 42 26 * DACH2 chrX 85629759 85629759 chrX 87289853 87289853 TCGA-EJ-5510 INV 24 6 * * chrX 86477539 86477539 chrX 88042209 88042209 TCGA-EJ-5510 DEL 26 30 DACH2 * chrX 87067428 87067429 chrX 87766398 87766399 TCGA-EJ-5510 DUP 3 43 * * chrX 87264500 87264504 chrX 87631371 87631375 TCGA-EJ-5510 INV 38 46 * KLHL4 chrX 87688259 87688265 chrX 87688550 87688556 TCGA-EJ-5510 DUP 26 6 * * chrX 97326094 97326095 chrX 97328351 97328352 TCGA-EJ-5510 DEL 2 28 DIAPH2 DIAPH2 chr12 23787244 23787244 chrX 66325665 66325665 TCGA-G9-6338 BND 31 47 SOX5 * chr13 92704173 92704173 chrX 66303157 66303157 TCGA-G9-6338 BND 39 38 GPC5 * chr16 15141357 15141359 chrX 68133371 68133373 TCGA-G9-6338 BND 46 35 PKD1P6 OPHN1 chr16 15143255 15143257 chrX 68237272 68237274 TCGA-G9-6338 BND 34 48 PKD1P6 OPHN1 chr16 1750681 1750682 chrX 68129489 68129490 TCGA-G9-6338 BND 20 20 MAPK8IP3 OPHN1 chr16 18200236 18200241 chrX 69596291 69596296 TCGA-G9-6338 BND 31 23 AC008785.1 * chr16 3987403 3987403 chrX 65700141 65700141 TCGA-G9-6338 BND 40 31 ADCY9 MSN chr22 36130766 36130767 chrX 92459762 92459763 TCGA-G9-6338 BND 31 22 * PCDH11X chr4 112207297 112207316 chrX 118280073 118280092 TCGA-G9-6338 BND 6 2 * AL391358.1 chr8 138227962 138227967 chrX 120065339 120065339 TCGA-G9-6338 BND 13 40 FAM135B RHOXF1-AS1 chrX 108664525 108664527 chrX 108664525 108664527 TCGA-G9-6338 INS 10 23 COL4A5 COL4A5 chrX 119806381 119806382 chrX 119806642 119806643 TCGA-G9-6338 DUP 42 24 UPF3B UPF3B chrX 125933495 125933495 chrX 129451219 129451219 TCGA-G9-6338 INV 47 33 * SMARCA1 chrX 126252223 126252225 chrX 127253925 127253927 TCGA-G9-6338 INV 2 27 * * chrX 126262014 126262016 chrX 127783400 127783402 TCGA-G9-6338 INV 46 30 * * chrX 127773581 127773581 chrX 129434233 129434233 TCGA-G9-6338 INV 43 7 * * chrX 66303226 66303227 chrX 75863589 75863590 TCGA-G9-6338 DEL 18 3 * * chrX 66325053 66325055 chrX 75863559 75863561 TCGA-G9-6338 INV 37 22 * * chrX 66597596 66597599 chrX 69597450 69597453 TCGA-G9-6338 DEL 33 8 EDA2R * chrX 66686929 66686930 chrX 67032745 67032746 TCGA-G9-6338 INV 47 7 * * chrX 66781205 66781210 chrX 66930906 66930911 TCGA-G9-6338 DUP 24 18 * * chrX 66881868 66881868 chrX 66886231 66886231 TCGA-G9-6338 INV 39 25 * * chrX 66897159 66897160 chrX 67078462 67078463 TCGA-G9-6338 DUP 1 26 * * chrX 67030217 67030221 chrX 67053245 67053249 TCGA-G9-6338 INV 1 44 * * chrX 67632967 67632970 chrX 67636451 67636454 TCGA-G9-6338 INV 3 15 AR AR chrX 68129936 68129938 chrX 69605842 69605844 TCGA-G9-6338 DUP 27 8 OPHN1 * chrX 68201063 68201063 chrX 68202717 68202717 TCGA-G9-6338 INV 44 14 OPHN1 OPHN1 chrX 68239897 68239899 chrX 68240760 68240762 TCGA-G9-6338 INV 33 44 OPHN1 OPHN1 chrX 68393205 68393208 chrX 68395528 68395531 TCGA-G9-6338 INV 38 46 OPHN1 OPHN1 chrX 69627631 69627633 chrX 69630240 69630242 TCGA-G9-6338 INV 3 49 EDA EDA chrX 87593955 87593955 chrX 87636320 87636320 TCGA-G9-6338 DEL 49 6 KLHL4 KLHL4 chrX 88179470 88179475 chrX 89386594 89386599 TCGA-G9-6338 DEL 25 14 * * chrX 88238393 88238394 chrX 126214802 126214803 TCGA-G9-6338 INV 3 9 * * chrX 89356368 89356368 chrX 91880169 91880169 TCGA-G9-6338 INV 48 18 * PCDH11X chrX 89589400 89589405 chrX 126897999 126898004 TCGA-G9-6338 DEL 8 10 * * chrX 89590728 89590730 chrX 90411971 90411973 TCGA-G9-6338 INV 48 47 * * chrX 89789329 89789332 chrX 89820192 89820195 TCGA-G9-6338 DEL 46 33 * * chrX 90350576 90350578 chrX 126878990 126878992 TCGA-G9-6338 INV 17 44 * * chrX 91328551 91328551 chrX 126188107 126188107 TCGA-G9-6338 INV 33 1 * * chrX 91360733 91360733 chrX 125917882 125917882 TCGA-G9-6338 DUP 26 16 * * chrX 91587889 91587890 chrX 127705146 127705147 TCGA-G9-6338 DEL 2 25 * * chrX 91639354 91639354 chrX 91904714 91904714 TCGA-G9-6338 INV 25 27 * PCDH11X chrX 91661188 91661188 chrX 91662420 91662420 TCGA-G9-6338 DEL 48 19 * * chr11 19618672 19619242 chrX 82104291 82104602 TCGA-4L-AA1F BND 35 28 NAV2 * chr12 102661847 102661853 chrX 91671578 91671584 TCGA-4L-AA1F BND 14 11 * * chr12 104391169 104391169 chrX 80191135 80191135 TCGA-4L-AA1F BND 35 43 * * chr12 104407493 104407494 chrX 66617277 66617278 TCGA-4L-AA1F BND 41 42 * EDA2R chr12 105090515 105090515 chrX 94543526 94543526 TCGA-4L-AA1F BND 29 26 * * chr12 105807225 105807226 chrX 95141531 95141532 TCGA-4L-AA1F BND 46 38 * * chr12 110755393 110755394 chrX 85153433 85153434 TCGA-4L-AA1F BND 13 25 * SATL1 chr12 111102843 111102843 chrX 66146768 66146768 TCGA-4L-AA1F BND 3 3 CUX2 * chr12 116419063 116419063 chrX 82158094 82158094 TCGA-4L-AA1F BND 39 37 * * chr12 117824971 117824974 chrX 94016109 94016112 TCGA-4L-AA1F BND 11 5 KSR2 * chr12 117825330 117825331 chrX 94016914 94016915 TCGA-4L-AA1F BND 9 14 KSR2 * chr12 117825516 117825518 chrX 94019670 94019672 TCGA-4L-AA1F BND 10 25 KSR2 * chr12 118932920 118932920 chrX 91467180 91467180 TCGA-4L-AA1F BND 20 15 * * chr12 129040479 129040480 chrX 11713174 11713178 TCGA-4L-AA1F BND 9 6 * AC004554.1 chr12 26070586 26070587 chrX 15758206 15758207 TCGA-4L-AA1F BND 10 33 RASSF8 CA5B chr12 92113226 92113226 chrX 95265202 95265202 TCGA-4L-AA1F BND 7 1 LINC01619 * chr12 92616550 92616550 chrX 92770571 92770571 TCGA-4L-AA1F BND 38 35 * TUSC2P2 chr12 95508230 95508237 chrX 66351304 66351311 TCGA-4L-AA1F BND 38 31 METAP2 * chr12 97664935 97664935 chrX 86159181 86159181 TCGA-4L-AA1F BND 6 8 * DACH2 chr12 99565360 99565361 chrX 65892095 65892096 TCGA-4L-AA1F BND 24 15 ANKS1B * chr14 45778691 45778691 chrX 66391146 66391146 TCGA-4L-AA1F BND 23 29 * * chr14 46305905 46305907 chrX 66419413 66419415 TCGA-4L-AA1F BND 27 32 LINC00871 * chr16 46786285 46786285 chrX 126251700 126251700 TCGA-4L-AA1F BND 46 44 MYLK3 * chr16 47033671 47033672 chrX 78938302 78938303 TCGA-4L-AA1F BND 40 35 AC018845.1 * chr16 49000116 49000119 chrX 58062043 58062046 TCGA-4L-AA1F BND 5 9 * * chr16 50977900 50977902 chrX 95008056 95008058 TCGA-4L-AA1F BND 20 21 * * chr16 6634381 6634381 chrX 34589645 34589645 TCGA-4L-AA1F BND 6 2 RBFOX1 * chr16 6647283 6647284 chrX 34566985 34566986 TCGA-4L-AA1F BND 2 7 RBFOX1 * chr18 21197665 21197668 chrX 98439940 98439943 TCGA-4L-AA1F BND 29 11 * * chr18 23256734 23256736 chrX 98440608 98440610 TCGA-4L-AA1F BND 4 12 CABLES1 * chr1 199883802 199883806 chrX 84700359 84700363 TCGA-4L-AA1F BND 23 38 * * chr2 108867227 108867227 chrX 140405720 140405720 TCGA-4L-AA1F BND 36 5 CCDC138 * chr4 85137708 85137711 chrX 119965204 119965207 TCGA-4L-AA1F BND 8 8 * RHOXF1P3 chr5 151891757 151891760 chrX 11713964 11713967 TCGA-4L-AA1F BND 30 41 GLRA1 AC004554.1 chr7 120401425 120401429 chrX 11714373 11714423 TCGA-4L-AA1F BND 8 35 KCND2 AC004554.1 chr8 63507818 63507821 chrX 11714494 11714502 TCGA-4L-AA1F BND 29 30 * AC004554.1 chr9 6946720 6946721 chrX 67983929 67983930 TCGA-4L-AA1F BND 20 8 KDM4C * chr9 8230413 8230414 chrX 23313588 23313589 TCGA-4L-AA1F BND 30 30 * * chrX 100024697 100024697 chrX 102923906 102923906 TCGA-4L-AA1F INV 10 20 * * chrX 102912466 102912469 chrX 125114182 125114185 TCGA-4L-AA1F INV 37 2 * * chrX 124780275 124780276 chrX 139234238 139234239 TCGA-4L-AA1F DUP 50 16 TENM1 * chrX 140528309 140528309 chrX 140800093 140800093 TCGA-4L-AA1F DEL 49 22 * * chrX 151063885 151063887 chrX 151063999 151063999 TCGA-4L-AA1F DEL 26 35 * * chrX 155524711 155524714 chrX 155525008 155525008 TCGA-4L-AA1F DEL 36 2 TMLHE-AS1 TMLHE-AS1 chrX 19174897 19174915 chrX 19175120 19175125 TCGA-4L-AA1F INV 46 9 * * chrX 19175162 19175162 chrX 19175359 19175359 TCGA-4L-AA1F DEL 21 5 * * chrX 19178239 19178240 chrX 65658717 65658718 TCGA-4L-AA1F DEL 50 3 * MSN chrX 27925804 27925804 chrX 27925918 27925918 TCGA-4L-AA1F DEL 4 32 * * chrX 28364688 28364688 chrX 80191135 80191135 TCGA-4L-AA1F DUP 8 24 * * chrX 30322995 30322996 chrX 34424531 34424532 TCGA-4L-AA1F INV 46 46 * * chrX 34588867 34588874 chrX 34589240 34589247 TCGA-4L-AA1F INV 18 47 * * chrX 41561679 41561681 chrX 41561732 41561732 TCGA-4L-AA1F DEL 8 10 CASK CASK chrX 49164592 49164597 chrX 49164704 49164704 TCGA-4L-AA1F DEL 5 14 MAGIX MAGIX chrX 5194198 5194198 chrX 5194901 5194901 TCGA-4L-AA1F DEL 38 14 * * chrX 58061884 58061893 chrX 58063635 58063644 TCGA-4L-AA1F DUP 7 40 * * chrX 63677865 63677865 chrX 68673807 68673807 TCGA-4L-AA1F INV 13 33 ARHGEF9 STARD8 chrX 64861983 64861983 chrX 64862388 64862388 TCGA-4L-AA1F INV 1 1 * * chrX 65005004 65005005 chrX 65005978 65005978 TCGA-4L-AA1F DEL 33 34 ZC4H2 ZC4H2 chrX 65474850 65474850 chrX 69520304 69520304 TCGA-4L-AA1F DUP 46 16 ZC3H12B FAM155B chrX 65633271 65633275 chrX 68155211 68155215 TCGA-4L-AA1F INV 37 3 MSN OPHN1 chrX 65890678 65890679 chrX 68405159 68405160 TCGA-4L-AA1F INV 13 16 * OPHN1 chrX 66076416 66076418 chrX 83488804 83488806 TCGA-4L-AA1F INV 18 37 EIF4BP9 * chrX 66191979 66191980 chrX 67397671 67397672 TCGA-4L-AA1F INV 16 45 HEPH * chrX 66474858 66474861 chrX 66476586 66476589 TCGA-4L-AA1F INV 42 23 * * chrX 66857628 66857629 chrX 67759772 67759773 TCGA-4L-AA1F DEL 34 21 * * chrX 66977441 66977442 chrX 67843585 67843586 TCGA-4L-AA1F INV 48 29 * * chrX 67253702 67253702 chrX 69156659 69156659 TCGA-4L-AA1F DUP 46 42 * * chrX 67802459 67802459 chrX 67805191 67805191 TCGA-4L-AA1F INV 44 44 * * chrX 67968453 67968453 chrX 76985119 76985119 TCGA-4L-AA1F INV 29 48 * MIR325HG chrX 68355140 68355141 chrX 68356205 68356206 TCGA-4L-AA1F INV 1 19 OPHN1 OPHN1 chrX 68406925 68406925 chrX 90056751 90056751 TCGA-4L-AA1F DEL 41 39 OPHN1 * chrX 68539696 68539696 chrX 85544924 85544924 TCGA-4L-AA1F INV 3 40 RNU6-245P * chrX 68893721 68893723 chrX 91229771 91229773 TCGA-4L-AA1F INV 27 26 * * chrX 68894040 68894040 chrX 70736865 70736865 TCGA-4L-AA1F DEL 13 30 * TEX11 chrX 69428229 69428229 chrX 85659267 85659267 TCGA-4L-AA1F INV 14 27 * * chrX 71284530 71284530 chrX 74201224 74201224 TCGA-4L-AA1F DEL 12 31 NONO FTX chrX 71285128 71285129 chrX 84201360 84201361 TCGA-4L-AA1F INV 3 29 NONO * chrX 71286632 71286633 chrX 71288851 71288852 TCGA-4L-AA1F INV 27 24 NONO NONO chrX 75871620 75871621 chrX 85667373 85667374 TCGA-4L-AA1F DUP 47 47 * * chrX 75920627 75920629 chrX 76312197 76312199 TCGA-4L-AA1F DUP 43 30 * * chrX 76397230 76397233 chrX 76398934 76398937 TCGA-4L-AA1F INV 24 50 * * chrX 76579419 76579419 chrX 76598690 76598690 TCGA-4L-AA1F DUP 34 36 * * chrX 78415448 78415448 chrX 126102806 126102806 TCGA-4L-AA1F DEL 16 16 * * chrX 84632217 84632218 chrX 93331227 93331228 TCGA-4L-AA1F DEL 40 10 * * chrX 85520601 85520603 chrX 86146731 86146733 TCGA-4L-AA1F INV 16 45 * * chrX 85521028 85521030 chrX 85544710 85544720 TCGA-4L-AA1F INV 10 28 * * chrX 85521028 85521030 chrX 85545064 85545069 TCGA-4L-AA1F INV 11 41 * * chrX 85521858 85521858 chrX 87302019 87302019 TCGA-4L-AA1F DEL 2 21 * * chrX 85544281 85544287 chrX 87304859 87304865 TCGA-4L-AA1F DUP 34 20 * * chrX 85544710 85544720 chrX 87304859 87304865 TCGA-4L-AA1F INV 4 47 * * chrX 85544812 85544815 chrX 85545064 85545069 TCGA-4L-AA1F DEL 22 14 * * chrX 85545064 85545069 chrX 87304307 87304307 TCGA-4L-AA1F INV 31 4 * * chrX 86140238 86140238 chrX 87304859 87304865 TCGA-4L-AA1F DEL 18 41 * * chrX 86174227 86174228 chrX 86552966 86552967 TCGA-4L-AA1F INV 24 27 DACH2 DACH2 chrX 94016505 94016506 chrX 94019697 94019698 TCGA-4L-AA1F DEL 48 38 * * chrX 94016552 94016555 chrX 94018523 94018526 TCGA-4L-AA1F INV 21 14 * * chrX 94016552 94016555 chrX 94016576 94016576 TCGA-4L-AA1F INS 39 25 * * chrX 94016665 94016665 chrX 94018021 94018021 TCGA-4L-AA1F DEL 26 10 * * chrX 94019195 94019199 chrX 94065364 94065368 TCGA-4L-AA1F DUP 18 12 * * chrX 98436950 98436950 chrX 125655836 125655836 TCGA-4L-AA1F DUP 34 31 * * chr11 19618907 19618931 chrX 82104275 82104299 TCGA-TP-A8TV BND 16 31 NAV2 * chr13 32253265 32253844 chrX 11934532 11934919 TCGA-TP-A8TV BND 42 25 FRY * chr13 32253631 32253631 chrX 11935013 11935072 TCGA-TP-A8TV BND 9 36 FRY * chr18 47352586 47353040 chrX 69834751 69835594 TCGA-TP-A8TV BND 6 22 MIR4527HG EDA chr1 149589644 149589648 chrX 69614684 69614688 TCGA-TP-A8TV BND 27 37 * EDA chr1 150774318 150774318 chrX 69610407 69610407 TCGA-TP-A8TV BND 49 6 * * chr1 151210105 151210106 chrX 69613913 69613914 TCGA-TP-A8TV BND 31 49 PIP5K1A * chr22 46101681 46101682 chrX 30326353 30326354 TCGA-TP-A8TV BND 37 48 MIRLET7BHG * chr6 72055826 72055828 chrX 141426632 141426634 TCGA-TP-A8TV BND 2 42 RIMS1 * chr7 98867659 98867663 chrX 68710897 68710901 TCGA-TP-A8TV BND 23 11 TMEM130 STARD8 chr7 98867704 98867707 chrX 69500782 69500785 TCGA-TP-A8TV BND 25 1 TMEM130 * chr8 91265461 91265461 chrX 141427245 141427247 TCGA-TP-A8TV BND 16 49 SLC26A7 * chrX 105830481 105830482 chrX 106438359 106438360 TCGA-TP-A8TV DUP 39 8 NRK * chrX 113249209 113249214 chrX 120231514 120231519 TCGA-TP-A8TV DUP 31 42 * NKAPP1 chrX 118298379 118298884 chrY 12322897 12323515 TCGA-TP-A8TV BND 11 38 * * chrX 124587683 124587706 chrX 148766700 148766723 TCGA-TP-A8TV INV 11 25 TENM1 AFF2 chrX 134411076 134411076 chrX 134873784 134873784 TCGA-TP-A8TV DUP 24 22 PHF6 * chrX 20519528 20519530 chrX 20713824 20713826 TCGA-TP-A8TV DUP 3 15 * * chrX 21365194 21365199 chrX 21628272 21628277 TCGA-TP-A8TV DEL 18 39 AL807742.1 CNKSR2 chrX 2197061 2197064 chrX 48672810 48672813 TCGA-TP-A8TV INV 24 28 * * chrX 23301801 23301802 chrX 23504577 23504578 TCGA-TP-A8TV DUP 29 14 * * chrX 2668451 2668452 chrX 3035984 3035985 TCGA-TP-A8TV DUP 3 25 * * chrX 2688736 2688738 chrX 4228942 4228944 TCGA-TP-A8TV DEL 37 29 * * chrX 29800192 29800192 chrX 30857722 30857722 TCGA-TP-A8TV DEL 17 13 IL1RAPL1 TAB3 chrX 30325017 30325020 chrX 30327272 30327275 TCGA-TP-A8TV DEL 8 2 * * chrX 32211784 32211784 chrX 32393385 32393385 TCGA-TP-A8TV DUP 9 16 DMD DMD chrX 43571033 43571036 chrX 43778114 43778117 TCGA-TP-A8TV DUP 38 2 * MAOB chrX 66698076 66698076 chrX 69947128 69947128 TCGA-TP-A8TV DUP 19 13 * EDA chrX 66730263 66730263 chrX 67124038 67124038 TCGA-TP-A8TV DUP 42 27 * * chrX 67000931 67000933 chrX 69163467 69163469 TCGA-TP-A8TV INV 11 44 * PJA1 chrX 67303147 67303148 chrX 67307478 67307479 TCGA-TP-A8TV DEL 35 34 * * chrX 69947244 69947244 chrX 69949103 69949103 TCGA-TP-A8TV DUP 4 23 EDA EDA chrX 73552377 73552378 chrX 73636078 73636079 TCGA-TP-A8TV DUP 4 45 MAP2K4P1 CHIC1 chrX 7579852 7579854 chrX 10219377 10219379 TCGA-TP-A8TV DEL 13 50 * CLCN4 chrX 9220850 9220850 chrX 9522753 9522753 TCGA-TP-A8TV DUP 38 18 * TBL1X chr11 71970852 71970852 chrX 96365269 96365291 TCGA-J9-A52D BND 15 33 RNF121 * chr12 56925075 56925080 chrX 70586542 70586553 TCGA-J9-A52D BND 18 40 SDR9C7 TEX11 chr12 56926271 56926293 chrX 70585609 70585611 TCGA-J9-A52D BND 14 15 SDR9C7 TEX11 chr12 56926271 56926293 chrX 70585778 70585785 TCGA-J9-A52D BND 27 49 SDR9C7 TEX11 chr13 19272600 19273382 chrX 87115980 87116429 TCGA-J9-A52D BND 50 35 * * chr15 67008737 67008738 chrX 1057644 1057645 TCGA-J9-A52D BND 6 49 AC087482.1 * chr17 15169676 15169691 chrX 11072143 11072145 TCGA-J9-A52D BND 44 32 * AC073529.1 chr17 15169676 15169691 chrX 9826683 9826683 TCGA-J9-A52D BND 18 41 * SHROOM2 chr1 225683458 225683459 chrX 125553110 125553111 TCGA-J9-A52D BND 12 28 * * chr1 225684227 225684230 chrX 125551051 125551054 TCGA-J9-A52D BND 22 45 * * chr1 63239717 63239717 chrX 152383943 152383943 TCGA-J9-A52D BND 44 6 LINC00466 GABRA3 chr20 39919165 39919179 chrX 112604901 112604915 TCGA-J9-A52D BND 28 25 * * chr2 19280800 19280806 chrX 96365269 96365291 TCGA-J9-A52D BND 2 39 LINC01376 * chr3 178766761 178766761 chrX 11935345 11935355 TCGA-J9-A52D BND 9 9 KCNMB2 * chr4 162215752 162215757 chrX 11934069 11934074 TCGA-J9-A52D BND 18 2 * * chr6 124900432 124900434 chrX 73326267 73326269 TCGA-J9-A52D BND 39 34 * * chr6 32491773 32491774 chrX 139341914 139341915 TCGA-J9-A52D BND 9 19 * * chr7 44992479 44992995 chrX 53721873 53722254 TCGA-J9-A52D BND 14 14 * * chr8 95882642 95882642 chrX 65801950 65801950 TCGA-J9-A52D BND 40 35 * * chr9 35456614 35456617 chrX 56685084 56685087 TCGA-J9-A52D BND 38 28 ATP8B5P * chrX 10085762 10085765 chrX 10403221 10403224 TCGA-J9-A52D INV 22 17 WWC3 * chrX 10805915 10805915 chrX 66856179 66856179 TCGA-J9-A52D DUP 7 20 MID1 * chrX 11029973 11029973 chrX 67770520 67770520 TCGA-J9-A52D INV 14 16 AC073529.1 * chrX 112235777 112235780 chrX 112290927 112290930 TCGA-J9-A52D DUP 35 24 * * chrX 116675982 116675982 chrX 116676723 116676723 TCGA-J9-A52D DEL 14 47 SLC6A14P1 SLC6A14P1 chrX 117944867 117944868 chrX 117947428 117947429 TCGA-J9-A52D DEL 23 22 KLHL13 KLHL13 chrX 121854996 121854996 chrX 121882278 121882278 TCGA-J9-A52D DEL 23 50 * * chrX 122415476 122415479 chrX 122415678 122415678 TCGA-J9-A52D DEL 17 17 * * chrX 123354833 123354836 chrX 123355680 123355680 TCGA-J9-A52D DEL 22 10 GRIA3 GRIA3 chrX 12382026 12382026 chrX 16429409 16429409 TCGA-J9-A52D INV 32 11 FRMPD4 * chrX 125552708 125552708 chrX 125553177 125553177 TCGA-J9-A52D INV 49 47 * * chrX 12970166 12970166 chrX 29946015 29946015 TCGA-J9-A52D DEL 24 50 * IL1RAPL1 chrX 13005306 13005309 chrX 67064403 67064406 TCGA-J9-A52D DUP 1 15 * * chrX 147784418 147784419 chrX 147784495 147784495 TCGA-J9-A52D DEL 41 44 * * chrX 15161976 15161976 chrX 67079304 67079304 TCGA-J9-A52D DEL 35 20 * * chrX 154556310 154556313 chrX 154613429 154613432 TCGA-J9-A52D DEL 28 44 IKBKG * chrX 15717961 15717961 chrX 50542732 50542732 TCGA-J9-A52D INV 17 47 CA5B * chrX 17508219 17508221 chrX 17508401 17508401 TCGA-J9-A52D DEL 25 16 NHS NHS chrX 1831292 1831292 chrX 7273462 7273462 TCGA-J9-A52D INV 48 32 * STS chrX 18357805 18357805 chrX 18574617 18574617 TCGA-J9-A52D DUP 20 24 * CDKL5 chrX 20142025 20142025 chrX 56334766 56334766 TCGA-J9-A52D DEL 48 11 EIF1AX * chrX 20146257 20146280 chrX 32812465 32812488 TCGA-J9-A52D INV 25 8 * DMD chrX 20146433 20146437 chrX 51202006 51202010 TCGA-J9-A52D DEL 5 10 * * chrX 21772032 21772033 chrX 67692906 67692907 TCGA-J9-A52D INV 5 37 * AR chrX 21846115 21846118 chrX 28355707 28355710 TCGA-J9-A52D DEL 2 30 MBTPS2 * chrX 24169497 24169499 chrX 67491772 67491774 TCGA-J9-A52D INV 33 41 ZFX * chrX 24445545 24445549 chrX 67349659 67349663 TCGA-J9-A52D DEL 26 45 * * chrX 24466070 24466070 chrX 25266999 25266999 TCGA-J9-A52D INV 48 48 PDK3 * chrX 24621210 24621213 chrX 24791721 24791724 TCGA-J9-A52D DEL 8 25 PCYT1B POLA1 chrX 24957271 24957271 chrX 67279136 67279136 TCGA-J9-A52D DEL 26 13 POLA1 * chrX 26956778 26956779 chrX 26958980 26958981 TCGA-J9-A52D INV 21 6 * * chrX 29249193 29249195 chrX 50682624 50682626 TCGA-J9-A52D INV 49 46 IL1RAPL1 SHROOM4 chrX 29848674 29849689 chrX 41153458 41154411 TCGA-J9-A52D DEL 30 45 IL1RAPL1 USP9X chrX 32860695 32860699 chrX 67621291 67621295 TCGA-J9-A52D INV 19 3 DMD AR chrX 36146371 36146371 chrX 36681934 36681934 TCGA-J9-A52D INV 25 1 CFAP47 * chrX 40211110 40211110 chrX 72559745 72559745 TCGA-J9-A52D INV 37 40 * HDAC8 chrX 42438415 42438415 chrX 57433029 57433029 TCGA-J9-A52D INV 20 9 Z93403.1 FAAH2 chrX 50946265 50946265 chrX 50960063 50960063 TCGA-J9-A52D DUP 12 46 * * chrX 56297077 56297077 chrX 56825810 56825810 TCGA-J9-A52D INV 35 15 * SPIN3 chrX 56353980 56353980 chrX 67602191 67602191 TCGA-J9-A52D DEL 14 23 * AR chrX 58187016 58187016 chrX 66510889 66510889 TCGA-J9-A52D DUP 48 41 * * chrX 58273727 58273732 chrX 58280202 58280207 TCGA-J9-A52D DEL 12 7 * * chrX 63193360 63193361 chrX 63208460 63208461 TCGA-J9-A52D DEL 13 37 * * chrX 64951128 64951128 chrX 64951295 64951295 TCGA-J9-A52D DEL 12 11 ZC4H2 ZC4H2 chrX 66752874 66752874 chrX 66754614 66754614 TCGA-J9-A52D INV 23 13 * * chrX 66811347 66811348 chrX 67052752 67052753 TCGA-J9-A52D INV 15 30 * * chrX 67665947 67665952 chrX 67670133 67670138 TCGA-J9-A52D DEL 35 31 AR AR chrX 67793744 67793745 chrX 67795653 67795654 TCGA-J9-A52D INV 18 2 BMI1P1 * chrX 71133440 71133442 chrX 71140055 71140057 TCGA-J9-A52D DEL 31 27 MED12 MED12 chrX 73324910 73324910 chrX 73326267 73326269 TCGA-J9-A52D DEL 28 27 * * chrX 77831421 77831421 chrX 77831565 77831565 TCGA-J9-A52D DEL 23 8 MAGT1 MAGT1 chrX 79621643 79621644 chrX 79650933 79650934 TCGA-J9-A52D DEL 3 2 * * chrX 91839381 91839383 chrX 93590008 93590010 TCGA-J9-A52D DUP 8 40 PCDH11X * chr13 33824884 33824887 chrX 69955839 69955846 TCGA-VP-A878 BND 29 8 RFC3 EDA chr20 39919512 39919512 chrX 112464062 112464062 TCGA-VP-A878 BND 1 6 * * chr4 169827995 169828450 chrX 40210688 40211464 TCGA-VP-A878 BND 29 40 * * chr5 78173653 78173664 chrX 76842160 76842171 TCGA-VP-A878 BND 38 45 AP3B1 MIR325HG chr7 32531214 32531852 chrX 148045027 148045484 TCGA-VP-A878 BND 35 19 AVL9 * chrX 110306700 110306701 chrX 143240324 143240325 TCGA-VP-A878 INV 39 27 AMMECR1 * chrX 110321988 110321992 chrX 143425254 143425258 TCGA-VP-A878 DUP 16 36 AMMECR1 AC239727.1 chrX 126134614 126134616 chrX 126134765 126134765 TCGA-VP-A878 DEL 41 30 * * chrX 143058159 143058160 chrX 143649469 143649470 TCGA-VP-A878 DEL 3 8 * * chrX 143097518 143097520 chrX 143295391 143295393 TCGA-VP-A878 DUP 50 22 * AC239727.1 chrX 143255034 143255035 chrX 143321208 143321209 TCGA-VP-A878 INV 14 50 * AC239727.1 chrX 22114007 22114008 chrX 62622439 62622440 TCGA-VP-A878 INV 6 11 PHEX * chrX 36279114 36279114 chrX 36279244 36279244 TCGA-VP-A878 DEL 38 45 CFAP47 CFAP47 chrX 48942753 48942757 chrX 48942850 48942850 TCGA-VP-A878 DEL 38 23 OTUD5 OTUD5 chrX 51141176 51141180 chrX 51424438 51424442 TCGA-VP-A878 INV 49 5 LINC01284 AL158055.1 chrX 66845721 66845721 chrX 67059132 67059132 TCGA-VP-A878 DUP 17 33 * * chrX 87974379 87974380 chrX 87979564 87979565 TCGA-VP-A878 DEL 8 46 * * chrX 97070598 97070598 chrX 97071889 97071889 TCGA-VP-A878 DEL 14 26 DIAPH2 DIAPH2 chr18 1701299 1701299 chrX 45394646 45394646 TCGA-HC-8262 BND 21 24 AC019183.1 * chr18 22321453 22321453 chrX 62826504 62826504 TCGA-HC-8262 BND 28 35 * * chr18 30544900 30544904 chrX 66348941 66348945 TCGA-HC-8262 BND 2 1 * * chr18 32224345 32224346 chrX 65024622 65024623 TCGA-HC-8262 BND 36 36 GAREM1 ZC4H2 chr18 35353936 35353936 chrX 1921208 1921208 TCGA-HC-8262 BND 26 11 * * chr18 36206666 36207571 chrX 64483465 64484477 TCGA-HC-8262 BND 18 17 MOCOS * chr18 36312242 36312242 chrX 67920811 67920811 TCGA-HC-8262 BND 8 10 FHOD3 * chr18 36323739 36323742 chrX 64840116 64840119 TCGA-HC-8262 BND 4 2 FHOD3 * chr18 36373360 36373362 chrX 64773732 64773734 TCGA-HC-8262 BND 13 10 FHOD3 * chr18 37510604 37510604 chrX 66611926 66611926 TCGA-HC-8262 BND 6 47 CELF4 EDA2R chr18 37900729 37900730 chrX 67858566 67858567 TCGA-HC-8262 BND 20 31 * * chr18 38533481 38533485 chrX 63913655 63913659 TCGA-HC-8262 BND 23 21 * * chr18 38678419 38678419 chrX 64919789 64919789 TCGA-HC-8262 BND 8 43 AC100781.1 ZC4H2 chr18 38719731 38719735 chrX 64114236 64114240 TCGA-HC-8262 BND 7 36 * * chr18 38766812 38766816 chrX 63976176 63976180 TCGA-HC-8262 BND 9 6 * * chr18 38865002 38865002 chrX 63910797 63910797 TCGA-HC-8262 BND 18 24 * * chr18 39071613 39071615 chrX 64659097 64659099 TCGA-HC-8262 BND 7 33 * * chr18 39072205 39072210 chrX 64566965 64566970 TCGA-HC-8262 BND 41 20 * * chr18 39178360 39178360 chrX 64006386 64006386 TCGA-HC-8262 BND 45 36 * * chr18 39586136 39586137 chrX 67925744 67925745 TCGA-HC-8262 BND 38 15 MIR924HG * chr18 39656632 39656632 chrX 68098936 68098936 TCGA-HC-8262 BND 39 6 MIR924HG OPHN1 chr18 40091062 40091063 chrX 66243080 66243081 TCGA-HC-8262 BND 35 7 LINC01477 HEPH chr18 40119941 40119943 chrX 66108376 66108378 TCGA-HC-8262 BND 40 20 * * chr18 40464007 40464009 chrX 65441714 65441716 TCGA-HC-8262 BND 11 41 * ZC3H12B chr18 40495405 40495405 chrX 66394848 66394848 TCGA-HC-8262 BND 21 14 * * chr18 40885804 40885805 chrX 66775641 66775642 TCGA-HC-8262 BND 27 2 * * chr18 40890473 40890473 chrX 67943257 67943257 TCGA-HC-8262 BND 15 5 * * chr18 41070923 41070924 chrX 67327943 67327944 TCGA-HC-8262 BND 40 10 * * chr18 41105345 41105345 chrX 67640166 67640166 TCGA-HC-8262 BND 36 32 * AR chr18 41172330 41172331 chrX 65129988 65129989 TCGA-HC-8262 BND 21 4 * * chr18 41194474 41194476 chrX 67289453 67289455 TCGA-HC-8262 BND 18 2 * * chr18 41216727 41216727 chrX 67343320 67343320 TCGA-HC-8262 BND 49 24 * * chr18 41249421 41249422 chrX 68630853 68630854 TCGA-HC-8262 BND 7 9 * * chr3 119637975 119637979 chrX 67765751 67765755 TCGA-HC-8262 BND 33 35 POPDC2 * chr3 122872942 122872942 chrX 67470747 67470747 TCGA-HC-8262 BND 48 40 SLC49A4 * chr3 137615433 137615435 chrX 66669373 66669375 TCGA-HC-8262 BND 8 16 * * chr3 148350747 148350747 chrX 67296017 67296017 TCGA-HC-8262 BND 42 33 LINC02046 * chr5 153947813 153948445 chrX 122140074 122140503 TCGA-HC-8262 BND 45 36 * * chr9 101625447 101625449 chrX 125581358 125581360 TCGA-HC-8262 BND 8 25 GRIN3A * chr9 40526479 40526981 chrX 58509184 58509563 TCGA-HC-8262 BND 21 14 BMS1P14 * chrX 1246343 1246343 chrX 1246682 1246682 TCGA-HC-8262 DEL 16 41 * * chrX 64126023 64126027 chrX 64142754 64142758 TCGA-HC-8262 INV 26 48 * * chrX 64802862 64802863 chrY 16806633 16806634 TCGA-HC-8262 BND 32 38 * * chrX 65037766 65037766 chrX 67404841 67404841 TCGA-HC-8262 INV 16 7 * * chrX 65160364 65160364 chrX 65769111 65769111 TCGA-HC-8262 DUP 20 20 * * chrX 65376922 65376929 chrY 12171709 12171709 TCGA-HC-8262 BND 5 12 ZC3H12B * chrX 65376922 65376929 chrY 19959703 19959704 TCGA-HC-8262 BND 2 21 ZC3H12B * chrX 66098646 66098648 chrX 66099432 66099434 TCGA-HC-8262 INV 42 33 * * chrX 66190307 66190307 chrX 66783950 66783950 TCGA-HC-8262 INV 40 40 HEPH * chrX 66405622 66405623 chrY 8047740 8047741 TCGA-HC-8262 BND 16 22 * * chrX 66489453 66489454 chrX 67811887 67811888 TCGA-HC-8262 DEL 47 14 * * chrX 67715380 67715383 chrX 68521980 68521983 TCGA-HC-8262 INV 26 12 AR YIPF6 chrX 68518357 68518360 chrX 89978929 89978932 TCGA-HC-8262 INV 23 33 YIPF6 * chrX 68518357 68518360 chrY 3636367 3636370 TCGA-HC-8262 BND 25 17 YIPF6 * chrX 74208984 74208986 chrX 74235296 74235298 TCGA-HC-8262 DUP 12 6 FTX FTX chrX 8107816 8107820 chrX 8512662 8512666 TCGA-HC-8262 DUP 49 25 AC079142.1 * chrX 85743738 85743741 chrX 85744271 85744271 TCGA-HC-8262 DEL 18 4 * * chr11 23083878 23083878 chrX 155158784 155158784 TCGA-2A-A8VO BND 40 28 * * chr13 34036306 34036306 chrX 44425144 44425144 TCGA-2A-A8VO BND 11 21 * * chr13 34411122 34411122 chrX 43505129 43505129 TCGA-2A-A8VO BND 36 17 LINC02343 * chr13 34412225 34412227 chrX 44428039 44428041 TCGA-2A-A8VO BND 11 1 LINC02343 * chr13 86269344 86269928 chrX 89073444 89073910 TCGA-2A-A8VO BND 37 46 * * chr15 86305323 86305323 chrX 11935182 11935182 TCGA-2A-A8VO BND 11 33 AGBL1 * chr1 161162206 161162210 chrX 130758883 130758887 TCGA-2A-A8VO BND 20 1 USP21 ENOX2 chr1 161162244 161162246 chrX 130758778 130758780 TCGA-2A-A8VO BND 47 14 USP21 ENOX2 chr2 192177251 192177777 chrX 11933176 11933671 TCGA-2A-A8VO BND 7 8 TMEFF2 * chr2 192177551 192177553 chrX 11933757 11933759 TCGA-2A-A8VO BND 50 24 TMEFF2 * chr2 71267074 71267082 chrX 57012424 57012432 TCGA-2A-A8VO BND 13 11 * * chr5 128540116 128540116 chrX 67415372 67415372 TCGA-2A-A8VO BND 21 14 FBN2 * chr7 73768108 73768110 chrX 45057770 45057772 TCGA-2A-A8VO BND 39 43 * KDM6A chrX 16182934 16183606 chrX 30453699 30454117 TCGA-2A-A8VO DUP 37 1 * * chrX 2197061 2197064 chrX 48672810 48672813 TCGA-2A-A8VO INV 3 8 * * chrX 25409408 25409408 chrX 125658023 125658023 TCGA-2A-A8VO INV 37 35 * * chrX 43492944 43492945 chrX 43495099 43495100 TCGA-2A-A8VO DEL 38 32 * * chrX 45086710 45086710 chrX 45102281 45102281 TCGA-2A-A8VO DEL 12 26 KDM6A KDM6A chrX 50022388 50022390 chrX 98762314 98762316 TCGA-2A-A8VO INV 39 42 CLCN5 AL157778.1 chrX 57012424 57012432 chrX 86006849 86006857 TCGA-2A-A8VO INV 19 48 * CHM chrX 65744020 65744022 chrX 67817089 67817091 TCGA-2A-A8VO DEL 19 31 * * chrX 66033304 66033306 chrX 67162971 67162973 TCGA-2A-A8VO INV 33 7 VSIG4 * chrX 66072889 66072891 chrX 66701233 66701235 TCGA-2A-A8VO INV 14 42 * * chrX 68145419 68145419 chrX 73872148 73872148 TCGA-2A-A8VO INV 25 38 OPHN1 * chrX 69293232 69293232 chrX 71584879 71584879 TCGA-2A-A8VO DEL 1 1 * GCNA chrX 69480869 69480869 chrX 70209608 70209614 TCGA-2A-A8VO INV 27 19 * * chrX 69481632 69481634 chrX 70209608 70209614 TCGA-2A-A8VO INV 9 12 * * chrX 72161605 72161606 chrX 73637660 73637661 TCGA-2A-A8VO DUP 12 40 NHSL2 CHIC1 chrX 72299048 72299048 chrX 72305734 72305734 TCGA-2A-A8VO DEL 43 16 PIN4 CITED1 chr11 100908940 100908968 chrX 65360476 65360504 TCGA-QU-A6IL BND 17 26 ARHGAP42 * chr11 100911738 100911740 chrX 139137259 139137261 TCGA-QU-A6IL BND 29 47 ARHGAP42 FGF13 chr11 107993783 107993792 chrX 74632985 74632994 TCGA-QU-A6IL BND 28 9 * * chr11 109250851 109250851 chrX 40370196 40370196 TCGA-QU-A6IL BND 13 10 * * chr11 129428532 129428537 chrX 55884283 55884288 TCGA-QU-A6IL BND 30 32 BARX2 * chr11 130370414 130370416 chrX 113770433 113770435 TCGA-QU-A6IL BND 9 38 ZBTB44-DT XACT chr11 134515898 134515898 chrX 5876881 5876881 TCGA-QU-A6IL BND 13 19 * NLGN4X chr11 134574318 134574318 chrX 46151495 46151495 TCGA-QU-A6IL BND 3 26 * * chr11 66682698 66682698 chrX 480019 480019 TCGA-QU-A6IL BND 34 26 * * chr11 69890678 69890684 chrX 131060695 131060701 TCGA-QU-A6IL BND 8 43 * ARHGAP36 chr11 76296829 76296829 chrX 79776772 79776772 TCGA-QU-A6IL BND 23 11 * * chr11 80774352 80774352 chrX 13553634 13553634 TCGA-QU-A6IL BND 27 3 * * chr11 80774872 80774874 chrX 40285928 40285930 TCGA-QU-A6IL BND 27 29 * AC091806.1 chr11 84479617 84479618 chrX 12182446 12182447 TCGA-QU-A6IL BND 49 40 DLG2 FRMPD4 chr11 86440820 86440823 chrX 99614408 99614411 TCGA-QU-A6IL BND 8 21 AP001831.1 * chr11 87046346 87046348 chrX 72701829 72701831 TCGA-QU-A6IL BND 16 10 TMEM135 PHKA1 chr12 83283568 83284500 chrX 94821871 94822392 TCGA-QU-A6IL BND 12 19 * * chr1 112640139 112640144 chrX 78265527 78265532 TCGA-QU-A6IL BND 17 40 CAPZA1 * chr4 54993734 54994380 chrX 45664616 45665065 TCGA-QU-A6IL BND 21 43 * * chr7 136834273 136834274 chrX 46149573 46149574 TCGA-QU-A6IL BND 8 39 AC009264.1 * chrX 10831072 10831078 chrX 130302623 130302629 TCGA-QU-A6IL DUP 24 8 MID1 * chrX 11369403 11369403 chrX 131065126 131065126 TCGA-QU-A6IL DUP 6 30 ARHGAP6 ARHGAP36 chrX 11374796 11374796 chrX 91868136 91868136 TCGA-QU-A6IL DEL 23 48 ARHGAP6 PCDH11X chrX 13556641 13556642 chrX 130297476 130297477 TCGA-QU-A6IL DEL 27 25 * * chrX 14731315 14731315 chrX 99031883 99031883 TCGA-QU-A6IL DUP 9 39 GLRA2 * chrX 14732205 14732207 chrX 146342935 146342937 TCGA-QU-A6IL INV 23 32 * * chrX 16888101 16888103 chrX 135082824 135082826 TCGA-QU-A6IL DEL 5 34 * SMIM10L2B-AS1 chrX 17144369 17144369 chrX 27079655 27079655 TCGA-QU-A6IL INV 4 12 REPS2 AC112493.1 chrX 20078946 20078949 chrX 47509216 47509219 TCGA-QU-A6IL INV 10 25 MAP7D2 * chrX 20083707 20083710 chrX 24168972 24168975 TCGA-QU-A6IL INV 7 49 MAP7D2 ZFX chrX 24166856 24166857 chrX 130247383 130247384 TCGA-QU-A6IL INV 39 39 ZFX ZNF280C chrX 2630053 2630072 chrX 2630195 2630195 TCGA-QU-A6IL DEL 38 44 CD99P1 CD99P1 chrX 27083265 27083269 chrX 57557372 57557376 TCGA-QU-A6IL DEL 30 42 AC112493.1 * chrX 40374413 40374414 chrX 89976130 89976131 TCGA-QU-A6IL INV 33 36 * * chrX 41474021 41474023 chrX 92803477 92803479 TCGA-QU-A6IL INV 11 24 NYX * chrX 57900173 57900173 chrX 122059188 122059188 TCGA-QU-A6IL DUP 3 18 * * chrX 65107506 65107508 chrX 68117007 68117009 TCGA-QU-A6IL DUP 7 49 * OPHN1 chrX 65583656 65583658 chrX 69620335 69620337 TCGA-QU-A6IL DUP 9 2 * EDA chrX 67299583 67299585 chrX 69493452 69493454 TCGA-QU-A6IL INV 36 9 * * chrX 67385423 67385423 chrX 67465359 67465359 TCGA-QU-A6IL DEL 33 18 * * chrX 68234187 68234188 chrX 139530747 139530748 TCGA-QU-A6IL INV 4 23 OPHN1 F9 chrX 74630449 74630450 chrX 89969728 89969729 TCGA-QU-A6IL INV 14 6 * * chrX 79773528 79773529 chrX 131761968 131761969 TCGA-QU-A6IL INV 22 41 * FIRRE chrX 83105174 83105174 chrX 83151317 83151317 TCGA-QU-A6IL DEL 25 41 * * chrX 87364398 87364399 chrX 87368211 87368212 TCGA-QU-A6IL DEL 33 39 * * chrX 87813321 87813322 chrX 87813900 87813900 TCGA-QU-A6IL DEL 50 17 * * chrX 91873816 91873822 chrX 99617440 99617446 TCGA-QU-A6IL INV 45 47 PCDH11X * chr13 49679296 49679297 chrX 66436424 66436425 TCGA-KK-A8ID BND 1 7 EBPL AL592049.1 chr17 3048950 3049457 chrX 68238933 68239667 TCGA-KK-A8ID BND 8 11 * OPHN1 chr5 25367222 25367224 chrX 68066253 68066255 TCGA-KK-A8ID BND 28 36 * OPHN1 chr7 73804096 73804096 chrX 67768709 67768709 TCGA-KK-A8ID BND 33 26 CLDN4 * chrX 121244796 121244797 chrX 121265787 121265788 TCGA-KK-A8ID DEL 46 18 * * chrX 139678119 139678119 chrX 139679001 139679001 TCGA-KK-A8ID DEL 49 12 MCF2 MCF2 chrX 5313021 5313022 chrX 5516225 5516226 TCGA-KK-A8ID DEL 47 20 * * chrX 6362750 6362751 chrX 7002798 7002799 TCGA-KK-A8ID DUP 38 45 * * chrX 66194922 66194922 chrX 66196235 66196235 TCGA-KK-A8ID INV 28 16 HEPH HEPH chrX 66380678 66380684 chrX 66391969 66391975 TCGA-KK-A8ID INV 35 27 * * chrX 66771243 66771243 chrX 66777174 66777174 TCGA-KK-A8ID INV 14 50 * * chrX 66835233 66835235 chrX 66836976 66836978 TCGA-KK-A8ID INV 9 32 * * chrX 67335813 67335814 chrX 67337007 67337008 TCGA-KK-A8ID INV 6 25 * * chrX 67641166 67641169 chrX 67655804 67655807 TCGA-KK-A8ID INV 26 37 AR AR chrX 68394891 68394925 chrX 68395202 68395202 TCGA-KK-A8ID DEL 13 47 OPHN1 OPHN1 chrX 68454611 68454613 chrX 68456111 68456113 TCGA-KK-A8ID INV 32 28 * * chrX 93025482 93025483 chrX 93025960 93025960 TCGA-KK-A8ID DEL 37 21 * * chrX 93390499 93390501 chrX 93390867 93390869 TCGA-KK-A8ID DUP 40 49 NT5DC1P1 NT5DC1P1 chr12 21856493 21856494 chrX 11707556 11707557 TCGA-CH-5748 BND 49 23 ABCC9 AC004554.1 chr12 27296390 27296390 chrX 2624860 2624860 TCGA-CH-5748 BND 20 50 STK38L CD99P1 chr12 76305252 76305252 chrX 11934864 11934864 TCGA-CH-5748 BND 47 7 * * chr13 108609648 108609650 chrX 11935564 11935566 TCGA-CH-5748 BND 31 31 MYO16 * chr13 61975704 61976172 chrX 11713764 11714278 TCGA-CH-5748 BND 42 45 * AC004554.1 chr13 61975809 61976464 chrX 11714389 11714935 TCGA-CH-5748 BND 25 25 * AC004554.1 chr13 61976358 61976359 chrX 11714134 11714146 TCGA-CH-5748 BND 2 42 * AC004554.1 chr14 19276701 19276701 chrX 20855122 20855122 TCGA-CH-5748 BND 38 38 DUXAP10 AL807742.1 chr15 41349337 41349341 chrX 90034287 90034308 TCGA-CH-5748 BND 3 24 AC087721.2 * chr15 87919180 87919184 chrX 67526423 67526424 TCGA-CH-5748 BND 18 20 NTRK3 * chr15 87919180 87919184 chrX 67526670 67526670 TCGA-CH-5748 BND 24 25 NTRK3 * chr18 74859080 74859080 chrX 106310343 106310343 TCGA-CH-5748 BND 18 41 ZNF407 * chr1 46540358 46540359 chrX 43267493 43267511 TCGA-CH-5748 BND 36 13 TMEM275 * chr22 28669336 28669337 chrX 147274683 147274684 TCGA-CH-5748 BND 17 31 TTC28 * chr22 28670133 28670133 chrX 147274708 147274708 TCGA-CH-5748 BND 32 34 TTC28 * chr2 230471696 230471712 chrX 101254936 101254945 TCGA-CH-5748 BND 11 35 SP100 DRP2 chr3 166739918 166739920 chrX 82134151 82134153 TCGA-CH-5748 BND 12 23 * * chr3 194429306 194429306 chrX 119084051 119084051 TCGA-CH-5748 BND 23 44 ATP13A3 KIAA1210 chr4 1613058 1613069 chrX 68635136 68635150 TCGA-CH-5748 BND 38 9 * * chr4 165774303 165774303 chrX 11935013 11935072 TCGA-CH-5748 BND 15 7 * * chr5 28417875 28418350 chrX 67981158 67982114 TCGA-CH-5748 BND 20 48 * * chr5 4771061 4771063 chrX 90034287 90034308 TCGA-CH-5748 BND 3 29 AC106799.2 * chr6 160235072 160235891 chrX 153013661 153014132 TCGA-CH-5748 BND 44 47 SLC22A2 * chr7 42786296 42786675 chrX 66137069 66137590 TCGA-CH-5748 BND 27 4 * * chr7 91814025 91814027 chrX 15698648 15698650 TCGA-CH-5748 BND 24 9 MTERF1 CA5BP1 chrX 11898238 11898241 chrX 11898375 11898375 TCGA-CH-5748 DEL 40 8 * * chrX 126387823 126387824 chrX 126403693 126403694 TCGA-CH-5748 DEL 6 44 * * chrX 136228352 136228355 chrX 136228555 136228555 TCGA-CH-5748 DEL 1 27 MAP7D3 MAP7D3 chrX 142797290 142797290 chrX 147922438 147922438 TCGA-CH-5748 INV 14 31 * FMR1 chrX 142797440 142797443 chrX 142797674 142797677 TCGA-CH-5748 INV 33 18 * * chrX 153684310 153684310 chrX 154583476 154583476 TCGA-CH-5748 DEL 16 32 PNCK * chrX 19429611 19429615 chrX 19430371 19430371 TCGA-CH-5748 DEL 7 44 MAP3K15 MAP3K15 chrX 2197061 2197064 chrX 48673107 48673110 TCGA-CH-5748 INV 22 23 * * chrX 35332275 35332276 chrX 35383073 35383074 TCGA-CH-5748 DEL 16 18 * * chrX 43266937 43266942 chrX 43267493 43267511 TCGA-CH-5748 INV 36 6 * * chrX 64542649 64542659 chrX 64542649 64542659 TCGA-CH-5748 INS 33 24 * * chrX 65623012 65623020 chrX 68138480 68138484 TCGA-CH-5748 DEL 34 42 MSN OPHN1 chrX 65623012 65623020 chrX 68138434 68138434 TCGA-CH-5748 DUP 27 42 MSN OPHN1 chrX 65624160 65624162 chrX 86591141 86591141 TCGA-CH-5748 DUP 42 22 MSN DACH2 chrX 65624160 65624162 chrX 66524594 66524596 TCGA-CH-5748 DUP 29 39 MSN * chrX 65746297 65746297 chrX 67557713 67557713 TCGA-CH-5748 DEL 23 5 * AR chrX 65889291 65889296 chrX 65892692 65892697 TCGA-CH-5748 DEL 23 6 * * chrX 65924084 65924084 chrX 67553172 67553172 TCGA-CH-5748 INV 49 24 * AR chrX 66031508 66031508 chrX 66888115 66888115 TCGA-CH-5748 DEL 40 5 VSIG4 * chrX 66032799 66033674 chrX 66651346 66652215 TCGA-CH-5748 DUP 9 22 VSIG4 * chrX 66042091 66042565 chrX 66449508 66450261 TCGA-CH-5748 INV 48 48 * * chrX 66137302 66137303 chrX 67398983 67398984 TCGA-CH-5748 INV 16 40 * * chrX 66137586 66137586 chrX 67713023 67713023 TCGA-CH-5748 DUP 40 12 * AR chrX 66274174 66274174 chrX 67367089 67367089 TCGA-CH-5748 INV 12 36 * * chrX 66343460 66343460 chrX 67030376 67030376 TCGA-CH-5748 INV 38 27 * * chrX 66525261 66526057 chrX 67557318 67558186 TCGA-CH-5748 DEL 9 22 * AR chrX 66598293 66598293 chrX 68132677 68132677 TCGA-CH-5748 INV 11 46 EDA2R OPHN1 chrX 66667811 66668827 chrX 67545517 67546421 TCGA-CH-5748 DUP 5 2 * AR chrX 66746803 66746804 chrX 67803682 67803683 TCGA-CH-5748 DUP 25 7 * * chrX 66854481 66854481 chrX 67113032 67113032 TCGA-CH-5748 INV 14 15 * * chrX 66854800 66854802 chrX 67016275 67016277 TCGA-CH-5748 DUP 48 44 * * chrX 67064595 67064595 chrX 67072305 67072309 TCGA-CH-5748 DEL 39 11 * * chrX 67116205 67116206 chrX 67356256 67356257 TCGA-CH-5748 DUP 16 29 * * chrX 67357676 67357677 chrX 67552620 67552621 TCGA-CH-5748 DUP 35 29 * AR chrX 67701059 67701059 chrX 67910276 67910276 TCGA-CH-5748 DUP 17 12 AR * chrX 67791173 67791173 chrX 67921075 67921075 TCGA-CH-5748 DUP 44 50 * * chrX 77256531 77256923 chrX 131466860 131467380 TCGA-CH-5748 INV 48 17 * IGSF1 chrX 81686985 81686987 chrX 81827323 81827325 TCGA-CH-5748 DEL 9 42 * * chrX 86100354 86100356 chrX 86100463 86100463 TCGA-CH-5748 DEL 8 1 * * chrX 86963541 86963541 chrX 86987626 86987626 TCGA-CH-5748 DEL 1 36 * * chrX 93807944 93807947 chrX 95148333 95148342 TCGA-CH-5748 INV 3 1 * * chrX 93808830 93808830 chrX 95148333 95148342 TCGA-CH-5748 INV 28 30 * * chrX 96209426 96209427 chrX 96210678 96210679 TCGA-CH-5748 DEL 19 39 * * chrX 97930593 97931174 chrX 99639149 99639947 TCGA-CH-5748 DEL 16 19 * * chrX 97930758 97930758 chrX 99640856 99640856 TCGA-CH-5748 INV 28 34 * * chrX 99639539 99639546 chrX 99640755 99640762 TCGA-CH-5748 INV 29 19 * * chr8 113776056 113776057 chrX 17519410 17519411 TCGA-EJ-A7NM BND 44 28 * NHS chrX 57012424 57012432 chrX 86006849 86006857 TCGA-EJ-A7NM INV 47 49 * CHM chrX 74789902 74790353 chrX 142124530 142125005 TCGA-EJ-A7NM INV 40 26 NEXMIF * chr11 109180849 109181195 chrX 109069945 109070567 TCGA-EJ-7789 BND 49 45 * * chr3 98195938 98196853 chrX 103761332 103761733 TCGA-EJ-7789 BND 29 42 OR5H5P * chr7 81261367 81261368 chrX 130621164 130621165 TCGA-EJ-7789 BND 49 10 * * chr8 4361556 4361557 chrX 11934119 11934120 TCGA-EJ-7789 BND 21 21 CSMD1 * chr9 134977412 134977412 chrX 99263214 99263214 TCGA-EJ-7789 BND 22 39 * * chrX 101672265 101672266 chrX 103231383 103231384 TCGA-EJ-7789 DUP 43 44 * * chrX 1101787 1101792 chrX 1102427 1102427 TCGA-EJ-7789 DEL 27 18 * * chrX 110432670 110432670 chrX 113757986 113757986 TCGA-EJ-7789 DUP 4 42 AMMECR1 XACT chrX 110468389 110468391 chrX 110470616 110470618 TCGA-EJ-7789 DEL 20 42 * * chrX 110471453 110471453 chrX 113751449 113751449 TCGA-EJ-7789 DEL 26 1 * XACT chrX 110522618 110522620 chrX 122746360 122746362 TCGA-EJ-7789 DUP 27 11 TDGF1P3 * chrX 110993409 110993410 chrX 121717453 121717454 TCGA-EJ-7789 INV 41 14 PAK3 * chrX 111951545 111951546 chrX 120029365 120029366 TCGA-EJ-7789 DUP 13 32 TRPC5 * chrX 114274829 114274833 chrX 115057713 115057717 TCGA-EJ-7789 DUP 24 31 * * chrX 119122212 119122212 chrX 119604451 119604451 TCGA-EJ-7789 DUP 34 2 KIAA1210 NKRF chrX 12344099 12344099 chrX 13852543 13852543 TCGA-EJ-7789 INV 37 45 FRMPD4 GPM6B chrX 12344289 12344289 chrX 111951174 111951174 TCGA-EJ-7789 DUP 2 19 FRMPD4 TRPC5 chrX 126443645 126443647 chrX 143037578 143037580 TCGA-EJ-7789 DUP 33 17 * * chrX 126884524 126884527 chrX 128357044 128357047 TCGA-EJ-7789 INV 47 36 * AL008633.1 chrX 1601733 1601735 chrX 1606602 1606604 TCGA-EJ-7789 DEL 35 37 AKAP17A * chrX 16727109 16727109 chrX 35135930 35135930 TCGA-EJ-7789 INV 9 23 SYAP1 * chrX 18878869 18878870 chrX 38687460 38687461 TCGA-EJ-7789 INV 3 35 * AF241726.1 chrX 18901972 18901976 chrX 20709505 20709509 TCGA-EJ-7789 INV 18 36 PHKA2 * chrX 2197061 2197064 chrX 48673107 48673110 TCGA-EJ-7789 INV 2 29 * * chrX 29013198 29013198 chrX 35692413 35692413 TCGA-EJ-7789 INV 45 49 IL1RAPL1 * chrX 29371672 29371673 chrX 107540033 107540034 TCGA-EJ-7789 DEL 46 40 IL1RAPL1 FRMPD3 chrX 34594493 34595142 chrX 63769724 63770404 TCGA-EJ-7789 INV 9 22 * ARHGEF9 chrX 35692782 35692786 chrX 48979512 48979516 TCGA-EJ-7789 DEL 38 43 * GRIPAP1 chrX 38737688 38737692 chrX 70579040 70579044 TCGA-EJ-7789 INV 3 49 * TEX11 chrX 38739959 38739961 chrX 70156756 70156758 TCGA-EJ-7789 INV 21 7 * IGBP1 chrX 38740735 38740735 chrX 48979984 48979984 TCGA-EJ-7789 INV 49 46 * GRIPAP1 chrX 41610076 41610770 chrX 111010339 111011154 TCGA-EJ-7789 INV 39 39 CASK PAK3 chrX 42517983 42518600 chrX 42933286 42933984 TCGA-EJ-7789 DEL 24 18 Z93403.1 * chrX 42519213 42519213 chrX 141620364 141620364 TCGA-EJ-7789 DEL 16 23 Z93403.1 SPANXA2-OT1 chrX 42942957 42942958 chrX 98838605 98838606 TCGA-EJ-7789 DEL 20 19 * AL157778.1 chrX 44335558 44335559 chrX 44376941 44376942 TCGA-EJ-7789 DUP 36 24 EFHC2 * chrX 45012045 45012045 chrX 98874547 98874547 TCGA-EJ-7789 DEL 38 13 KDM6A AL157778.1 chrX 45334624 45334624 chrX 96594507 96594507 TCGA-EJ-7789 DEL 50 40 * * chrX 59336937 59336937 chrX 88127304 88127304 TCGA-EJ-7789 INV 31 49 * * chrX 62688752 62688753 chrX 62971743 62971744 TCGA-EJ-7789 DEL 42 41 * * chrX 63306844 63306850 chrX 153873485 153873491 TCGA-EJ-7789 DEL 49 42 * L1CAM chrX 63792825 63792826 chrX 64373239 64373240 TCGA-EJ-7789 DEL 37 1 ARHGEF9 MTMR8 chrX 65457295 65457303 chrX 74167361 74167369 TCGA-EJ-7789 DEL 31 16 ZC3H12B FTX chrX 67316316 67316317 chrX 67342509 67342510 TCGA-EJ-7789 DUP 29 29 * * chrX 70681003 70681003 chrX 71460852 71460852 TCGA-EJ-7789 DUP 19 49 TEX11 TAF1 chrX 7070903 7070903 chrX 102295881 102295881 TCGA-EJ-7789 DUP 4 24 PUDP NXF2 chrX 73326018 73326021 chrX 100747729 100747732 TCGA-EJ-7789 DEL 32 16 * * chrX 75097087 75097087 chrX 127916517 127916517 TCGA-EJ-7789 INV 30 10 ABCB7 * chrX 75645530 75645533 chrX 88090643 88090646 TCGA-EJ-7789 INV 10 23 * * chrX 76520245 76520912 chrX 101330306 101331097 TCGA-EJ-7789 INV 6 26 * * chrX 79633169 79633172 chrX 82986488 82986491 TCGA-EJ-7789 DUP 37 20 * * chrX 80370419 80370419 chrX 80370700 80370700 TCGA-EJ-7789 DEL 25 12 TENT5D TENT5D chrX 8043892 8043892 chrX 122035209 122035209 TCGA-EJ-7789 INV 23 2 AC079142.1 * chrX 82481075 82481075 chrX 82987155 82987155 TCGA-EJ-7789 DEL 17 5 * * chrX 84095053 84095892 chrX 84149212 84150133 TCGA-EJ-7789 DUP 40 47 RPS6KA6 RPS6KA6 chrX 8903052 8903054 chrX 42518782 42518784 TCGA-EJ-7789 INV 27 15 AC074281.1 Z93403.1 chrX 89349989 89349992 chrX 101671735 101671738 TCGA-EJ-7789 INV 11 47 * * chrX 89350785 89350785 chrX 110522238 110522238 TCGA-EJ-7789 DUP 36 44 * TDGF1P3 chrX 8945029 8945030 chrX 64398538 64398539 TCGA-EJ-7789 INV 22 13 * * chrX 93128924 93128925 chrX 120029551 120029552 TCGA-EJ-7789 DEL 6 45 * * chrX 9793417 9793417 chrX 98874411 98874411 TCGA-EJ-7789 DUP 33 10 SHROOM2 AL157778.1 chrX 9823883 9823884 chrX 101812273 101812274 TCGA-EJ-7789 INV 34 22 SHROOM2 * chrX 98620173 98620174 chrX 102018023 102018024 TCGA-EJ-7789 DUP 38 45 AL157778.1 * chrX 98650877 98650879 chrX 141617878 141617880 TCGA-EJ-7789 DEL 10 45 AL157778.1 SPANXA2-OT1 chrX 98875193 98875194 chrX 141649256 141649257 TCGA-EJ-7789 INV 18 16 AL157778.1 SPANXA2-OT1 chr11 55335297 55335297 chrX 86675121 86675121 TCGA-YL-A8S9 BND 29 38 * DACH2 chr11 55890152 55890152 chrX 87066075 87066075 TCGA-YL-A8S9 BND 45 23 TRIM51 * chr17 2045231 2045231 chrX 96540805 96540805 TCGA-YL-A8S9 BND 19 48 AC090617.5 * chr17 3673617 3673619 chrX 45092191 45092193 TCGA-YL-A8S9 BND 38 1 P2RX5-TAX1BP3 KDM6A chr17 4055362 4055373 chrX 96542204 96542215 TCGA-YL-A8S9 BND 22 14 ZZEF1 * chr17 4055470 4055472 chrX 45092234 45092236 TCGA-YL-A8S9 BND 34 33 ZZEF1 KDM6A chr17 79158620 79158622 chrX 12589410 12589412 TCGA-YL-A8S9 BND 39 44 RBFOX3 FRMPD4 chr1 100907714 100907714 chrX 97152056 97152056 TCGA-YL-A8S9 BND 43 1 SLC30A7 DIAPH2 chr1 100907812 100907815 chrX 96542764 96542767 TCGA-YL-A8S9 BND 24 40 SLC30A7 * chr21 19826070 19826072 chrX 69235879 69235881 TCGA-YL-A8S9 BND 29 29 * * chr21 19826120 19826121 chrX 79414793 79414794 TCGA-YL-A8S9 BND 34 11 * * chr22 10662463 10662463 chrX 2627159 2627159 TCGA-YL-A8S9 BND 12 29 * CD99P1 chr4 13803074 13803074 chrX 147905057 147905057 TCGA-YL-A8S9 BND 17 15 LINC01182 * chr4 16111400 16111402 chrX 66461428 66461430 TCGA-YL-A8S9 BND 31 32 * * chr4 18343823 18343824 chrX 149233075 149233076 TCGA-YL-A8S9 BND 45 6 * * chr4 54993522 54994327 chrX 45664636 45665010 TCGA-YL-A8S9 BND 36 20 * * chr5 125937776 125937777 chrX 43083338 43083339 TCGA-YL-A8S9 BND 49 38 * * chr7 117337528 117337529 chrX 67814203 67814204 TCGA-YL-A8S9 BND 20 48 * * chr7 127139791 127139793 chrX 66209729 66209731 TCGA-YL-A8S9 BND 25 30 GRM8 HEPH chr8 102275361 102275361 chrX 12677612 12677612 TCGA-YL-A8S9 BND 42 6 UBR5 FRMPD4 chrX 147808810 147808812 chrX 147815332 147815334 TCGA-YL-A8S9 INV 45 1 * * chrX 148171884 148171887 chrX 148378978 148378981 TCGA-YL-A8S9 INV 39 33 * * chrX 148257009 148257009 chrX 148260836 148260836 TCGA-YL-A8S9 INV 42 26 * * chrX 148604324 148604326 chrX 148990904 148990906 TCGA-YL-A8S9 INV 6 18 AFF2 AFF2 chrX 18868814 18868814 chrX 154054266 154054266 TCGA-YL-A8S9 INV 50 23 * MECP2 chrX 19135593 19135594 chrX 19135825 19135826 TCGA-YL-A8S9 INV 39 20 * * chrX 2530283 2530287 chrX 2536118 2536122 TCGA-YL-A8S9 INV 22 8 * * chrX 2762810 2762811 chrY 4279937 4279938 TCGA-YL-A8S9 BND 43 4 XG * chrX 66045418 66045418 chrX 66046698 66046698 TCGA-YL-A8S9 INV 50 14 * * chrX 66072889 66072891 chrX 66701233 66701235 TCGA-YL-A8S9 INV 14 16 * * chrX 66992262 66992264 chrX 67011018 67011020 TCGA-YL-A8S9 INV 4 18 * * chrX 68145419 68145419 chrX 73872148 73872148 TCGA-YL-A8S9 INV 27 26 OPHN1 * chrX 68186382 68186384 chrX 115274938 115274940 TCGA-YL-A8S9 INV 37 6 OPHN1 * chrX 68317881 68317882 chrX 68319401 68319402 TCGA-YL-A8S9 INV 44 10 OPHN1 OPHN1 chrX 69293232 69293232 chrX 71584879 71584879 TCGA-YL-A8S9 DEL 19 19 * GCNA chrX 69545917 69545922 chrX 69838674 69838679 TCGA-YL-A8S9 DEL 38 43 * EDA chrX 74418283 74418286 chrX 74422581 74422584 TCGA-YL-A8S9 INV 6 43 * SLC16A2 chrX 74822960 74822960 chrX 149100964 149100964 TCGA-YL-A8S9 INV 14 1 NEXMIF * chrX 76375693 76375744 chrX 155932847 155932898 TCGA-YL-A8S9 DUP 41 47 * VAMP7 chrX 76379871 76379874 chrX 76382182 76382185 TCGA-YL-A8S9 INV 28 20 * * chrX 96540857 96540861 chrX 103818756 103818760 TCGA-YL-A8S9 INV 26 40 * * chrX 97151285 97151286 chrX 106872964 106872965 TCGA-YL-A8S9 DEL 44 3 DIAPH2 TBC1D8B chr15 29935228 29935232 chrX 58004193 58004197 TCGA-KK-A59Z BND 29 35 TJP1 * chr15 98354732 98354732 chrX 19452157 19452157 TCGA-KK-A59Z BND 23 2 * MAP3K15 chr17 16950931 16950933 chrX 42249931 42249933 TCGA-KK-A59Z BND 5 10 TNFRSF13B * chr1 199883802 199883806 chrX 84700359 84700363 TCGA-KK-A59Z BND 38 28 * * chr1 33656204 33656975 chrX 12187306 12187765 TCGA-KK-A59Z BND 24 32 CSMD2 FRMPD4 chr1 69615293 69616075 chrX 152954636 152955082 TCGA-KK-A59Z BND 32 44 LRRC7 ZNF185 chr3 139715794 139715796 chrX 39442530 39442532 TCGA-KK-A59Z BND 13 12 * * chr3 98195978 98196615 chrX 103761277 103761733 TCGA-KK-A59Z BND 17 28 OR5H5P * chr6 115358552 115358553 chrX 104385249 104385250 TCGA-KK-A59Z BND 21 50 AL606845.1 * chr6 136162657 136163113 chrX 143497203 143497960 TCGA-KK-A59Z BND 3 34 PDE7B AC239727.1 chr7 38245015 38245016 chrX 66921030 66921031 TCGA-KK-A59Z BND 4 34 TRGC2 * chr7 53584163 53584164 chrX 76265073 76265074 TCGA-KK-A59Z BND 16 43 * * chr8 1415255 1415255 chrX 39444306 39444306 TCGA-KK-A59Z BND 10 41 DLGAP2 * chr8 497595 497597 chrX 39456857 39456859 TCGA-KK-A59Z BND 27 39 TDRP * chr8 501794 501794 chrX 55621349 55621349 TCGA-KK-A59Z BND 31 15 TDRP * chr8 63091521 63092262 chrX 84692165 84692534 TCGA-KK-A59Z BND 16 8 * * chrX 1013424 1013476 chrX 1013812 1013812 TCGA-KK-A59Z DEL 46 21 * * chrX 113790289 113790300 chrX 113790289 113790300 TCGA-KK-A59Z INS 31 20 XACT XACT chrX 136789625 136789626 chrX 136811954 136811955 TCGA-KK-A59Z INV 8 18 RPL7P56 * chrX 136796965 136796965 chrX 137052874 137052874 TCGA-KK-A59Z INV 50 31 * * chrX 14941840 14941847 chrX 70252257 70252263 TCGA-KK-A59Z INV 6 22 * RNA5SP507 chrX 31597401 31597401 chrX 31597803 31597803 TCGA-KK-A59Z DEL 27 35 DMD DMD chrX 31722402 31722403 chrX 32397568 32397569 TCGA-KK-A59Z DEL 48 20 DMD DMD chrX 38972177 38972179 chrX 56351280 56351282 TCGA-KK-A59Z DEL 39 38 * * chrX 66409827 66410747 chrX 69213497 69214206 TCGA-KK-A59Z DUP 41 5 * * chrX 66759153 66759155 chrX 67072305 67072309 TCGA-KK-A59Z DUP 1 1 * * chrX 66828610 66828615 chrX 66926005 66926010 TCGA-KK-A59Z DUP 38 25 * * chrX 69024582 69024584 chrX 69379845 69379847 TCGA-KK-A59Z DUP 27 12 * * chrX 77899590 77899593 chrX 77902639 77902642 TCGA-KK-A59Z DEL 49 33 COX7B COX7B chrX 8323693 8323695 chrX 108012977 108012979 TCGA-KK-A59Z INV 35 2 * * chrX 85843825 85843825 chrX 85867225 85867225 TCGA-KK-A59Z DEL 25 26 * CHM chrX 92665786 92665790 chrX 92698781 92698785 TCGA-KK-A59Z DEL 38 40 * * chrX 94502416 94502416 chrX 94619872 94619872 TCGA-KK-A59Z DUP 40 16 * * chrX 95666507 95666510 chrX 95670714 95670717 TCGA-KK-A59Z DEL 11 16 * * chr4 54765963 54765963 chrX 21304828 21304828 TCGA-YL-A8HM BND 11 19 * AL807742.1 chrX 105636095 105636095 chrX 105644314 105644314 TCGA-YL-A8HM DEL 50 27 IL1RAPL2 IL1RAPL2 chrX 127689850 127689852 chrX 127689966 127689966 TCGA-YL-A8HM DEL 27 45 * * chrX 47942744 47942744 chrX 47942821 47942821 TCGA-YL-A8HM DEL 35 34 ZNF81 ZNF81 chr9 116840418 116840421 chrX 53967332 53967335 TCGA-HC-A6AP BND 26 5 ASTN2 PHF8 chrX 131816622 131816634 chrX 135565547 135565547 TCGA-HC-A6AP INV 6 22 FIRRE INTS6L chr16 1426795 1426795 chrX 48472707 48472707 TCGA-J4-A6G3 BND 18 7 * * chr16 1427724 1427724 chrX 48474379 48474379 TCGA-J4-A6G3 BND 43 28 * * chr16 1428337 1428338 chrX 48474618 48474619 TCGA-J4-A6G3 BND 12 23 * FTSJ1 chr16 8393364 8393369 chrX 3235843 3235848 TCGA-J4-A6G3 BND 47 13 * * chr4 170117031 170117477 chrX 16182864 16183701 TCGA-J4-A6G3 BND 45 31 * * chrX 10717903 10717904 chrX 10718589 10718589 TCGA-J4-A6G3 DEL 36 48 MID1 MID1 chrX 10948079 10948081 chrX 10948156 10948156 TCGA-J4-A6G3 DEL 20 32 AC073529.1 AC073529.1 chrX 116176010 116176013 chrX 116176229 116176229 TCGA-J4-A6G3 DEL 32 10 * * chrX 128698319 128698319 chrX 128698448 128698448 TCGA-J4-A6G3 DEL 21 46 * * chrX 129831194 129831197 chrX 129831293 129831293 TCGA-J4-A6G3 DEL 44 12 ZDHHC9 ZDHHC9 chrX 16182914 16183705 chrX 30453691 30454222 TCGA-J4-A6G3 DUP 46 18 * * chrX 1685770 1685773 chrX 1742046 1742049 TCGA-J4-A6G3 DEL 37 20 * AL683807.1 chrX 1736356 1736358 chrX 1742995 1742997 TCGA-J4-A6G3 DUP 45 49 AL683807.1 AL683807.1 chrX 1736952 1736973 chrX 1742990 1743011 TCGA-J4-A6G3 DEL 23 16 AL683807.1 AL683807.1 chrX 18553710 18553710 chrX 18554221 18554221 TCGA-J4-A6G3 DEL 9 9 CDKL5 CDKL5 chrX 21001130 21001134 chrX 21001364 21001364 TCGA-J4-A6G3 DEL 42 15 AL807742.1 AL807742.1 chrX 23972012 23972012 chrX 57216651 57216651 TCGA-J4-A6G3 DUP 41 44 * * chrX 25003799 25003804 chrX 25086582 25086587 TCGA-J4-A6G3 DEL 40 48 ARX * chrX 27079111 27079112 chrX 27079167 27079167 TCGA-J4-A6G3 DEL 36 34 AC112493.1 AC112493.1 chrX 34248397 34248398 chrX 34414852 34414853 TCGA-J4-A6G3 INV 14 9 AL592043.1 AL592043.1 chrX 34260534 34260538 chrX 34414883 34414887 TCGA-J4-A6G3 INV 36 17 AL592043.1 AL592043.1 chrX 53072959 53072962 chrX 53073011 53073011 TCGA-J4-A6G3 DEL 40 42 GPR173 GPR173 chrX 66833252 66833254 chrX 66939049 66939051 TCGA-J4-A6G3 DUP 40 16 * * chrX 77110782 77110787 chrX 77110918 77110918 TCGA-J4-A6G3 DEL 23 16 * * chrX 83862497 83862501 chrX 83862631 83862631 TCGA-J4-A6G3 DEL 25 24 CYLC1 CYLC1 chr5 107080509 107080509 chrX 98493978 98493978 TCGA-Y6-A8TL BND 22 49 * AL157778.1 chr5 114056235 114056235 chrX 98499607 98499607 TCGA-Y6-A8TL BND 38 13 KCNN2 AL157778.1 chr5 153947864 153948391 chrX 122140123 122140489 TCGA-Y6-A8TL BND 31 24 * * chr5 155323262 155323264 chrX 98493854 98493856 TCGA-Y6-A8TL BND 22 25 * AL157778.1 chr7 38952737 38952740 chrX 97932116 97932119 TCGA-Y6-A8TL BND 37 34 * * chrX 141877962 141877965 chrX 146425146 146425149 TCGA-Y6-A8TL INV 45 4 MAGEC3 * chrX 146769660 146769662 chrX 146791543 146791545 TCGA-Y6-A8TL DEL 2 22 * * chrX 147048824 147048826 chrX 147048960 147048962 TCGA-Y6-A8TL DUP 36 43 * * chrX 25409408 25409408 chrX 125658023 125658023 TCGA-Y6-A8TL INV 36 31 * * chrX 29882413 29882413 chrX 29954447 29954447 TCGA-Y6-A8TL INV 33 27 IL1RAPL1 IL1RAPL1 chrX 34699528 34699541 chrX 34699528 34699541 TCGA-Y6-A8TL INS 6 44 * * chrX 66668466 66668466 chrX 66668645 66668645 TCGA-Y6-A8TL DUP 8 25 * * chrX 66929036 66929036 chrX 131249123 131249123 TCGA-Y6-A8TL DUP 18 14 * * chr11 109180848 109181193 chrX 109070031 109070669 TCGA-ZG-A9LB BND 14 3 * * chr12 106209787 106210196 chrX 141252069 141252416 TCGA-ZG-A9LB BND 22 38 * * chr14 34047231 34047997 chrX 106354297 106354770 TCGA-ZG-A9LB BND 23 18 EGLN3 * chr15 56669876 56669876 chrX 126035804 126035804 TCGA-ZG-A9LB BND 12 14 ZNF280D * chr16 72695350 72695359 chrX 55270268 55270277 TCGA-ZG-A9LB BND 2 5 AC004943.2 * chr17 68736683 68737419 chrX 69940081 69940515 TCGA-ZG-A9LB BND 15 18 LINC01482 EDA chr19 55388623 55389097 chrX 102596060 102596704 TCGA-ZG-A9LB BND 36 18 RPL28 * chr19 55388987 55388990 chrX 70043179 70043182 TCGA-ZG-A9LB BND 2 50 RPL28 AWAT2 chr19 55389856 55389859 chrX 111131600 111131603 TCGA-ZG-A9LB BND 34 39 RPL28 PAK3 chr2 137280498 137280498 chrX 11713174 11713178 TCGA-ZG-A9LB BND 44 39 THSD7B AC004554.1 chr4 63061720 63062417 chrX 27001987 27002370 TCGA-ZG-A9LB BND 31 50 * * chrX 10885367 10885370 chrX 11037157 11037160 TCGA-ZG-A9LB DUP 5 7 AC073529.1 AC073529.1 chrX 11969427 11969427 chrX 11969852 11969852 TCGA-ZG-A9LB DEL 18 9 * * chrX 128748387 128748387 chrX 128984014 128984014 TCGA-ZG-A9LB DUP 5 27 * * chrX 141929089 141929091 chrX 145360589 145360591 TCGA-ZG-A9LB DUP 31 27 * * chrX 16182976 16183626 chrX 30453701 30454217 TCGA-ZG-A9LB DUP 24 42 * * chrX 18312042 18312045 chrX 18599474 18599477 TCGA-ZG-A9LB DUP 36 45 SCML2 CDKL5 chrX 21824544 21824544 chrX 77554446 77554446 TCGA-ZG-A9LB INV 28 11 * ATRX chrX 2197061 2197064 chrX 48672810 48672813 TCGA-ZG-A9LB INV 34 40 * * chrX 2197061 2197064 chrX 48673107 48673110 TCGA-ZG-A9LB INV 29 24 * * chrX 3261922 3261935 chrX 3261922 3261935 TCGA-ZG-A9LB INS 14 14 * * chrX 41814838 41814841 chrX 82541870 82541873 TCGA-ZG-A9LB INV 49 15 CASK * chrX 4326515 4326519 chrX 9274684 9274688 TCGA-ZG-A9LB DUP 33 37 * AC003684.1 chrX 4336031 4336032 chrX 4336113 4336113 TCGA-ZG-A9LB DEL 37 20 * * chrX 47230044 47230044 chrX 47231371 47231371 TCGA-ZG-A9LB DEL 6 42 * USP11 chrX 49765789 49765789 chrX 51946388 51946388 TCGA-ZG-A9LB DEL 45 31 * * chrX 5225389 5225390 chrX 5301478 5301479 TCGA-ZG-A9LB DUP 11 6 * * chrX 57592489 57592939 chrX 57909711 57910186 TCGA-ZG-A9LB INV 2 32 ZXDB ZXDA chrX 67492286 67492288 chrX 67891246 67891248 TCGA-ZG-A9LB DUP 38 21 * * chrX 70043344 70043347 chrX 102596458 102596461 TCGA-ZG-A9LB DEL 25 48 AWAT2 * chrX 7679080 7679094 chrX 7679080 7679094 TCGA-ZG-A9LB INS 14 47 * * chrX 8338963 8338963 chrX 8952829 8952829 TCGA-ZG-A9LB DUP 33 32 * * chrX 8838244 8838244 chrX 11970949 11970949 TCGA-ZG-A9LB DUP 15 45 * * chrX 88722525 88722528 chrX 88926160 88926163 TCGA-ZG-A9LB DUP 7 27 * * chrX 91724749 91724749 chrX 106636408 106636408 TCGA-ZG-A9LB INV 9 8 * RADX chr10 13845211 13845211 chrX 69362809 69362809 TCGA-2A-A8VX BND 39 9 FRMD4A * chr10 3107088 3107088 chrX 40974256 40974256 TCGA-2A-A8VX BND 9 31 PFKP * chr12 102621289 102621297 chrX 124124140 124124148 TCGA-2A-A8VX BND 4 2 * STAG2 chr18 47352586 47353031 chrX 69834779 69835678 TCGA-2A-A8VX BND 32 16 MIR4527HG EDA chr18 57204144 57204145 chrX 23681197 23681198 TCGA-2A-A8VX BND 38 16 * PRDX4 chr19 4415682 4416027 chrX 18868615 18869099 TCGA-2A-A8VX BND 2 37 CHAF1A * chr2 103276792 103276792 chrX 40961339 40961339 TCGA-2A-A8VX BND 17 28 * * chr2 56062925 56062933 chrX 141252391 141252399 TCGA-2A-A8VX BND 20 19 AC011306.1 * chr2 79176011 79176011 chrX 24745524 24745524 TCGA-2A-A8VX BND 2 4 AC011754.1 POLA1 chr3 131016245 131016248 chrX 20450313 20450316 TCGA-2A-A8VX BND 46 39 ATP2C1 AL807740.1 chr3 131016333 131016334 chrX 20451524 20451525 TCGA-2A-A8VX BND 3 4 ATP2C1 AL807740.1 chr4 169828549 169828933 chrX 40211076 40211470 TCGA-2A-A8VX BND 7 17 * * chr4 85137708 85137711 chrX 119965204 119965207 TCGA-2A-A8VX BND 46 43 * RHOXF1P3 chr8 39995196 39995196 chrX 104761848 104761848 TCGA-2A-A8VX BND 49 21 AC007991.3 IL1RAPL2 chr9 36680918 36680922 chrX 20974700 20974704 TCGA-2A-A8VX BND 30 11 * AL807742.1 chr9 36681070 36681070 chrX 20225533 20225533 TCGA-2A-A8VX BND 43 31 * RPS6KA3 chrX 11714349 11714349 chrX 66354878 66354878 TCGA-2A-A8VX DUP 43 44 AC004554.1 * chrX 1296247 1296627 chrX 1298516 1299097 TCGA-2A-A8VX DEL 26 19 CSF2RA CSF2RA chrX 1356094 1356097 chrX 1356198 1356201 TCGA-2A-A8VX INV 7 32 IL3RA IL3RA chrX 136879121 136879121 chrX 136879318 136879318 TCGA-2A-A8VX DEL 14 1 RBMX RBMX chrX 14517102 14517105 chrX 14518045 14518048 TCGA-2A-A8VX INV 6 43 * * chrX 14618561 14618564 chrX 14619100 14619103 TCGA-2A-A8VX INV 31 46 GLRA2 GLRA2 chrX 14995643 14995648 chrX 15016668 15016673 TCGA-2A-A8VX INV 35 24 * * chrX 15511592 15511593 chrX 22672926 22672927 TCGA-2A-A8VX INV 8 14 BMX PTCHD1-AS chrX 16193816 16193820 chrX 16194961 16194965 TCGA-2A-A8VX INV 19 26 * * chrX 16424081 16424085 chrX 16427404 16427408 TCGA-2A-A8VX INV 42 25 * * chrX 18335601 18335602 chrX 22673701 22673702 TCGA-2A-A8VX DUP 41 19 SCML2 PTCHD1-AS chrX 20196073 20196075 chrX 20209039 20209041 TCGA-2A-A8VX INV 19 23 RPS6KA3 RPS6KA3 chrX 21650703 21650706 chrX 21652271 21652274 TCGA-2A-A8VX INV 26 39 CNKSR2 CNKSR2 chrX 21775948 21775950 chrX 21855524 21855526 TCGA-2A-A8VX DEL 13 8 * MBTPS2 chrX 22097242 22097242 chrX 22097698 22097698 TCGA-2A-A8VX DEL 47 3 PHEX PHEX chrX 22097855 22097859 chrX 22098577 22098581 TCGA-2A-A8VX INV 37 10 PHEX PHEX chrX 22718631 22718632 chrX 23056495 23056496 TCGA-2A-A8VX DEL 50 38 PTCHD1-AS PTCHD1-AS chrX 26310974 26310975 chrX 39563824 39563825 TCGA-2A-A8VX DEL 50 27 * * chrX 26568445 26568446 chrX 32976377 32976378 TCGA-2A-A8VX DEL 39 9 * DMD chrX 37296942 37296944 chrX 38010927 38010929 TCGA-2A-A8VX DEL 2 41 * AF241726.1 chrX 37959464 37959465 chrX 42442243 42442244 TCGA-2A-A8VX DUP 16 50 AF241726.1 Z93403.1 chrX 39161375 39161376 chrX 46690980 46690981 TCGA-2A-A8VX INV 34 37 * SLC9A7 chrX 39170345 39170347 chrX 41148765 41148767 TCGA-2A-A8VX DUP 17 3 * USP9X chrX 39180070 39180071 chrX 65726309 65726310 TCGA-2A-A8VX DEL 46 43 * MSN chrX 39490104 39490104 chrX 67289058 67289058 TCGA-2A-A8VX INV 11 23 * * chrX 39504586 39504586 chrX 67289079 67289079 TCGA-2A-A8VX INV 16 17 * * chrX 39507669 39507670 chrX 67171807 67171808 TCGA-2A-A8VX DEL 5 34 * * chrX 40916095 40916098 chrX 41044349 41044352 TCGA-2A-A8VX INV 40 46 * * chrX 40925546 40925546 chrX 69233937 69233937 TCGA-2A-A8VX INV 15 8 * * chrX 41186299 41186301 chrX 69171369 69171371 TCGA-2A-A8VX INV 44 35 USP9X * chrX 41204207 41204207 chrX 41205707 41205707 TCGA-2A-A8VX INV 2 46 USP9X USP9X chrX 41805640 41805641 chrX 42416278 42416279 TCGA-2A-A8VX INV 21 45 CASK Z93403.1 chrX 41837407 41837409 chrX 42167325 42167327 TCGA-2A-A8VX INV 14 40 CASK * chrX 41976855 41976857 chrX 42045713 42045713 TCGA-2A-A8VX INV 9 2 * * chrX 41976855 41976857 chrX 41978338 41978340 TCGA-2A-A8VX INV 22 2 * * chrX 41988921 41988923 chrX 42019067 42019069 TCGA-2A-A8VX INV 1 14 * * chrX 42006960 42006960 chrX 42047341 42047341 TCGA-2A-A8VX INV 5 5 * * chrX 42011982 42011986 chrX 42026739 42026743 TCGA-2A-A8VX DUP 24 37 * * chrX 42035325 42035327 chrX 42043384 42043386 TCGA-2A-A8VX INV 11 27 * * chrX 42162782 42162783 chrX 65347952 65347953 TCGA-2A-A8VX INV 25 41 * * chrX 42577754 42578761 chrX 64961785 64962637 TCGA-2A-A8VX DEL 38 31 Z93403.1 ZC4H2 chrX 45640156 45640156 chrX 45641061 45641061 TCGA-2A-A8VX INV 18 24 * * chrX 45653358 45653361 chrX 45655459 45655462 TCGA-2A-A8VX DEL 40 43 * * chrX 45775964 45775964 chrX 67287225 67287225 TCGA-2A-A8VX INV 7 32 * * chrX 45834441 45834443 chrX 67959723 67959725 TCGA-2A-A8VX INV 12 23 * * chrX 45877098 45877098 chrX 69299639 69299639 TCGA-2A-A8VX DUP 50 14 * * chrX 45877218 45877851 chrX 69169536 69170015 TCGA-2A-A8VX INV 29 27 * * chrX 45877229 45877840 chrX 46469776 46470711 TCGA-2A-A8VX INV 15 13 * KRBOX4 chrX 45877324 45877335 chrX 46471105 46471105 TCGA-2A-A8VX INV 16 23 * KRBOX4 chrX 45877324 45877335 chrX 45877324 45877335 TCGA-2A-A8VX INS 5 16 * * chrX 45877324 45877335 chrX 46485273 46485274 TCGA-2A-A8VX DEL 48 17 * KRBOX4 chrX 45877522 45877522 chrX 46471826 46471826 TCGA-2A-A8VX DUP 7 41 * KRBOX4 chrX 45878004 45878015 chrX 69300770 69300774 TCGA-2A-A8VX DUP 30 2 * * chrX 45878004 45878015 chrX 68892709 68892718 TCGA-2A-A8VX DEL 39 5 * * chrX 45881814 45881814 chrX 46471629 46471634 TCGA-2A-A8VX INV 20 35 * KRBOX4 chrX 45965707 45965711 chrX 68235201 68235205 TCGA-2A-A8VX INV 27 3 * OPHN1 chrX 45976947 45976948 chrX 69477290 69477291 TCGA-2A-A8VX INV 5 43 * * chrX 46020043 46020044 chrX 69164252 69164253 TCGA-2A-A8VX INV 43 13 * PJA1 chrX 46240102 46240102 chrX 70038300 70038300 TCGA-2A-A8VX DUP 40 34 * EDA chrX 46413429 46413481 chrX 112604901 112604953 TCGA-2A-A8VX INV 42 48 * * chrX 46468902 46468905 chrX 68633137 68633140 TCGA-2A-A8VX INV 25 49 KRBOX4 * chrX 46469828 46469829 chrX 46485160 46485161 TCGA-2A-A8VX DUP 10 31 KRBOX4 KRBOX4 chrX 46470291 46470293 chrX 46485427 46485438 TCGA-2A-A8VX INV 36 6 KRBOX4 KRBOX4 chrX 46471492 46471492 chrX 46485427 46485438 TCGA-2A-A8VX DEL 22 30 KRBOX4 KRBOX4 chrX 46471629 46471634 chrX 69300007 69300007 TCGA-2A-A8VX INV 21 47 KRBOX4 * chrX 46486189 46486189 chrX 70047524 70047524 TCGA-2A-A8VX INV 33 47 KRBOX4 AWAT2 chrX 46486373 46486374 chrX 68892414 68892415 TCGA-2A-A8VX INV 6 30 KRBOX4 * chrX 46486490 46486954 chrX 69169725 69170430 TCGA-2A-A8VX DEL 23 8 KRBOX4 * chrX 46708219 46708239 chrX 46711397 46711399 TCGA-2A-A8VX INV 37 46 SLC9A7 SLC9A7 chrX 46791446 46791450 chrX 70161828 70161832 TCGA-2A-A8VX INV 37 3 * IGBP1 chrX 65211475 65211475 chrX 65224789 65224789 TCGA-2A-A8VX DEL 7 34 * * chrX 65328785 65328788 chrX 65370795 65370798 TCGA-2A-A8VX INV 44 19 MORF4L1P5 ZC3H12B chrX 65350917 65350917 chrX 65365676 65365676 TCGA-2A-A8VX INV 44 27 * ZC3H12B chrX 65425015 65425017 chrX 65426914 65426916 TCGA-2A-A8VX INV 14 22 ZC3H12B ZC3H12B chrX 65919627 65919628 chrX 65920723 65920724 TCGA-2A-A8VX INV 44 26 * * chrX 65936973 65936973 chrX 65962790 65962790 TCGA-2A-A8VX DUP 1 49 * * chrX 66061596 66061597 chrX 67576688 67576689 TCGA-2A-A8VX DEL 10 13 * AR chrX 66177852 66177852 chrX 67649748 67649748 TCGA-2A-A8VX INV 41 48 HEPH AR chrX 66816440 66816443 chrX 66824902 66824914 TCGA-2A-A8VX INV 26 42 * * chrX 66824902 66824914 chrX 66952841 66952841 TCGA-2A-A8VX INV 40 37 * * chrX 66852366 66852369 chrX 66855344 66855347 TCGA-2A-A8VX INV 7 23 * * chrX 66854205 66854205 chrX 66855022 66855022 TCGA-2A-A8VX INV 50 29 * * chrX 66857722 66857724 chrX 66941636 66941638 TCGA-2A-A8VX INV 32 30 * * chrX 66916100 66916100 chrX 66920112 66920112 TCGA-2A-A8VX INV 27 35 * * chrX 66948352 66948355 chrX 67145092 67145095 TCGA-2A-A8VX DUP 42 19 * * chrX 66949083 66949084 chrX 69968232 69968233 TCGA-2A-A8VX INV 26 42 * EDA chrX 66957175 66957175 chrX 68547779 68547779 TCGA-2A-A8VX INV 13 31 * * chrX 66957960 66957962 chrX 69279694 69279696 TCGA-2A-A8VX INV 25 9 * * chrX 67078012 67078014 chrX 69253047 69253049 TCGA-2A-A8VX INV 31 13 * * chrX 67092579 67092581 chrX 70091014 70091016 TCGA-2A-A8VX INV 23 4 * * chrX 67100017 67100019 chrX 68193550 68193552 TCGA-2A-A8VX DEL 40 38 * OPHN1 chrX 67197599 67197599 chrX 67199125 67199125 TCGA-2A-A8VX INV 36 1 * * chrX 67432352 67432354 chrX 69288194 69288196 TCGA-2A-A8VX DUP 21 21 * * chrX 67466106 67466107 chrX 68621601 68621602 TCGA-2A-A8VX DUP 25 48 * * chrX 67638390 67638392 chrX 69521818 69521820 TCGA-2A-A8VX DUP 3 30 AR FAM155B chrX 67964079 67964081 chrX 69598976 69598978 TCGA-2A-A8VX DUP 21 40 * * chrX 68083914 68083916 chrX 68413519 68413521 TCGA-2A-A8VX INV 9 43 OPHN1 OPHN1 chrX 68107305 68107308 chrX 68405936 68405939 TCGA-2A-A8VX INV 30 42 OPHN1 OPHN1 chrX 68176138 68176139 chrX 69408109 69408110 TCGA-2A-A8VX INV 46 21 OPHN1 * chrX 68185941 68185942 chrX 70114395 70114396 TCGA-2A-A8VX DEL 7 22 OPHN1 * chrX 68218911 68218911 chrX 68247429 68247429 TCGA-2A-A8VX INV 43 47 OPHN1 OPHN1 chrX 68332083 68332083 chrX 68538245 68538245 TCGA-2A-A8VX DUP 4 27 OPHN1 * chrX 68610859 68610859 chrX 68888623 68888623 TCGA-2A-A8VX INV 29 14 * * chrX 68834310 68834329 chrX 70037989 70037993 TCGA-2A-A8VX DEL 22 32 EFNB1 EDA chrX 68834310 68834329 chrX 69300007 69300007 TCGA-2A-A8VX INV 25 3 EFNB1 * chrX 68892709 68892718 chrX 70047666 70047671 TCGA-2A-A8VX INV 22 22 * AWAT2 chrX 68927253 68927253 chrX 69151538 69151538 TCGA-2A-A8VX INV 4 24 * * chrX 69067045 69067049 chrX 69068744 69068748 TCGA-2A-A8VX INV 34 48 * * chrX 69170092 69170096 chrX 69304802 69304805 TCGA-2A-A8VX DEL 20 34 * * chrX 69170092 69170096 chrX 69299935 69299936 TCGA-2A-A8VX INV 46 38 * * chrX 69444101 69444101 chrX 69450450 69450450 TCGA-2A-A8VX INV 43 43 * * chrX 69820140 69820605 chrX 69923891 69924751 TCGA-2A-A8VX INV 42 48 EDA EDA chrX 907508 907508 chrX 908083 908083 TCGA-2A-A8VX DEL 32 19 * * chrX 95123220 95123220 chrX 95270199 95270199 TCGA-2A-A8VX INV 18 29 * * chrX 95243221 95243222 chrX 95246918 95246919 TCGA-2A-A8VX INV 21 46 * * chr17 5058441 5058441 chrX 22682604 22682604 TCGA-V1-A9ZK BND 36 42 * PTCHD1-AS chr2 171866465 171866470 chrX 78265527 78265532 TCGA-V1-A9ZK BND 42 22 SLC25A12 * chrX 10318992 10318992 chrX 10319568 10319568 TCGA-V1-A9ZK DEL 31 5 AC003666.1 AC003666.1 chrX 12846856 12846858 chrX 153655912 153655914 TCGA-V1-A9ZK INV 39 17 MRPL35P4 * chrX 427313 427315 chrX 427655 427655 TCGA-V1-A9ZK DEL 33 8 * * chrX 48673055 48673059 chrX 95551524 95551528 TCGA-V1-A9ZK DEL 36 29 * * chrX 66730981 66730984 chrX 68088937 68088940 TCGA-V1-A9ZK DUP 29 39 * OPHN1 chrX 66897911 66897916 chrX 67233896 67233901 TCGA-V1-A9ZK DUP 40 10 * * chrX 76671970 76671972 chrX 83502524 83502526 TCGA-V1-A9ZK INV 46 18 MIR325HG * chr10 36754038 36754038 chrX 48280881 48280881 TCGA-KK-A8IA BND 13 3 * AC245047.4 chr5 176305757 176306151 chrX 42285416 42285983 TCGA-KK-A8IA BND 36 44 SIMC1 AL023875.1 chrX 11421051 11421054 chrX 11524001 11524004 TCGA-KK-A8IA DUP 31 14 ARHGAP6 ARHGAP6 chrX 114521239 114521243 chrX 114522429 114522433 TCGA-KK-A8IA DEL 18 40 * * chrX 57592512 57592918 chrX 57909471 57910160 TCGA-KK-A8IA INV 28 12 ZXDB ZXDA chrX 66857939 66857941 chrX 66927903 66927905 TCGA-KK-A8IA DUP 21 18 * * chrX 66884426 66884427 chrX 66888517 66888518 TCGA-KK-A8IA DEL 43 41 * * chrX 7483131 7483132 chrX 8260760 8260761 TCGA-KK-A8IA DUP 37 25 * * chrX 86274653 86274653 chrX 135894479 135894479 TCGA-KK-A8IA DEL 50 12 DACH2 SAGE1 chr1 212312937 212312938 chrX 91126241 91126242 TCGA-M7-A722 BND 16 1 PPP2R5A * chr20 8742605 8742605 chrX 73077016 73077016 TCGA-M7-A722 BND 21 16 PLCB1 * chr2 15741234 15741235 chrX 11934864 11934864 TCGA-M7-A722 BND 27 41 LINC01804 * chr2 15741234 15741235 chrX 11935013 11935072 TCGA-M7-A722 BND 45 25 LINC01804 * chr3 73131142 73131142 chrX 65397224 65397224 TCGA-M7-A722 BND 43 20 * ZC3H12B chr4 36697467 36697478 chrX 566865 566876 TCGA-M7-A722 BND 43 22 * * chr6 160235023 160235679 chrX 153013661 153014125 TCGA-M7-A722 BND 39 28 SLC22A2 * chrX 104855667 104855670 chrX 104855805 104855805 TCGA-M7-A722 DEL 12 48 IL1RAPL2 IL1RAPL2 chrX 121900926 121900926 chrX 121959736 121959736 TCGA-M7-A722 DEL 36 2 * * chrX 24902888 24902892 chrX 70499566 70499570 TCGA-M7-A722 DUP 15 4 POLA1 DLG3 chrX 25389957 25389957 chrX 63526917 63526917 TCGA-M7-A722 INV 48 35 * LINC01278 chrX 26027375 26027380 chrX 26127619 26127624 TCGA-M7-A722 DEL 11 50 * * chrX 28464067 28464072 chrX 63801031 63801036 TCGA-M7-A722 INV 6 29 * ARHGEF9 chrX 41375914 41375917 chrX 41376408 41376408 TCGA-M7-A722 DEL 21 29 * * chrX 41818189 41818189 chrX 66729622 66729622 TCGA-M7-A722 DUP 49 23 CASK * chrX 41818344 41818344 chrX 44995791 44995791 TCGA-M7-A722 DEL 16 29 CASK KDM6A chrX 44976017 44976019 chrX 63770280 63770282 TCGA-M7-A722 INV 39 22 KDM6A ARHGEF9 chrX 44979241 44979243 chrX 63778740 63778742 TCGA-M7-A722 DEL 21 44 KDM6A ARHGEF9 chrX 45009931 45009933 chrX 68076612 68076614 TCGA-M7-A722 DEL 45 5 KDM6A OPHN1 chrX 50322046 50322046 chrX 50331439 50331439 TCGA-M7-A722 DEL 34 22 CCNB3 CCNB3 chrX 53587784 53587785 chrX 63534437 63534438 TCGA-M7-A722 INV 12 43 HUWE1 LINC01278 chrX 63514078 63514080 chrX 66729317 66729319 TCGA-M7-A722 DEL 35 17 LINC01278 * chrX 63535503 63535506 chrX 67801910 67801913 TCGA-M7-A722 INV 15 5 LINC01278 * chrX 64215689 64215693 chrX 64216177 64216181 TCGA-M7-A722 DUP 26 50 * * chrX 64474880 64474880 chrX 64577199 64577199 TCGA-M7-A722 INV 3 49 * * chrX 64568896 64568896 chrX 79493036 79493036 TCGA-M7-A722 INV 48 2 * * chrX 65914488 65914492 chrX 65915272 65915272 TCGA-M7-A722 DEL 30 40 * * chrX 66320870 66320872 chrX 66722397 66722399 TCGA-M7-A722 INV 21 31 * * chrX 66828497 66828499 chrX 66829368 66829370 TCGA-M7-A722 INV 5 23 * * chrX 68069039 68069039 chrX 68091155 68091155 TCGA-M7-A722 INV 10 16 OPHN1 OPHN1 chrX 68236142 68236143 chrX 68237833 68237834 TCGA-M7-A722 INV 50 25 OPHN1 OPHN1 chr4 54460169 54460840 chrX 82767254 82767749 TCGA-YL-A9WY BND 38 22 * * chr4 54460193 54460961 chrX 82766781 82767269 TCGA-YL-A9WY BND 29 45 * * chrX 2197061 2197064 chrX 48672810 48672813 TCGA-YL-A9WY INV 26 22 * * chrX 57012424 57012432 chrX 86006849 86006857 TCGA-YL-A9WY INV 30 12 * CHM chrX 65626975 65626978 chrX 67803593 67803596 TCGA-YL-A9WY DUP 14 12 MSN * chrX 66460529 66460529 chrX 67877963 67877963 TCGA-YL-A9WY INV 35 32 * * chrX 66815063 66815064 chrX 66910476 66910477 TCGA-YL-A9WY DUP 24 21 * * chrX 67682040 67682041 chrX 67682099 67682099 TCGA-YL-A9WY DEL 39 26 AR AR chr11 5880452 5881145 chrX 148895691 148896188 TCGA-YL-A9WI BND 27 45 TRIM5 AFF2 chr11 8978672 8978672 chrX 147999981 147999981 TCGA-YL-A9WI BND 45 6 * FMR1NB chr12 59909108 59909579 chrX 67349485 67350216 TCGA-YL-A9WI BND 27 32 * * chr13 29433374 29433374 chrX 68151578 68151578 TCGA-YL-A9WI BND 42 31 MTUS2 OPHN1 chr18 2492651 2492651 chrX 129172018 129172018 TCGA-YL-A9WI BND 8 9 * * chr1 24267584 24268061 chrX 66791476 66792439 TCGA-YL-A9WI BND 36 35 * * chr1 98155010 98155481 chrX 10569308 10570235 TCGA-YL-A9WI BND 45 18 * MID1 chr3 84925502 84925980 chrX 67981458 67982380 TCGA-YL-A9WI BND 44 17 * * chr4 112207297 112207316 chrX 118280073 118280092 TCGA-YL-A9WI BND 7 11 * AL391358.1 chr4 35494821 35495311 chrX 66891587 66892414 TCGA-YL-A9WI BND 4 32 RNU6-573P * chr5 28417875 28418354 chrX 67981192 67982190 TCGA-YL-A9WI BND 16 41 * * chr6 146031907 146032376 chrX 67349502 67350188 TCGA-YL-A9WI BND 4 36 GRM1 * chr6 146032363 146032835 chrX 67349290 67350068 TCGA-YL-A9WI BND 1 22 GRM1 * chr8 116387758 116387761 chrX 28519760 28519763 TCGA-YL-A9WI BND 37 6 * * chr8 120039294 120039765 chrX 67349457 67350316 TCGA-YL-A9WI BND 34 2 DEPTOR * chr8 69602742 69602743 chrX 79566512 79566513 TCGA-YL-A9WI BND 33 20 SULF1 * chr8 71662821 71662823 chrX 91667698 91667700 TCGA-YL-A9WI BND 3 47 * * chr9 23210932 23210932 chrX 143604707 143604707 TCGA-YL-A9WI BND 16 35 AL391117.1 * chr9 23302702 23302702 chrX 144669914 144669914 TCGA-YL-A9WI BND 25 44 AL391117.1 * chr9 24108368 24108812 chrX 10569430 10570263 TCGA-YL-A9WI BND 29 4 * MID1 chrX 102514459 102514460 chrX 102802218 102802219 TCGA-YL-A9WI DUP 26 11 TMSB15A LINC00630 chrX 102937846 102937847 chrX 103002474 103002475 TCGA-YL-A9WI DEL 30 17 RAB40AL * chrX 10569352 10570443 chrX 152585280 152585784 TCGA-YL-A9WI DUP 48 24 MID1 * chrX 10569724 10569724 chrX 66791793 66791793 TCGA-YL-A9WI INV 15 11 MID1 * chrX 10572886 10573693 chrX 67599480 67600273 TCGA-YL-A9WI DUP 16 18 MID1 AR chrX 10573951 10574622 chrX 66791417 66792252 TCGA-YL-A9WI INV 10 44 MID1 * chrX 10578059 10578061 chrX 67983577 67983579 TCGA-YL-A9WI INV 18 38 MID1 * chrX 116229168 116229168 chrX 116694598 116694598 TCGA-YL-A9WI INV 4 17 * BX119904.1 chrX 139782104 139782104 chrX 140497852 140497852 TCGA-YL-A9WI DUP 4 17 ATP11C * chrX 142965055 142965058 chrX 143515523 143515526 TCGA-YL-A9WI INV 34 7 * AC239727.1 chrX 142981810 142981812 chrX 143844042 143844044 TCGA-YL-A9WI DUP 21 5 * * chrX 143927475 143927478 chrX 144503218 144503221 TCGA-YL-A9WI DUP 33 27 * * chrX 144359222 144359222 chrX 144521862 144521862 TCGA-YL-A9WI DEL 31 7 * * chrX 144364618 144364620 chrX 144520163 144520165 TCGA-YL-A9WI DEL 25 14 * * chrX 146015096 146015097 chrX 146042986 146042987 TCGA-YL-A9WI DEL 14 43 * * chrX 57097930 57097930 chrX 84700359 84700363 TCGA-YL-A9WI DEL 2 38 * * chrX 5790528 5790531 chrX 6976124 6976127 TCGA-YL-A9WI DUP 2 46 * * chrX 63831233 63831234 chrX 67346144 67346145 TCGA-YL-A9WI DUP 47 47 * * chrX 64378281 64378282 chrX 66506846 66506847 TCGA-YL-A9WI DUP 43 42 MTMR8 * chrX 64649748 64649750 chrX 68151438 68151440 TCGA-YL-A9WI INV 50 30 * OPHN1 chrX 64717265 64717267 chrX 64718627 64718629 TCGA-YL-A9WI INV 3 4 * * chrX 64779391 64779393 chrX 65291705 65291707 TCGA-YL-A9WI DEL 4 26 * * chrX 65501925 65501929 chrX 65503413 65503417 TCGA-YL-A9WI INV 45 33 ZC3H12B ZC3H12B chrX 65708327 65708377 chrX 65708717 65708717 TCGA-YL-A9WI DEL 3 43 MSN MSN chrX 65726404 65726404 chrX 65728434 65728434 TCGA-YL-A9WI DEL 1 13 MSN MSN chrX 66860208 66860209 chrX 67791395 67791396 TCGA-YL-A9WI INV 37 4 * * chrX 66909126 66909126 chrX 67790356 67790356 TCGA-YL-A9WI DUP 5 26 * * chrX 66942606 66942608 chrX 67282553 67282555 TCGA-YL-A9WI INV 9 39 * * chrX 67296055 67296055 chrX 67570771 67570771 TCGA-YL-A9WI DEL 12 2 * AR chrX 67299974 67299974 chrX 67764652 67764652 TCGA-YL-A9WI INV 28 37 * * chrX 68151689 68152275 chrX 69393151 69393922 TCGA-YL-A9WI INV 4 6 OPHN1 * chrX 68390796 68390797 chrX 68727461 68727462 TCGA-YL-A9WI DEL 44 24 OPHN1 * chrX 69951909 69951913 chrX 69953533 69953537 TCGA-YL-A9WI INV 43 29 EDA EDA chrX 91471868 91471870 chrX 102729660 102729662 TCGA-YL-A9WI INV 45 34 * BHLHB9 chrX 91626668 91626671 chrX 102933815 102933818 TCGA-YL-A9WI INV 3 13 * * chrX 92105889 92105889 chrX 92560030 92560030 TCGA-YL-A9WI DEL 42 31 PCDH11X PCDH11X chrX 92560030 92560030 chrY 5330399 5330399 TCGA-YL-A9WI BND 26 13 PCDH11X PCDH11Y chrX 971188 971188 chrX 971285 971285 TCGA-YL-A9WI DEL 6 8 * * chr18 54413567 54413906 chrX 81945311 81945926 TCGA-G9-7510 BND 37 17 CUPIN1P * chr19 11909492 11909494 chrX 105220571 105220591 TCGA-G9-7510 BND 17 13 ZNF69 IL1RAPL2 chr19 11910657 11910657 chrX 105220571 105220591 TCGA-G9-7510 BND 36 32 ZNF69 IL1RAPL2 chr2 167868556 167868556 chrX 65044990 65044990 TCGA-G9-7510 BND 45 50 B3GALT1 * chrX 22385 22387 chrX 23286 23288 TCGA-G9-7510 INV 27 14 * * chrX 2450177 2450179 chrX 2465899 2465901 TCGA-G9-7510 INV 20 44 DHRSX DHRSX chrX 36934347 36934352 chrX 36943095 36943100 TCGA-G9-7510 DEL 8 2 * * chrX 40049257 40049258 chrX 40177076 40177077 TCGA-G9-7510 DUP 21 18 * BCOR chrX 54262086 54262086 chrX 82069218 82069218 TCGA-G9-7510 INV 17 34 WNK3 * chrX 66889353 66890077 chrX 67006162 67006985 TCGA-G9-7510 DEL 25 28 * * chrX 67188396 67188399 chrX 67230384 67230387 TCGA-G9-7510 DUP 10 46 * * chrX 69392421 69392424 chrX 69393271 69393274 TCGA-G9-7510 INV 28 7 * * chrX 78523800 78523813 chrX 78523800 78523813 TCGA-G9-7510 INS 41 16 * * chrX 82060294 82060299 chrX 82071552 82071557 TCGA-G9-7510 INV 26 31 * * chr12 8793816 8793816 chrX 151556631 151556631 TCGA-KK-A8IF BND 10 42 AC092490.1 * chr3 33348970 33348972 chrX 81907735 81907737 TCGA-KK-A8IF BND 2 30 FBXL2 * chr3 33349167 33349168 chrX 81909730 81909731 TCGA-KK-A8IF BND 48 38 FBXL2 * chr5 60287779 60287781 chrX 130362785 130362787 TCGA-KK-A8IF BND 8 26 PDE4D SLC25A14 chr5 60388018 60388019 chrX 129528862 129528863 TCGA-KK-A8IF BND 26 45 PDE4D * chr6 132162948 132162949 chrX 129522616 129522617 TCGA-KK-A8IF BND 30 36 LINC01013 SMARCA1 chr6 158549964 158549964 chrX 129529129 129529129 TCGA-KK-A8IF BND 30 25 TMEM181 * chrX 48673055 48673059 chrX 95551524 95551528 TCGA-KK-A8IF DEL 32 36 * * chrX 57012424 57012432 chrX 86006849 86006857 TCGA-KK-A8IF INV 16 8 * CHM chrX 79325081 79325081 chrX 79688189 79688189 TCGA-KK-A8IF INV 35 21 KIF4CP * chrX 81397654 81397656 chrX 81414296 81414298 TCGA-KK-A8IF INV 32 12 * AL445213.1 chr13 38550556 38550556 chrX 11934038 11934038 TCGA-ZG-A8QX BND 25 38 * * chr15 36089702 36089703 chrX 28884044 28884045 TCGA-ZG-A8QX BND 26 41 AC021351.1 IL1RAPL1 chr18 22273915 22273915 chrX 1169320 1169320 TCGA-ZG-A8QX BND 47 44 * * chr20 17328123 17328123 chrX 143950447 143950447 TCGA-ZG-A8QX BND 43 50 PCSK2 * chr2 115137226 115137226 chrX 120344033 120344033 TCGA-ZG-A8QX BND 27 5 DPP10 * chr2 118817802 118817802 chrX 124823112 124823112 TCGA-ZG-A8QX BND 36 11 LINC01956 TENM1 chr2 119250458 119250462 chrX 124586898 124586902 TCGA-ZG-A8QX BND 16 14 STEAP3 TENM1 chr2 126392717 126392719 chrX 122343712 122343714 TCGA-ZG-A8QX BND 30 33 * * chr3 120736858 120736859 chrX 83653969 83653970 TCGA-ZG-A8QX BND 14 44 RABL3 * chr4 170117049 170117477 chrX 16182928 16183558 TCGA-ZG-A8QX BND 11 23 * * chr5 8867782 8867791 chrX 11935013 11935072 TCGA-ZG-A8QX BND 43 32 LINC02199 * chr5 8867782 8867791 chrX 11935345 11935355 TCGA-ZG-A8QX BND 11 12 LINC02199 * chr6 114501089 114501092 chrX 145034970 145034973 TCGA-ZG-A8QX BND 20 7 * * chr6 125176728 125176728 chrX 122156625 122156625 TCGA-ZG-A8QX BND 10 15 TPD52L1 * chr6 31427654 31427654 chrX 53026074 53026074 TCGA-ZG-A8QX BND 50 34 HCP5 * chrX 109376659 109376659 chrX 112595349 112595349 TCGA-ZG-A8QX DEL 17 13 GUCY2F * chrX 116518774 116518775 chrX 135604807 135604808 TCGA-ZG-A8QX DUP 42 17 * SAGE4P chrX 124569037 124569038 chrX 124569587 124569590 TCGA-ZG-A8QX INV 36 34 TENM1 TENM1 chrX 124569587 124569590 chrX 132896176 132896176 TCGA-ZG-A8QX DEL 1 17 TENM1 HS6ST2 chrX 124587021 124587023 chrX 133006339 133006341 TCGA-ZG-A8QX DUP 29 33 TENM1 * chrX 128041147 128041147 chrX 128041224 128041224 TCGA-ZG-A8QX INV 41 21 * * chrX 1330043 1330080 chrX 1330311 1330348 TCGA-ZG-A8QX INV 6 41 * * chrX 143271673 143271674 chrX 143272435 143272436 TCGA-ZG-A8QX INV 37 28 * * chrX 145102549 145102551 chrX 145103499 145103501 TCGA-ZG-A8QX INV 19 41 * * chrX 32471005 32471007 chrX 111587258 111587260 TCGA-ZG-A8QX DEL 26 21 DMD * chrX 32699891 32699892 chrX 79169670 79169671 TCGA-ZG-A8QX DUP 1 14 DMD GPR174 chrX 57592569 57592910 chrX 57909666 57910168 TCGA-ZG-A8QX INV 49 37 ZXDB ZXDA chrX 64456962 64456965 chrX 64458187 64458190 TCGA-ZG-A8QX INV 33 11 * * chrX 64667405 64667405 chrX 64668890 64668890 TCGA-ZG-A8QX INV 49 27 * * chrX 64744767 64744768 chrX 67649369 67649370 TCGA-ZG-A8QX INV 39 36 * AR chrX 64831547 64831550 chrX 67687632 67687635 TCGA-ZG-A8QX DUP 32 45 * AR chrX 65105917 65105917 chrX 65107025 65107025 TCGA-ZG-A8QX INV 7 3 * * chrX 66186464 66186466 chrX 66188260 66188262 TCGA-ZG-A8QX INV 7 10 HEPH HEPH chrX 66644051 66644053 chrX 66683769 66683771 TCGA-ZG-A8QX INV 28 19 * * chrX 66814055 66814056 chrX 66863933 66863934 TCGA-ZG-A8QX INV 13 32 * * chrX 66846502 66846505 chrX 66847891 66847894 TCGA-ZG-A8QX INV 34 3 * * chrX 67028063 67028065 chrX 67687687 67687689 TCGA-ZG-A8QX DEL 25 47 * AR chrX 67032972 67032973 chrX 67076859 67076860 TCGA-ZG-A8QX DUP 20 1 * * chrX 67216767 67216768 chrX 67303598 67303599 TCGA-ZG-A8QX DUP 13 12 * * chrX 67625230 67625232 chrX 67728010 67728012 TCGA-ZG-A8QX INV 31 15 AR AR chrX 67732739 67732741 chrX 67735075 67735077 TCGA-ZG-A8QX INV 28 7 * * chrX 79169641 79169644 chrX 79188938 79188941 TCGA-ZG-A8QX DUP 9 4 GPR174 * chrX 79170364 79170368 chrX 79188760 79188765 TCGA-ZG-A8QX INV 3 25 GPR174 * chrX 79188760 79188765 chrX 86675237 86675242 TCGA-ZG-A8QX INV 30 49 * DACH2 chrX 80685651 80685655 chrX 112595062 112595066 TCGA-ZG-A8QX INV 30 20 BRWD3 * chrX 80721402 80721404 chrX 112604053 112604055 TCGA-ZG-A8QX DUP 20 27 BRWD3 * chrX 84991627 84991629 chrX 109358108 109358110 TCGA-ZG-A8QX INV 29 32 * * chrX 87028343 87028344 chrX 111859744 111859745 TCGA-ZG-A8QX DUP 2 46 * TRPC5 chrX 87328692 87328694 chrX 109444498 109444500 TCGA-ZG-A8QX INV 29 9 * GUCY2F chrX 90280579 90280579 chrX 94795511 94795511 TCGA-ZG-A8QX INV 9 6 * * chrX 92253359 92253361 chrX 98528337 98528339 TCGA-ZG-A8QX DUP 48 44 PCDH11X AL157778.1 chrX 9404547 9404549 chrX 9414313 9414315 TCGA-ZG-A8QX DUP 17 28 AC073488.1 AC073488.6 chrX 94246315 94246317 chrX 94332014 94332016 TCGA-ZG-A8QX DEL 49 20 * * chrX 96268941 96268943 chrX 99081570 99081572 TCGA-ZG-A8QX INV 16 44 * * chr2 68987231 68987231 chrX 123770782 123770782 TCGA-KC-A7F3 BND 41 30 * * chr3 98195943 98196621 chrX 100787792 100788209 TCGA-KC-A7F3 BND 33 43 OR5H5P * chrX 16105615 16105615 chrX 80397853 80397853 TCGA-KC-A7F3 INV 27 5 * TENT5D chrX 66806585 66806588 chrX 67133072 67133075 TCGA-KC-A7F3 DUP 22 5 * * chr4 35494821 35495282 chrX 66891692 66892536 TCGA-V1-A9OX BND 18 13 RNU6-573P * chr5 159922371 159923125 chrX 67762459 67763304 TCGA-V1-A9OX BND 23 13 ADRA1B * chr6 117687088 117687090 chrX 129483764 129483766 TCGA-V1-A9OX BND 37 34 NUS1 SMARCA1 chr6 117687124 117687125 chrX 129483706 129483707 TCGA-V1-A9OX BND 16 10 NUS1 SMARCA1 chrX 129487825 129487827 chrX 129492439 129492441 TCGA-V1-A9OX DEL 32 15 SMARCA1 SMARCA1 chrX 136293659 136294173 chrX 136295202 136295697 TCGA-V1-A9OX DEL 34 49 * STK24P1 chrX 65517017 65517017 chrX 68050246 68050246 TCGA-V1-A9OX DUP 17 50 LAS1L OPHN1 chrX 65535735 65535735 chrX 67749759 67749759 TCGA-V1-A9OX INV 49 44 LAS1L * chrX 65617600 65617617 chrX 67706541 67706558 TCGA-V1-A9OX DEL 2 12 MSN AR chrX 65873730 65873732 chrX 66839926 66839928 TCGA-V1-A9OX INV 39 27 * * chrX 65905000 65905003 chrX 66875087 66875090 TCGA-V1-A9OX INV 26 50 * * chrX 65913621 65913625 chrX 66294094 66294098 TCGA-V1-A9OX INV 10 9 * * chrX 65916376 65916378 chrX 67626044 67626046 TCGA-V1-A9OX DUP 47 34 * AR chrX 65986646 65986646 chrX 67318394 67318394 TCGA-V1-A9OX DUP 30 8 * * chrX 66058591 66058592 chrX 66772831 66772832 TCGA-V1-A9OX DEL 39 14 * * chrX 67749150 67750148 chrX 67898287 67898749 TCGA-V1-A9OX INV 13 9 * * chr10 39337519 39337523 chrX 11714134 11714146 TCGA-VP-A87J BND 2 36 * AC004554.1 chr12 58075681 58075719 chrX 27198526 27198564 TCGA-VP-A87J BND 35 28 * AC107419.1 chr22 30495262 30495262 chrX 70167896 70167896 TCGA-VP-A87J BND 44 3 SEC14L4 * chr22 37020618 37020621 chrX 73117042 73117045 TCGA-VP-A87J BND 18 42 TST * chr22 37924002 37924003 chrX 74167880 74167881 TCGA-VP-A87J BND 25 35 MICALL1 FTX chr22 37924737 37924742 chrX 65825785 65825791 TCGA-VP-A87J BND 37 16 MICALL1 * chr22 37924737 37924742 chrX 74173158 74173158 TCGA-VP-A87J BND 4 39 MICALL1 FTX chr22 37926657 37926659 chrX 65825785 65825791 TCGA-VP-A87J BND 16 4 MICALL1 * chr2 178984154 178984158 chrX 68522723 68522727 TCGA-VP-A87J BND 34 21 CCDC141 YIPF6 chr3 69517365 69517369 chrX 44227382 44227386 TCGA-VP-A87J BND 45 26 FRMD4B EFHC2 chr4 170117030 170117477 chrX 16182941 16183600 TCGA-VP-A87J BND 44 2 * * chr5 120335929 120335930 chrX 70998177 70998178 TCGA-VP-A87J BND 31 3 * * chr5 12362762 12362765 chrX 11713285 11713320 TCGA-VP-A87J BND 9 16 * AC004554.1 chr8 63091603 63092279 chrX 84692168 84692508 TCGA-VP-A87J BND 17 37 * * chrX 113867980 113867994 chrX 113867980 113867994 TCGA-VP-A87J INS 29 45 XACT XACT chrX 118638922 118638924 chrX 118638991 118638991 TCGA-VP-A87J DEL 19 33 DOCK11 DOCK11 chrX 13976504 13976505 chrX 25317303 25317304 TCGA-VP-A87J INV 28 27 * * chrX 23972012 23972012 chrX 57216651 57216651 TCGA-VP-A87J DUP 41 42 * * chrX 342300 342326 chrX 342894 342894 TCGA-VP-A87J DEL 8 10 PPP2R3B PPP2R3B chrX 3747332 3747334 chrX 3748277 3748279 TCGA-VP-A87J INV 43 22 * * chrX 44693736 44693738 chrX 50057753 50057755 TCGA-VP-A87J DEL 18 10 * CLCN5 chrX 50179806 50179806 chrX 50180441 50180441 TCGA-VP-A87J DEL 16 44 * * chrX 62510767 62511209 chrX 62512634 62512991 TCGA-VP-A87J DEL 12 38 * * chrX 62515176 62515177 chrX 62527841 62527842 TCGA-VP-A87J INV 26 17 * * chrX 62578768 62578770 chrX 62578768 62578770 TCGA-VP-A87J INS 11 26 * * chrX 63315867 63315870 chrX 63316885 63316888 TCGA-VP-A87J INV 47 25 * * chrX 63439228 63439228 chrX 63440816 63440816 TCGA-VP-A87J INV 17 28 LINC01278 LINC01278 chrX 63565842 63565846 chrX 64723496 64723500 TCGA-VP-A87J DEL 25 41 * * chrX 63808121 63808124 chrX 63808561 63808564 TCGA-VP-A87J INV 42 31 ARHGEF9 ARHGEF9 chrX 64867059 64867061 chrX 65177588 65177590 TCGA-VP-A87J DEL 5 8 * * chrX 66728321 66728321 chrX 69737273 69737273 TCGA-VP-A87J INV 28 48 * EDA chrX 66870235 66870240 chrX 66881645 66881650 TCGA-VP-A87J INV 6 27 * * chrX 66879959 66879964 chrX 66881356 66881361 TCGA-VP-A87J INV 15 22 * * chrX 66940591 66940591 chrX 66963867 66963867 TCGA-VP-A87J INV 50 32 * * chrX 66964373 66964373 chrX 67765990 67765990 TCGA-VP-A87J INV 2 11 * * chrX 67098066 67098068 chrX 67224951 67224953 TCGA-VP-A87J INV 32 12 * * chrX 67223402 67223404 chrX 68105723 68105725 TCGA-VP-A87J DEL 6 30 * OPHN1 chrX 67602736 67602739 chrX 67633185 67633188 TCGA-VP-A87J INV 39 17 AR AR chrX 67777654 67777654 chrX 68124972 68124972 TCGA-VP-A87J DEL 31 34 * OPHN1 chrX 67958564 67958566 chrX 67971710 67971712 TCGA-VP-A87J INV 3 29 * * chrX 68134355 68134355 chrX 68210266 68210266 TCGA-VP-A87J DEL 47 44 OPHN1 OPHN1 chrX 68522723 68522727 chrX 86971327 86971331 TCGA-VP-A87J INV 49 15 YIPF6 * chrX 68623823 68623825 chrX 68625474 68625476 TCGA-VP-A87J INV 31 46 * * chrX 69046543 69046545 chrX 69056286 69056288 TCGA-VP-A87J INV 34 49 * * chrX 69051808 69051813 chrX 69236160 69236165 TCGA-VP-A87J DUP 39 33 * * chrX 69244452 69244453 chrX 69871608 69871609 TCGA-VP-A87J INV 28 14 * EDA chrX 69551125 69551127 chrX 69560387 69560389 TCGA-VP-A87J INV 47 8 * * chrX 69575294 69575297 chrX 69586505 69586508 TCGA-VP-A87J INV 12 16 * * chrX 69740901 69740906 chrX 69755128 69755133 TCGA-VP-A87J INV 22 15 EDA EDA chrX 69773797 69773797 chrX 71369082 71369082 TCGA-VP-A87J DEL 11 23 EDA TAF1 chrX 69829911 69829913 chrX 69831735 69831737 TCGA-VP-A87J INV 1 35 EDA EDA chrX 70089041 70089043 chrX 70092250 70092252 TCGA-VP-A87J INV 21 19 * * chrX 70356829 70356830 chrX 70399931 70399932 TCGA-VP-A87J INV 49 3 KIF4A KIF4A chrX 70505696 70505696 chrX 70629419 70629419 TCGA-VP-A87J INV 1 2 * TEX11 chrX 71301006 71301007 chrX 71328789 71328790 TCGA-VP-A87J DUP 37 34 NONO * chrX 71313569 71313579 chrX 71342976 71342986 TCGA-VP-A87J INV 2 19 * * chrX 71432079 71432079 chrX 71433740 71433740 TCGA-VP-A87J INV 44 22 TAF1 TAF1 chr12 52163542 52163543 chrX 57305893 57305894 TCGA-V1-A8MM BND 28 48 LINC00592 FAAH2 chr12 97761212 97761224 chrX 44272743 44272747 TCGA-V1-A8MM BND 25 27 PAFAH1B2P2 EFHC2 chr12 97761212 97761224 chrX 44272197 44272201 TCGA-V1-A8MM BND 25 38 PAFAH1B2P2 EFHC2 chr3 115784179 115784183 chrX 67955849 67955853 TCGA-V1-A8MM BND 47 46 * * chr4 48086705 48086705 chrX 67626637 67626637 TCGA-V1-A8MM BND 19 11 TXK AR chr5 153947788 153948399 chrX 104408939 104409368 TCGA-V1-A8MM BND 49 45 * * chr9 40526544 40526910 chrX 58509258 58509563 TCGA-V1-A8MM BND 42 7 BMS1P14 * chrX 27486573 27486573 chrX 27488053 27488059 TCGA-V1-A8MM DUP 34 48 * * chrX 27487682 27487688 chrX 27488053 27488059 TCGA-V1-A8MM DEL 18 38 * * chrX 27489405 27489407 chrX 27490318 27490320 TCGA-V1-A8MM INV 47 50 * * chrX 27492747 27492749 chrX 27492803 27492803 TCGA-V1-A8MM DEL 30 37 * * chrX 38577994 38577997 chrX 38579431 38579434 TCGA-V1-A8MM INV 30 4 AF241726.1 AF241726.1 chrX 48673055 48673059 chrX 95551524 95551528 TCGA-V1-A8MM DEL 24 24 * * chrX 66753330 66753330 chrX 67484624 67484624 TCGA-V1-A8MM INV 40 16 * * chrX 67083170 67083173 chrX 67251269 67251272 TCGA-V1-A8MM DEL 46 42 * * chrX 67121556 67121558 chrX 67483487 67483489 TCGA-V1-A8MM INV 29 33 * * chrX 67135974 67135976 chrX 67157757 67157759 TCGA-V1-A8MM INV 18 42 * * chrX 67582618 67582621 chrX 67604368 67604371 TCGA-V1-A8MM INV 20 30 AR AR chrX 68197832 68197834 chrX 68201436 68201438 TCGA-V1-A8MM INV 21 40 OPHN1 OPHN1 chrX 71233294 71233300 chrX 71282217 71282223 TCGA-V1-A8MM DUP 37 35 * NONO chrX 75176594 75176594 chrX 116245473 116245473 TCGA-V1-A8MM INV 2 24 * * chrX 75426218 75426231 chrX 75426218 75426231 TCGA-V1-A8MM INS 26 8 ZDHHC15 ZDHHC15 chrX 80141576 80141578 chrX 80142396 80142398 TCGA-V1-A8MM INV 42 6 * * chrX 80141771 80141776 chrX 80143323 80143328 TCGA-V1-A8MM INV 24 46 * * chrX 93832828 93832831 chrX 94024384 94024387 TCGA-V1-A8MM DUP 26 8 * * chr12 106209577 106210207 chrX 141252039 141252416 TCGA-EJ-A65E BND 14 21 * * chr2 52974089 52974101 chrX 11933508 11933508 TCGA-EJ-A65E BND 9 3 * * chr2 52974089 52974101 chrX 11933693 11933693 TCGA-EJ-A65E BND 46 20 * * chr7 44992490 44992907 chrX 53721860 53722231 TCGA-EJ-A65E BND 38 47 * * chr8 107739358 107739358 chrX 11935013 11935072 TCGA-EJ-A65E BND 48 34 * * chr8 114480881 114480881 chrX 11935489 11935489 TCGA-EJ-A65E BND 11 44 * * chrX 11935393 11935393 chrX 62644042 62644042 TCGA-EJ-A65E DEL 7 40 * * chrX 66851648 66851648 chrX 67147799 67147799 TCGA-EJ-A65E DUP 9 8 * * chrX 78946148 78946149 chrX 78946234 78946234 TCGA-EJ-A65E DEL 49 43 P2RY10 P2RY10 chr10 86600946 86600948 chrX 103320317 103320319 TCGA-J4-A83J BND 17 35 * * chr12 48112215 48112215 chrX 96627672 96627672 TCGA-J4-A83J BND 33 18 PFKM * chr13 71028728 71029048 chrX 78215873 78216262 TCGA-J4-A83J BND 26 26 LINC00348 * chr19 22709972 22710609 chrX 64728877 64729451 TCGA-J4-A83J BND 15 4 AC024563.1 * chr22 28669376 28669809 chrX 147726626 147726932 TCGA-J4-A83J BND 14 19 TTC28 * chr2 3877727 3877732 chrX 4991607 4991612 TCGA-J4-A83J BND 24 16 * * chr2 99123472 99123472 chrX 65476833 65476833 TCGA-J4-A83J BND 26 35 TSGA10 ZC3H12B chr3 166534058 166534058 chrX 5488675 5488675 TCGA-J4-A83J BND 21 25 * * chr3 31104958 31104958 chrX 141427245 141427247 TCGA-J4-A83J BND 4 30 * * chr6 43785436 43785439 chrX 129502118 129502121 TCGA-J4-A83J BND 12 24 VEGFA SMARCA1 chr6 43785498 43785498 chrX 129501536 129501536 TCGA-J4-A83J BND 26 45 VEGFA SMARCA1 chr8 63091606 63092257 chrX 84692165 84692485 TCGA-J4-A83J BND 18 29 * * chrX 107850043 107850046 chrX 107850222 107850222 TCGA-J4-A83J DEL 42 12 MID2 MID2 chrX 11506478 11506478 chrX 11506628 11506628 TCGA-J4-A83J DEL 4 8 ARHGAP6 ARHGAP6 chrX 141403607 141403610 chrX 141404616 141404619 TCGA-J4-A83J DEL 5 8 * * chrX 151738024 151738025 chrX 151750795 151750796 TCGA-J4-A83J DEL 41 15 CNGA2 * chrX 2197061 2197064 chrX 48673107 48673110 TCGA-J4-A83J INV 2 18 * * chrX 22944480 22944482 chrX 22944616 22944616 TCGA-J4-A83J DEL 7 6 PTCHD1-AS PTCHD1-AS chrX 3228983 3228984 chrX 3229709 3229709 TCGA-J4-A83J DEL 19 33 * * chrX 34174548 34174549 chrX 34185460 34185461 TCGA-J4-A83J DEL 28 35 * * chrX 44341531 44341531 chrX 44341961 44341961 TCGA-J4-A83J DEL 16 16 EFHC2 EFHC2 chrX 47831754 47831757 chrX 47831875 47831875 TCGA-J4-A83J DEL 47 5 * * chrX 49717397 49717400 chrX 49718331 49718331 TCGA-J4-A83J DEL 39 21 * * chrX 51805441 51805441 chrX 51805510 51805510 TCGA-J4-A83J DEL 49 46 MAGED1 MAGED1 chrX 58395851 58395851 chrX 58395927 58395927 TCGA-J4-A83J DEL 43 25 * * chrX 64734977 64734977 chrX 65494336 65494336 TCGA-J4-A83J DUP 49 47 * ZC3H12B chrX 68438100 68438103 chrX 69009663 69009666 TCGA-J4-A83J DUP 34 8 * * chrX 88139290 88139295 chrX 88139599 88139599 TCGA-J4-A83J DEL 25 39 * * chr20 39919165 39919179 chrX 112604901 112604915 TCGA-FC-7961 BND 32 16 * * chr2 166310076 166310076 chrX 139068833 139068833 TCGA-FC-7961 BND 50 47 SCN9A FGF13 chr5 108905243 108905243 chrX 11713394 11713394 TCGA-FC-7961 BND 16 25 FER AC004554.1 chr5 164233330 164233330 chrX 31159527 31159540 TCGA-FC-7961 BND 27 1 AC008662.1 DMD chr5 164233351 164233353 chrX 31159527 31159540 TCGA-FC-7961 BND 19 11 AC008662.1 DMD chr5 82665496 82666178 chrX 11714015 11714441 TCGA-FC-7961 BND 6 13 * AC004554.1 chr5 82665781 82665796 chrX 11714577 11714586 TCGA-FC-7961 BND 1 40 * AC004554.1 chr5 82665781 82665796 chrX 11713661 11713671 TCGA-FC-7961 BND 17 9 * AC004554.1 chrX 112340886 112340886 chrX 112340977 112340977 TCGA-FC-7961 DEL 41 14 * * chrX 11713472 11713476 chrX 11714373 11714423 TCGA-FC-7961 INV 14 27 AC004554.1 AC004554.1 chrX 129504297 129504303 chrX 142505440 142505449 TCGA-FC-7961 INV 34 40 SMARCA1 * chrX 136931231 136931231 chrX 138724005 138724005 TCGA-FC-7961 INV 42 12 AL390879.1 FGF13 chrX 136931608 136931609 chrX 138060814 138060815 TCGA-FC-7961 DEL 37 21 AL390879.1 * chrX 138060773 138060776 chrX 138060905 138060908 TCGA-FC-7961 INV 1 50 * * chrX 152111456 152111458 chrX 152113432 152113447 TCGA-FC-7961 INV 39 49 * * chrX 244617 245039 chrX 247876 248256 TCGA-FC-7961 DEL 26 2 * * chrX 34424531 34424532 chrX 134044953 134044953 TCGA-FC-7961 INV 21 16 * * chrX 48526841 48526841 chrX 48526922 48526922 TCGA-FC-7961 DEL 22 49 EBP EBP chrX 66829684 66829687 chrX 66829923 66829926 TCGA-FC-7961 INV 40 16 * * chrX 66877213 66877213 chrX 68002821 68002821 TCGA-FC-7961 DUP 46 35 * * chrX 66882883 66882883 chrX 66884121 66884121 TCGA-FC-7961 DEL 45 27 * * chrX 67283954 67283954 chrX 67726820 67726820 TCGA-FC-7961 DEL 48 47 * AR chrX 73005797 73005799 chrX 74605272 74605274 TCGA-FC-7961 DEL 42 19 * RLIM chr10 89788681 89788681 chrX 27403012 27403012 TCGA-HC-7738 BND 12 21 * * chr12 106209632 106210177 chrX 141252086 141252410 TCGA-HC-7738 BND 4 20 * * chr20 13300581 13300584 chrX 64584678 64584681 TCGA-HC-7738 BND 7 6 ISM1 * chr3 133406256 133406258 chrX 155532751 155532753 TCGA-HC-7738 BND 34 44 BFSP2 TMLHE-AS1 chr4 19078728 19078729 chrX 51188172 51188173 TCGA-HC-7738 BND 25 33 * * chr4 54460121 54460719 chrX 82767254 82767718 TCGA-HC-7738 BND 11 44 * * chr4 54460271 54461045 chrX 82766815 82767269 TCGA-HC-7738 BND 32 45 * * chr4 63061740 63062394 chrX 27002004 27002374 TCGA-HC-7738 BND 42 24 * * chr7 12253516 12254237 chrX 148177274 148177638 TCGA-HC-7738 BND 34 4 * * chr9 29948744 29948744 chrX 69178045 69178068 TCGA-HC-7738 BND 2 7 * LINC00269 chrX 110643562 110643562 chrX 154477489 154477489 TCGA-HC-7738 INV 41 18 * PLXNA3 chrX 154477489 154477489 chrX 155424584 155424584 TCGA-HC-7738 DUP 17 16 PLXNA3 * chrX 155155311 155155316 chrX 155615284 155615289 TCGA-HC-7738 DEL 38 21 BX293995.1 TMLHE chrX 155532084 155532084 chrX 155615316 155615316 TCGA-HC-7738 INV 38 23 TMLHE-AS1 TMLHE chrX 155984138 155984138 chrX 155984222 155984222 TCGA-HC-7738 DEL 43 31 * * chrX 17637775 17637781 chrX 18412638 18412644 TCGA-HC-7738 DEL 17 15 NHS * chrX 48016840 48017562 chrX 48139393 48139819 TCGA-HC-7738 DUP 46 8 ZNF630 * chrX 64060039 64060039 chrX 64062842 64062842 TCGA-HC-7738 INV 30 49 * * chrX 64113041 64113041 chrX 64132775 64132775 TCGA-HC-7738 INV 38 9 * * chrX 64138348 64138351 chrX 64894914 64894917 TCGA-HC-7738 DUP 4 4 * * chrX 64179407 64179411 chrX 64197979 64197983 TCGA-HC-7738 INV 33 34 * AMER1 chrX 66285788 66285790 chrX 66293706 66293708 TCGA-HC-7738 INV 9 12 * * chrX 66321819 66321821 chrX 66322333 66322335 TCGA-HC-7738 INV 14 16 * * chrX 66748626 66748626 chrX 67715654 67715654 TCGA-HC-7738 DUP 15 5 * AR chrX 66762470 66762472 chrX 67036179 67036181 TCGA-HC-7738 INV 19 23 * * chrX 66890345 66890347 chrX 66943176 66943178 TCGA-HC-7738 DUP 25 12 * * chrX 67033027 67033031 chrX 67034455 67034459 TCGA-HC-7738 INV 29 32 * * chrX 67287974 67287976 chrX 67289352 67289354 TCGA-HC-7738 INV 4 45 * * chrX 67297286 67297289 chrX 67316564 67316567 TCGA-HC-7738 INV 34 40 * * chrX 67564587 67564588 chrX 67574521 67574522 TCGA-HC-7738 INV 20 36 AR AR chrX 67957898 67957900 chrX 67958732 67958734 TCGA-HC-7738 INV 1 42 * * chrX 69176536 69176539 chrX 69178045 69178068 TCGA-HC-7738 INV 27 39 * LINC00269 chrX 76732467 76732470 chrX 76732467 76732470 TCGA-HC-7738 INS 5 11 MIR325HG MIR325HG chrX 83767557 83767557 chrX 83768052 83768052 TCGA-HC-7738 DEL 30 43 * * chrX 87125534 87125547 chrX 87125534 87125547 TCGA-HC-7738 INS 2 49 * * chrX 91203157 91203159 chrX 96058114 96058116 TCGA-HC-7738 INV 19 49 * * chr15 46084321 46084323 chrX 47116356 47116358 TCGA-XK-AAIW BND 14 5 * * chrX 10604333 10604333 chrX 10604434 10604434 TCGA-XK-AAIW DEL 36 25 MID1 MID1 chrX 63093049 63093075 chrX 63286795 63286821 TCGA-XK-AAIW DUP 32 50 * * chr11 109180868 109181195 chrX 109069987 109070508 TCGA-VP-A87H BND 36 22 * * chr11 65690592 65690592 chrX 65457729 65457729 TCGA-VP-A87H BND 17 48 * ZC3H12B chr19 56389302 56389310 chrX 9072447 9072455 TCGA-VP-A87H BND 22 29 ZNF582 FAM9B chr1 70160880 70160880 chrX 84084224 84084224 TCGA-VP-A87H BND 50 27 LRRC40 RPS6KA6 chr1 70217875 70217876 chrX 85754162 85754163 TCGA-VP-A87H BND 42 36 SRSF11 * chr22 28670047 28670048 chrX 128233714 128233715 TCGA-VP-A87H BND 38 41 TTC28 * chr2 31624094 31624094 chrX 68619560 68619560 TCGA-VP-A87H BND 28 5 * * chr3 94612153 94612155 chrX 68619203 68619203 TCGA-VP-A87H BND 20 22 * * chr3 94612153 94612155 chrX 68619020 68619020 TCGA-VP-A87H BND 28 35 * * chr4 18272641 18272644 chrX 76002332 76002335 TCGA-VP-A87H BND 20 46 * * chr4 45128687 45128688 chrX 142747719 142747720 TCGA-VP-A87H BND 34 17 * * chr4 54460045 54460892 chrX 82767254 82767709 TCGA-VP-A87H BND 42 10 * * chr4 54460264 54460904 chrX 82766820 82767269 TCGA-VP-A87H BND 28 2 * * chr6 17608756 17608758 chrX 101187696 101187698 TCGA-VP-A87H BND 16 7 FAM8A1 * chr7 21036383 21036385 chrX 139492039 139492041 TCGA-VP-A87H BND 30 25 * * chr8 88473260 88473832 chrX 68618960 68619327 TCGA-VP-A87H BND 45 38 AC090578.1 * chr8 88473564 88473565 chrX 68619459 68619460 TCGA-VP-A87H BND 35 48 AC090578.1 * chr9 32204313 32204314 chrX 2761379 2761380 TCGA-VP-A87H BND 11 39 * XG chrX 114482256 114482256 chrX 119539303 119539303 TCGA-VP-A87H INV 32 21 * CXorf56 chrX 118532893 118532893 chrX 135317621 135317621 TCGA-VP-A87H INV 14 16 DOCK11 ZNF75D chrX 12474189 12474189 chrX 79210270 79210270 TCGA-VP-A87H INV 26 12 FRMPD4 * chrX 134590094 134590099 chrX 134590729 134590729 TCGA-VP-A87H INV 16 6 PLAC1 PLAC1 chrX 134590094 134590099 chrX 136236903 136236904 TCGA-VP-A87H DUP 44 8 PLAC1 MAP7D3 chrX 135457589 135457591 chrX 135470833 135470835 TCGA-VP-A87H DEL 43 6 * * chrX 136020434 136020434 chrX 136041359 136041359 TCGA-VP-A87H DEL 39 42 SLC9A6 SLC9A6 chrX 1581882 1581906 chrX 1582223 1582223 TCGA-VP-A87H DEL 45 42 * * chrX 1838878 1838879 chrY 7421048 7421049 TCGA-VP-A87H BND 36 39 * * chrX 2201980 2201980 chrX 2471305 2471305 TCGA-VP-A87H INV 42 26 * DHRSX chrX 2423148 2423148 chrX 89536320 89536320 TCGA-VP-A87H DUP 46 16 DHRSX * chrX 2423148 2423148 chrY 3192194 3192194 TCGA-VP-A87H BND 24 18 DHRSX * chrX 2477357 2477359 chrX 89565880 89565882 TCGA-VP-A87H INV 36 1 DHRSX * chrX 2477357 2477359 chrY 3221927 3221929 TCGA-VP-A87H BND 38 23 DHRSX * chrX 2733203 2733203 chrY 7168053 7168053 TCGA-VP-A87H BND 16 43 CD99 * chrX 41797268 41797273 chrX 45203296 45203301 TCGA-VP-A87H DEL 18 38 CASK AC136489.1 chrX 64866093 64866093 chrX 64867434 64867434 TCGA-VP-A87H INV 6 50 * * chrX 65397370 65397373 chrX 72566822 72566825 TCGA-VP-A87H INV 46 4 ZC3H12B HDAC8 chrX 66028872 66028873 chrX 72965133 72965134 TCGA-VP-A87H DEL 19 31 VSIG4 * chrX 66088538 66088540 chrX 72750550 72750552 TCGA-VP-A87H DEL 4 26 * * chrX 66088538 66088540 chrX 72970277 72970279 TCGA-VP-A87H INV 10 29 * * chrX 66929036 66929036 chrX 131249123 131249123 TCGA-VP-A87H DUP 6 46 * * chrX 72543443 72543445 chrX 72700245 72700247 TCGA-VP-A87H DUP 45 6 HDAC8 PHKA1 chrX 72544741 72544743 chrX 72545558 72545560 TCGA-VP-A87H INV 15 37 HDAC8 HDAC8 chrX 73060698 73060698 chrX 73061597 73061597 TCGA-VP-A87H INV 26 9 * * chrX 74044617 74044621 chrX 74045613 74045617 TCGA-VP-A87H INV 28 16 JPX JPX chrX 77256531 77256908 chrX 131466821 131467461 TCGA-VP-A87H INV 9 3 * IGSF1 chrX 80581093 80581094 chrX 80583780 80583781 TCGA-VP-A87H DEL 4 50 * * chrX 90380128 90380128 chrX 92692226 92692226 TCGA-VP-A87H DEL 41 42 * * chr12 63102267 63102280 chrX 26960403 26960416 TCGA-CH-5788 BND 17 18 * * chr15 24767594 24767594 chrX 45136631 45136631 TCGA-CH-5788 BND 14 13 * * chr3 120736858 120736859 chrX 83653969 83653970 TCGA-CH-5788 BND 49 13 RABL3 * chr5 24370579 24370579 chrX 89402436 89402436 TCGA-CH-5788 BND 21 10 * * chrX 105224390 105224393 chrX 105224479 105224479 TCGA-CH-5788 DEL 22 36 IL1RAPL2 IL1RAPL2 chrX 11310727 11310728 chrX 67717390 67717391 TCGA-CH-5788 DUP 40 28 ARHGAP6 AR chrX 138089231 138089237 chrX 138092428 138092434 TCGA-CH-5788 DEL 31 5 * * chrX 146013154 146013158 chrX 146864366 146864370 TCGA-CH-5788 DEL 23 38 * * chrX 148142363 148142365 chrX 148153066 148153068 TCGA-CH-5788 DEL 17 46 * * chrX 26996699 26996701 chrX 26996801 26996801 TCGA-CH-5788 DEL 34 24 * * chrX 56674792 56674792 chrX 63959199 63959199 TCGA-CH-5788 INV 36 39 * * chrX 57701739 57701739 chrX 58328299 58328299 TCGA-CH-5788 DEL 31 17 * * chrX 57703675 57703679 chrX 62545141 62545145 TCGA-CH-5788 DUP 42 14 * * chrX 58160052 58160052 chrX 65420138 65420138 TCGA-CH-5788 DUP 43 30 * ZC3H12B chrX 60111453 60111453 chrX 63116390 63116390 TCGA-CH-5788 DUP 32 11 * * chrX 62539704 62539704 chrX 63097338 63097338 TCGA-CH-5788 INV 49 14 * * chrX 62620882 62620883 chrX 69136772 69136773 TCGA-CH-5788 INV 31 36 * * chrX 62682810 62682811 chrX 67973618 67973619 TCGA-CH-5788 INV 6 44 * * chrX 62684850 62684850 chrX 63762389 63762389 TCGA-CH-5788 DUP 7 9 * ARHGEF9 chrX 63070354 63070356 chrX 66246374 66246376 TCGA-CH-5788 DUP 18 28 * HEPH chrX 63117138 63117833 chrX 65048004 65048710 TCGA-CH-5788 DUP 19 3 * * chrX 63390840 63390840 chrX 63519949 63519949 TCGA-CH-5788 INV 39 22 LINC01278 LINC01278 chrX 63473417 63473417 chrX 64924775 64924775 TCGA-CH-5788 DEL 19 39 LINC01278 ZC4H2 chrX 63476641 63476641 chrX 66497678 66497678 TCGA-CH-5788 INV 34 18 LINC01278 PKMP2 chrX 63685504 63685504 chrX 65062779 65062779 TCGA-CH-5788 DEL 32 23 ARHGEF9 * chrX 63766092 63766095 chrX 63793234 63793237 TCGA-CH-5788 INV 26 10 ARHGEF9 ARHGEF9 chrX 63903872 63903872 chrX 65551430 65551430 TCGA-CH-5788 INV 20 22 * FRMD8P1 chrX 64203675 64203677 chrX 66017739 66017741 TCGA-CH-5788 INV 35 49 AMER1 MIR223HG chrX 64220244 64220244 chrX 65975651 65975651 TCGA-CH-5788 INV 49 47 * * chrX 64250298 64250298 chrX 64839817 64839817 TCGA-CH-5788 DEL 30 44 * * chrX 64271158 64271158 chrX 65572258 65572258 TCGA-CH-5788 INV 45 15 MTMR8 * chrX 64605751 64605753 chrX 67717498 67717500 TCGA-CH-5788 INV 3 45 * AR chrX 64840320 64840323 chrX 65432336 65432339 TCGA-CH-5788 DUP 32 49 * ZC3H12B chrX 64991245 64991245 chrX 65833484 65833484 TCGA-CH-5788 INV 22 4 ZC4H2 * chrX 65150630 65150650 chrX 67972821 67972841 TCGA-CH-5788 INV 24 49 * * chrX 65195596 65195597 chrX 65216681 65216682 TCGA-CH-5788 DUP 29 26 * * chrX 65195694 65195695 chrX 65243182 65243183 TCGA-CH-5788 DUP 17 29 * * chrX 65391893 65391893 chrX 66859645 66859645 TCGA-CH-5788 INV 20 50 ZC3H12B * chrX 65438978 65438978 chrX 67272591 67272591 TCGA-CH-5788 DEL 44 7 ZC3H12B * chrX 65511140 65511142 chrX 65887518 65887520 TCGA-CH-5788 DEL 8 18 * * chrX 65512461 65512461 chrX 65799443 65799443 TCGA-CH-5788 DEL 20 30 * * chrX 65542788 65542788 chrX 65577473 65577473 TCGA-CH-5788 DUP 19 45 * * chrX 65609123 65609123 chrX 67371266 67371266 TCGA-CH-5788 DUP 42 21 MSN * chrX 65873448 65873449 chrX 66178185 66178186 TCGA-CH-5788 INV 34 35 * HEPH chrX 66104426 66104427 chrX 68868100 68868101 TCGA-CH-5788 INV 48 20 * * chrX 66141940 66141941 chrX 66173592 66173593 TCGA-CH-5788 DEL 12 45 * HEPH chrX 66471620 66471621 chrX 66938711 66938712 TCGA-CH-5788 INV 7 21 * * chrX 67205981 67205984 chrX 67756381 67756384 TCGA-CH-5788 DEL 2 23 * * chrX 67697048 67697048 chrX 67950482 67950482 TCGA-CH-5788 DUP 9 14 AR * chrX 68133817 68133820 chrX 68836048 68836051 TCGA-CH-5788 DEL 50 42 OPHN1 EFNB1 chrX 69235332 69235334 chrX 69253228 69253230 TCGA-CH-5788 DUP 23 43 * * chrX 69274164 69274165 chrX 69582618 69582619 TCGA-CH-5788 INV 22 46 * * chrX 69539477 69539477 chrX 154343721 154343721 TCGA-CH-5788 INV 44 37 * * chrX 69539477 69539477 chrX 154388392 154388392 TCGA-CH-5788 DEL 27 1 * * chrX 71366670 71366670 chrX 153738995 153738995 TCGA-CH-5788 DEL 29 25 TAF1 ABCD1 chrX 87577379 87577380 chrX 87579417 87579418 TCGA-CH-5788 DEL 50 23 KLHL4 KLHL4 chrX 912654 912656 chrX 913513 913513 TCGA-CH-5788 DEL 47 39 * * chrX 95215982 95215982 chrX 95252883 95252883 TCGA-CH-5788 DEL 8 3 * * chr10 54513118 54513118 chrX 136562567 136562567 TCGA-VP-AA1N BND 1 13 PCDH15 * chr11 54747466 54747910 chrX 11933196 11933722 TCGA-VP-AA1N BND 30 24 * * chr11 54747600 54747601 chrX 11933958 11933959 TCGA-VP-AA1N BND 22 18 * * chr14 30680337 30680337 chrX 55635739 55635749 TCGA-VP-AA1N BND 38 41 SCFD1 AL159987.2 chr14 30681352 30681352 chrX 55635739 55635749 TCGA-VP-AA1N BND 11 8 SCFD1 AL159987.2 chr15 22074347 22074350 chrX 74876411 74876414 TCGA-VP-AA1N BND 10 46 AC134980.2 NEXMIF chr1 125126776 125126776 chrX 73063517 73063517 TCGA-VP-AA1N BND 44 19 * * chr21 14261959 14261960 chrX 75101106 75101107 TCGA-VP-AA1N BND 25 25 ABCC13 ABCB7 chr21 16283364 16283365 chrX 69545086 69545087 TCGA-VP-AA1N BND 29 6 MIR99AHG * chr22 28669924 28669924 chrX 4702819 4702819 TCGA-VP-AA1N BND 27 30 TTC28 * chr2 56864255 56864770 chrX 11934533 11934953 TCGA-VP-AA1N BND 8 42 * * chr2 56864568 56864570 chrX 11935013 11935072 TCGA-VP-AA1N BND 22 39 * * chr4 12882 12882 chrX 67794498 67794498 TCGA-VP-AA1N BND 46 31 * * chr4 54993617 54994282 chrX 45664638 45665039 TCGA-VP-AA1N BND 22 24 * * chr7 32531087 32531787 chrX 148045481 148045940 TCGA-VP-AA1N BND 50 47 AVL9 * chr7 32531270 32531886 chrX 148045019 148045484 TCGA-VP-AA1N BND 36 40 AVL9 * chr8 111983988 111983989 chrX 83758689 83758690 TCGA-VP-AA1N BND 27 45 * * chr8 114049363 114049365 chrX 111347166 111347168 TCGA-VP-AA1N BND 33 11 * DCX chr8 41595901 41595902 chrX 73112334 73112335 TCGA-VP-AA1N BND 6 36 GPAT4 * chr8 74378549 74379185 chrX 10025858 10026353 TCGA-VP-AA1N BND 46 28 GDAP1 WWC3 chr8 81184778 81184779 chrX 79787411 79787412 TCGA-VP-AA1N BND 21 32 * * chr8 81185836 81185836 chrX 81782568 81782586 TCGA-VP-AA1N BND 35 18 * * chrX 62671851 62671857 chrX 62674423 62674429 TCGA-VP-AA1N DEL 26 10 * * chrX 65524942 65524944 chrX 87818030 87818032 TCGA-VP-AA1N INV 6 17 LAS1L * chrX 65745920 65745922 chrX 65757360 65757362 TCGA-VP-AA1N INV 43 19 * * chrX 65757419 65757419 chrX 81467586 81467586 TCGA-VP-AA1N INV 44 28 * * chrX 66039816 66039819 chrX 81782568 81782586 TCGA-VP-AA1N INV 8 30 VSIG4 * chrX 66063154 66063154 chrX 66073407 66073407 TCGA-VP-AA1N INV 20 38 * * chrX 66580605 66580606 chrX 75271082 75271083 TCGA-VP-AA1N DUP 42 46 * * chrX 66843485 66843487 chrX 66844882 66844884 TCGA-VP-AA1N INV 9 4 * * chrX 66844882 66844884 chrX 105739828 105739830 TCGA-VP-AA1N DUP 5 49 * IL1RAPL2 chrX 67723452 67723454 chrX 72580599 72580601 TCGA-VP-AA1N DEL 34 36 AR PHKA1 chrX 68765228 68765228 chrX 72037485 72037485 TCGA-VP-AA1N INV 41 40 * NHSL2 chrX 68765868 68765871 chrX 68939549 68939552 TCGA-VP-AA1N INV 40 18 * * chrX 69361211 69361215 chrX 69363404 69363408 TCGA-VP-AA1N INV 32 45 * * chrX 69689432 69689435 chrX 69691420 69691423 TCGA-VP-AA1N INV 5 18 EDA EDA chrX 69763329 69763335 chrX 69780323 69780329 TCGA-VP-AA1N DUP 9 38 EDA EDA chrX 69967139 69967142 chrX 69968398 69968401 TCGA-VP-AA1N INV 6 34 EDA EDA chrX 72403043 72403043 chrX 89542397 89542397 TCGA-VP-AA1N INV 13 13 HDAC8 * chrX 73708771 73708775 chrX 97154283 97154287 TCGA-VP-AA1N DEL 46 7 * DIAPH2 chrX 75052196 75052196 chrX 75053051 75053051 TCGA-VP-AA1N INV 21 30 ABCB7 ABCB7 chrX 78503504 78503505 chrX 81214337 81214338 TCGA-VP-AA1N DEL 15 17 * SH3BGRL chrX 81386823 81386824 chrX 85720097 85720098 TCGA-VP-AA1N INV 46 12 * * chrX 81430932 81430935 chrX 81467931 81467944 TCGA-VP-AA1N INV 29 29 * * chrX 81463962 81463965 chrX 81465348 81465351 TCGA-VP-AA1N INV 15 9 * * chrX 81465372 81465375 chrX 81465585 81465585 TCGA-VP-AA1N DEL 5 8 * * chrX 81467586 81467586 chrX 81467931 81467944 TCGA-VP-AA1N INV 31 12 * * chrX 82448256 82448256 chrX 85721973 85721973 TCGA-VP-AA1N INV 20 21 * * chrX 89194696 89194696 chrX 89196862 89196862 TCGA-VP-AA1N INV 16 22 * * chr10 56704408 56704408 chrX 1627502 1627502 TCGA-V1-A9OF BND 50 8 * ASMT chr1 112639966 112639968 chrX 80396906 80396908 TCGA-V1-A9OF BND 27 50 CAPZA1 TENT5D chr1 63239797 63239798 chrX 147325620 147325621 TCGA-V1-A9OF BND 35 30 LINC00466 * chr20 57633158 57633158 chrX 27605385 27605385 TCGA-V1-A9OF BND 36 17 * DCAF8L2 chr22 28669563 28670045 chrX 27605047 27605901 TCGA-V1-A9OF BND 16 5 TTC28 DCAF8L2 chr2 205178264 205178265 chrX 125863590 125863591 TCGA-V1-A9OF BND 24 45 PARD3B * chr3 174587744 174587744 chrX 122902186 122902186 TCGA-V1-A9OF BND 16 22 NAALADL2 * chr4 110402286 110402286 chrX 107910840 107910840 TCGA-V1-A9OF BND 34 50 ENPEP MID2 chr4 42837105 42837106 chrX 44816473 44816474 TCGA-V1-A9OF BND 34 3 * * chr4 49179087 49179090 chrX 45492358 45492361 TCGA-V1-A9OF BND 13 26 * * chr5 12645955 12645957 chrX 69661331 69661333 TCGA-V1-A9OF BND 26 9 LINC01194 EDA chr5 165330517 165330522 chrX 4606195 4606200 TCGA-V1-A9OF BND 26 40 * * chr8 66040143 66040151 chrX 148670536 148670544 TCGA-V1-A9OF BND 25 18 DNAJC5B AFF2 chr8 74403107 74403114 chrX 108765328 108765335 TCGA-V1-A9OF BND 46 45 GDAP1 * chr9 30492005 30492005 chrX 18296057 18296057 TCGA-V1-A9OF BND 46 10 LINC01242 SCML2 chrX 137586580 137586593 chrX 137586580 137586593 TCGA-V1-A9OF INS 7 37 Z96074.1 Z96074.1 chrX 142673334 142673335 chrX 143587427 143587428 TCGA-V1-A9OF DEL 33 32 * * chrX 17115267 17115267 chrX 29234913 29234913 TCGA-V1-A9OF INV 20 36 REPS2 IL1RAPL1 chrX 17115305 17115306 chrX 29234983 29234984 TCGA-V1-A9OF INV 2 13 REPS2 IL1RAPL1 chrX 25628635 25628638 chrX 25630193 25630196 TCGA-V1-A9OF INV 13 12 * * chrX 32399371 32399373 chrX 71592761 71592763 TCGA-V1-A9OF DUP 32 23 DMD GCNA chrX 38624042 38624044 chrX 44996731 44996733 TCGA-V1-A9OF INV 7 7 AF241726.1 KDM6A chrX 38894178 38894178 chrX 44980951 44980951 TCGA-V1-A9OF DEL 43 11 * KDM6A chrX 43200063 43200064 chrX 47948571 47948572 TCGA-V1-A9OF INV 6 47 PINCR ZNF81 chrX 43812356 43812357 chrX 45008522 45008523 TCGA-V1-A9OF INV 16 27 MAOB KDM6A chrX 44983314 44983314 chrX 45009108 45009108 TCGA-V1-A9OF DEL 50 45 KDM6A KDM6A chrX 48673055 48673059 chrX 95551524 95551528 TCGA-V1-A9OF DEL 7 29 * * chrX 58063443 58063443 chrX 65013671 65013671 TCGA-V1-A9OF INV 15 32 * ZC4H2 chrX 64824921 64824922 chrX 65147199 65147200 TCGA-V1-A9OF INV 24 50 * * chrX 64974107 64974108 chrX 70811410 70811411 TCGA-V1-A9OF INV 7 5 ZC4H2 TEX11 chrX 67715167 67715167 chrX 67723520 67723520 TCGA-V1-A9OF DEL 20 13 AR AR chrX 83369675 83369680 chrX 94149108 94149113 TCGA-V1-A9OF DEL 6 18 * * chrX 89204246 89204595 chrX 89205600 89205940 TCGA-V1-A9OF DEL 25 6 * * chr3 79291578 79292012 chrX 46084231 46084858 TCGA-YL-A8SH BND 35 20 ROBO1 * chr6 136162657 136163103 chrX 143497200 143497881 TCGA-YL-A8SH BND 25 34 PDE7B AC239727.1 chr6 29717709 29717709 chrX 68325639 68325639 TCGA-YL-A8SH BND 50 14 * OPHN1 chr7 136575815 136576605 chrX 7976397 7977014 TCGA-YL-A8SH BND 17 27 * * chrX 100537158 100537561 chrX 100537998 100538259 TCGA-YL-A8SH DEL 29 2 * * chrX 110474364 110474364 chrX 110722595 110722595 TCGA-YL-A8SH DUP 46 5 * CHRDL1 chrX 145427825 145427828 chrX 145532458 145532461 TCGA-YL-A8SH DUP 7 37 * * chrX 145994327 145994328 chrX 146175966 146175967 TCGA-YL-A8SH DUP 1 24 MIR890 * chrX 19408875 19408879 chrX 19408966 19408966 TCGA-YL-A8SH DEL 1 47 MAP3K15 MAP3K15 chrX 24143856 24143857 chrX 24845587 24845588 TCGA-YL-A8SH DUP 19 38 * POLA1 chrX 34819697 34820120 chrX 67762545 67763236 TCGA-YL-A8SH DEL 46 31 * * chrX 44493414 44493416 chrX 44745411 44745413 TCGA-YL-A8SH DUP 33 5 * * chrX 66343490 66343491 chrX 76632149 76632150 TCGA-YL-A8SH INV 33 50 * * chrX 66366788 66366788 chrX 66370537 66370537 TCGA-YL-A8SH DEL 10 47 * * chrX 66736356 66736357 chrX 67009547 67009548 TCGA-YL-A8SH DUP 16 46 * * chrX 66737317 66737320 chrX 66764214 66764217 TCGA-YL-A8SH DEL 13 33 * * chrX 66755548 66755550 chrX 67004824 67004826 TCGA-YL-A8SH DUP 19 23 * * chrX 66809926 66809927 chrX 67017614 67017615 TCGA-YL-A8SH DUP 32 6 * * chrX 68131369 68131370 chrX 76714476 76714477 TCGA-YL-A8SH INV 45 32 OPHN1 MIR325HG chrX 7899946 7899950 chrX 8077350 8077354 TCGA-YL-A8SH DUP 50 16 PNPLA4 AC079142.1 chrX 80711103 80711103 chrX 84904928 84904928 TCGA-YL-A8SH INV 39 42 BRWD3 * chrX 80718188 80718190 chrX 84904697 84904699 TCGA-YL-A8SH INV 23 29 BRWD3 * chrX 8281801 8281805 chrX 8960980 8960984 TCGA-YL-A8SH DUP 20 21 * * chrX 99079002 99079003 chrX 99235385 99235386 TCGA-YL-A8SH DUP 32 47 * * chr12 26565863 26565863 chrX 1154542 1154542 TCGA-ZG-A9L0 BND 16 11 ITPR2 * chr15 21041440 21041444 chrX 84700359 84700363 TCGA-ZG-A9L0 BND 17 22 * * chr15 55303854 55303854 chrX 42285701 42285701 TCGA-ZG-A9L0 BND 32 8 RAB27A AL023875.1 chr1 112640139 112640144 chrX 78265527 78265532 TCGA-ZG-A9L0 BND 21 38 CAPZA1 * chr1 868470 868470 chrX 77278631 77278631 TCGA-ZG-A9L0 BND 25 9 FAM41C * chr20 29386928 29386928 chrX 25345322 25345322 TCGA-ZG-A9L0 BND 11 37 * * chr20 29434145 29434145 chrX 25844183 25844183 TCGA-ZG-A9L0 BND 36 44 * * chr20 29852916 29852916 chrX 24940834 24940834 TCGA-ZG-A9L0 BND 49 30 * POLA1 chr20 31737822 31737824 chrX 95329 95331 TCGA-ZG-A9L0 BND 5 17 TPX2 * chr2 72830298 72830298 chrX 114643978 114643978 TCGA-ZG-A9L0 BND 33 32 * HTR2C chr3 196243754 196243754 chrX 126640973 126640973 TCGA-ZG-A9L0 BND 14 40 PCYT1A * chr4 68261066 68261988 chrX 73623852 73624336 TCGA-ZG-A9L0 BND 39 46 * CHIC1 chr6 148319560 148319561 chrX 6875025 6875026 TCGA-ZG-A9L0 BND 27 40 SASH1 * chr6 148667091 148667091 chrX 6875734 6875734 TCGA-ZG-A9L0 BND 14 32 * * chrX 10084184 10084191 chrX 16052418 16052425 TCGA-ZG-A9L0 INV 20 33 WWC3 * chrX 101327529 101327531 chrX 101327979 101327979 TCGA-ZG-A9L0 DEL 11 4 * * chrX 11021138 11021141 chrX 13309415 13309418 TCGA-ZG-A9L0 DEL 15 24 AC073529.1 GS1-600G8.3 chrX 13176808 13176810 chrX 13189031 13189033 TCGA-ZG-A9L0 DUP 25 19 * * chrX 13734392 13734394 chrX 15866452 15866454 TCGA-ZG-A9L0 INV 32 20 TRAPPC2 * chrX 14027993 14027993 chrX 103126325 103126325 TCGA-ZG-A9L0 DEL 12 20 GEMIN8 * chrX 14027993 14027993 chrX 15873244 15873244 TCGA-ZG-A9L0 DEL 35 19 GEMIN8 * chrX 15038267 15038267 chrX 16170391 16170391 TCGA-ZG-A9L0 DEL 29 3 * MAGEB17 chrX 15043104 15043106 chrX 22527808 22527810 TCGA-ZG-A9L0 INV 4 7 * PTCHD1-AS chrX 15237520 15237523 chrX 16170870 16170873 TCGA-ZG-A9L0 DUP 33 40 ASB9 MAGEB17 chrX 15784125 15784134 chrX 21858660 21858669 TCGA-ZG-A9L0 INV 8 45 CA5B MBTPS2 chrX 15873244 15873244 chrX 103126420 103126420 TCGA-ZG-A9L0 DUP 5 19 * * chrX 16173223 16173224 chrX 16863172 16863173 TCGA-ZG-A9L0 DUP 16 5 * RBBP7 chrX 17000263 17000268 chrX 103179189 103179194 TCGA-ZG-A9L0 INV 2 33 REPS2 * chrX 17497602 17497602 chrX 99528414 99528414 TCGA-ZG-A9L0 INV 32 22 NHS * chrX 17543130 17543131 chrX 18740989 18740990 TCGA-ZG-A9L0 DUP 25 37 NHS PPEF1 chrX 17645869 17645869 chrX 99305216 99305216 TCGA-ZG-A9L0 INV 6 7 NHS * chrX 17977835 17977835 chrX 99530618 99530618 TCGA-ZG-A9L0 DUP 1 28 LINC01456 * chrX 17989049 17989696 chrX 18691907 18692501 TCGA-ZG-A9L0 DEL 19 27 LINC01456 PPEF1 chrX 17989297 17989298 chrX 103464216 103464217 TCGA-ZG-A9L0 INV 12 19 LINC01456 * chrX 17990005 17990005 chrX 18010182 18010182 TCGA-ZG-A9L0 DUP 44 36 LINC01456 LINC01456 chrX 18009874 18009874 chrX 19896294 19896294 TCGA-ZG-A9L0 DUP 7 5 LINC01456 * chrX 18692307 18692308 chrX 103464028 103464029 TCGA-ZG-A9L0 INV 42 36 PPEF1 * chrX 19179547 19179548 chrX 99533083 99533084 TCGA-ZG-A9L0 INV 38 42 * * chrX 25338801 25338802 chrX 25339180 25339180 TCGA-ZG-A9L0 DEL 34 26 * * chrX 27004891 27004891 chrX 72179444 72179444 TCGA-ZG-A9L0 DUP 25 13 * * chrX 28377199 28377199 chrX 28527466 28527466 TCGA-ZG-A9L0 INV 50 36 * * chrX 3108854 3108854 chrX 7358458 7358458 TCGA-ZG-A9L0 DUP 22 17 ARSF * chrX 3171063 3171063 chrX 6747320 6747320 TCGA-ZG-A9L0 INV 22 2 * * chrX 39184401 39184402 chrX 54741260 54741261 TCGA-ZG-A9L0 DEL 6 31 * * chrX 4855273 4855273 chrX 4941792 4941792 TCGA-ZG-A9L0 DEL 41 41 * * chrX 4890317 4890317 chrX 7792221 7792221 TCGA-ZG-A9L0 DEL 16 6 * * chrX 5343875 5343876 chrX 63346739 63346740 TCGA-ZG-A9L0 DEL 13 47 * LINC01278 chrX 54741632 54741635 chrX 54742361 54742361 TCGA-ZG-A9L0 DEL 5 44 * * chrX 54742110 54742110 chrX 54743515 54743515 TCGA-ZG-A9L0 DUP 47 24 * * chrX 54742568 54742568 chrX 54743273 54743273 TCGA-ZG-A9L0 DEL 6 8 * * chrX 597315 598121 chrX 598954 599657 TCGA-ZG-A9L0 DEL 49 14 * * chrX 6874962 6874962 chrX 7012341 7012341 TCGA-ZG-A9L0 DEL 23 25 * * chrX 70076635 70076636 chrX 70087413 70087414 TCGA-ZG-A9L0 INV 38 11 * * chrX 70177105 70177105 chrX 70178691 70178691 TCGA-ZG-A9L0 INV 43 19 DGAT2L6 DGAT2L6 chrX 7116973 7116973 chrX 7858579 7858579 TCGA-ZG-A9L0 INV 3 11 PUDP * chrX 7347869 7347871 chrX 7419875 7419877 TCGA-ZG-A9L0 INV 42 24 STS * chrX 73892040 73892045 chrX 73892607 73892607 TCGA-ZG-A9L0 DEL 18 49 * * chrX 7446975 7446980 chrX 24138326 24138331 TCGA-ZG-A9L0 DEL 11 30 * * chrX 7532414 7532414 chrX 7533470 7533470 TCGA-ZG-A9L0 INV 50 39 * * chrX 7532770 7532771 chrX 7543569 7543570 TCGA-ZG-A9L0 DEL 22 45 * * chrX 7542516 7542517 chrX 7543819 7543820 TCGA-ZG-A9L0 INV 38 20 * * chrX 8319487 8319489 chrX 8338921 8338923 TCGA-ZG-A9L0 DUP 2 29 * * chrX 8450959 8450959 chrX 17502135 17502135 TCGA-ZG-A9L0 DUP 1 34 * NHS chrX 96049 96049 chrX 24240615 24240615 TCGA-ZG-A9L0 DUP 18 21 * * chrX 9818884 9818888 chrX 27438284 27438288 TCGA-ZG-A9L0 INV 30 48 SHROOM2 * chr6 62109156 62109156 chrX 11713358 11713358 TCGA-EJ-A65M BND 9 5 KHDRBS2 AC004554.1 chr6 69971584 69971585 chrX 11713285 11713320 TCGA-EJ-A65M BND 2 43 COL19A1 AC004554.1 chrX 146066143 146066144 chrX 146818157 146818158 TCGA-EJ-A65M DEL 25 13 * * chrX 149026733 149026748 chrX 149026733 149026748 TCGA-EJ-A65M INS 18 17 * * chr6 162855381 162855381 chrX 68056810 68056810 TCGA-EJ-7782 BND 25 14 PACRG OPHN1 chr7 21074075 21074076 chrX 88800113 88800114 TCGA-EJ-7782 BND 14 21 * * chrX 13976504 13976505 chrX 25317303 25317304 TCGA-EJ-7782 INV 30 26 * * chrX 1609732 1609746 chrX 1609801 1609801 TCGA-EJ-7782 DEL 39 27 * * chrX 66675854 66675855 chrX 66677286 66677287 TCGA-EJ-7782 INV 9 28 * RNU6-394P chrX 66735798 66735800 chrX 66736609 66736611 TCGA-EJ-7782 INV 32 26 * * chrX 66736543 66736545 chrX 66737090 66737090 TCGA-EJ-7782 DEL 50 16 * * chrX 67594406 67594406 chrX 67630338 67630338 TCGA-EJ-7782 INV 8 43 AR AR chrX 67771422 67771425 chrX 67854610 67854613 TCGA-EJ-7782 INV 1 20 * * chrX 67982501 67982506 chrX 68021191 68021196 TCGA-EJ-7782 INV 19 47 * * chrX 67985908 67986796 chrX 68023039 68023991 TCGA-EJ-7782 DEL 2 32 * * chrX 68064293 68064297 chrX 68109584 68109588 TCGA-EJ-7782 DUP 48 29 OPHN1 OPHN1 chrX 68076415 68076416 chrX 68116251 68116252 TCGA-EJ-7782 INV 29 41 OPHN1 OPHN1 chrX 68248554 68248558 chrX 68273083 68273087 TCGA-EJ-7782 INV 24 38 OPHN1 OPHN1 chrX 69494985 69494986 chrX 69495131 69495150 TCGA-EJ-7782 DEL 14 29 * * chrX 69495131 69495150 chrX 69495878 69495881 TCGA-EJ-7782 INV 34 15 * * chr12 21012594 21012594 chrX 35434528 35434528 TCGA-XJ-A83G BND 26 4 SLCO1B3-SLCO1B7 * chr14 44417279 44417831 chrX 78215874 78216320 TCGA-XJ-A83G BND 21 29 * * chr4 41988916 41988916 chrX 915373 915373 TCGA-XJ-A83G BND 8 33 AC106052.1 * chrX 133079538 133079540 chrX 133079951 133079951 TCGA-XJ-A83G DEL 7 26 USP26 USP26 chrX 1871241 1871264 chrX 1873028 1873051 TCGA-XJ-A83G DEL 40 26 * * chrX 48285657 48285659 chrX 48286025 48286025 TCGA-XJ-A83G DEL 14 31 * * chrX 66887741 66887783 chrX 66933463 66933505 TCGA-XJ-A83G DUP 16 46 * * chr11 101763697 101763698 chrX 25340466 25340467 TCGA-KK-A6E0 BND 12 16 TRPC6 * chr11 115693974 115693974 chrX 66428676 66428676 TCGA-KK-A6E0 BND 7 6 LINC02698 * chr11 115758468 115758468 chrX 66310041 66310041 TCGA-KK-A6E0 BND 28 16 LINC02698 * chr11 115806538 115806539 chrX 147001101 147001102 TCGA-KK-A6E0 BND 15 8 LINC02698 * chr11 116036848 116036849 chrX 66576723 66576724 TCGA-KK-A6E0 BND 36 43 * * chr11 116037633 116037636 chrX 66542443 66542446 TCGA-KK-A6E0 BND 45 4 * * chr11 116038393 116038394 chrX 66548374 66548375 TCGA-KK-A6E0 BND 50 37 * * chr11 116616180 116616182 chrX 68840668 68840670 TCGA-KK-A6E0 BND 17 47 * EFNB1 chr11 134482297 134482297 chrX 66422801 66422801 TCGA-KK-A6E0 BND 8 34 B3GAT1-DT * chr11 134490848 134490850 chrX 67832614 67832616 TCGA-KK-A6E0 BND 1 16 B3GAT1-DT * chr11 134639082 134639082 chrX 145986569 145986569 TCGA-KK-A6E0 BND 35 43 * * chr11 20455831 20455831 chrX 113070515 113070515 TCGA-KK-A6E0 BND 28 39 PRMT3 * chr11 22797101 22797101 chrX 109090616 109090616 TCGA-KK-A6E0 BND 27 15 GAS2 * chr11 22892385 22892385 chrX 67865061 67865061 TCGA-KK-A6E0 BND 29 14 AC006299.1 * chr11 23199594 23199594 chrX 66541425 66541425 TCGA-KK-A6E0 BND 46 21 LINC02718 * chr11 50766858 50766861 chrX 20710987 20710990 TCGA-KK-A6E0 BND 2 32 * * chr11 54986918 54986922 chrX 145465759 145465763 TCGA-KK-A6E0 BND 5 2 * * chr11 55003185 55003185 chrX 156009460 156009460 TCGA-KK-A6E0 BND 15 42 * IL9R chr11 55079655 55079656 chrX 110107180 110107181 TCGA-KK-A6E0 BND 23 50 * TMEM164 chr11 59081971 59081974 chrX 112731847 112731850 TCGA-KK-A6E0 BND 47 50 * * chr11 59423946 59423949 chrX 138931096 138931099 TCGA-KK-A6E0 BND 38 27 OR5A2 FGF13 chr11 5997719 5997719 chrX 145279611 145279611 TCGA-KK-A6E0 BND 44 14 * * chr11 6167908 6167908 chrX 58125129 58125129 TCGA-KK-A6E0 BND 37 43 AC022762.1 * chr11 99864356 99864356 chrX 140079022 140079022 TCGA-KK-A6E0 BND 13 14 CNTN5 * chr14 44417377 44417813 chrX 78215890 78216301 TCGA-KK-A6E0 BND 10 14 * * chr17 28760033 28760033 chrX 68569715 68569715 TCGA-KK-A6E0 BND 24 40 FAM222B * chr1 109221421 109221424 chrX 69563821 69563824 TCGA-KK-A6E0 BND 6 26 SARS1 * chr20 8944088 8944092 chrX 109608615 109608619 TCGA-KK-A6E0 BND 37 8 PLCB1 * chr7 3408534 3408534 chrX 37634140 37634140 TCGA-KK-A6E0 BND 3 16 SDK1 AF241726.1 chr7 3409510 3409514 chrX 37634342 37634346 TCGA-KK-A6E0 BND 31 37 SDK1 AF241726.1 chr8 64641334 64641340 chrX 11713661 11713671 TCGA-KK-A6E0 BND 36 6 CYP7B1 AC004554.1 chr9 22058093 22058093 chrX 21972079 21972079 TCGA-KK-A6E0 BND 12 28 CDKN2B-AS1 SMS chr9 42031088 42031089 chrX 26471692 26471693 TCGA-KK-A6E0 BND 42 19 CNTNAP3B * chr9 6268745 6268745 chrX 26809445 26809450 TCGA-KK-A6E0 BND 24 34 * * chr9 63978154 63978160 chrX 28440141 28440147 TCGA-KK-A6E0 BND 16 14 AL163540.1 * chr9 9898150 9898152 chrX 11713202 11713204 TCGA-KK-A6E0 BND 41 10 PTPRD AC004554.1 chrX 109210632 109210634 chrX 145939649 145939651 TCGA-KK-A6E0 DEL 12 1 * * chrX 110076800 110076801 chrX 112701774 112701775 TCGA-KK-A6E0 INV 30 25 TMEM164 * chrX 129592790 129592791 chrX 129592925 129592925 TCGA-KK-A6E0 DEL 37 41 * * chrX 146013154 146013158 chrX 146864366 146864370 TCGA-KK-A6E0 DEL 35 22 * * chrX 16183248 16183259 chrX 142427625 142427636 TCGA-KK-A6E0 DEL 15 19 * * chrX 26470154 26470155 chrX 31041307 31041308 TCGA-KK-A6E0 DEL 9 43 * * chrX 26809445 26809450 chrX 28438306 28438306 TCGA-KK-A6E0 INV 41 11 * * chrX 28438281 28438281 chrX 28438306 28438306 TCGA-KK-A6E0 INS 20 12 * * chrX 34819697 34820102 chrX 67762538 67763142 TCGA-KK-A6E0 DEL 29 45 * * chrX 439992 439992 chrX 440055 440055 TCGA-KK-A6E0 DEL 33 4 * * chrX 66321224 66321224 chrX 68585749 68585749 TCGA-KK-A6E0 DEL 32 5 * * chrX 66421213 66421213 chrX 66528970 66528970 TCGA-KK-A6E0 DEL 28 39 * * chrX 66561795 66561797 chrX 66808738 66808740 TCGA-KK-A6E0 INV 12 43 * * chrX 66706216 66706218 chrX 66732929 66732931 TCGA-KK-A6E0 INV 29 26 * * chrX 67433344 67433344 chrX 67900345 67900345 TCGA-KK-A6E0 INV 29 41 * * chrX 67879314 67879315 chrX 67880448 67880449 TCGA-KK-A6E0 INV 49 45 * * chrX 68499119 68499126 chrX 68499793 68499800 TCGA-KK-A6E0 INV 34 40 YIPF6 YIPF6 chrX 68519265 68519266 chrX 68521040 68521041 TCGA-KK-A6E0 INV 26 7 YIPF6 YIPF6 chrX 68980193 68980945 chrX 68985280 68985869 TCGA-KK-A6E0 INV 49 19 * * chrX 68981562 68981563 chrX 68994753 68994754 TCGA-KK-A6E0 DUP 37 24 * * chr12 106209623 106210204 chrX 141252074 141252414 TCGA-VN-A88R BND 18 8 * * chr15 43115622 43115622 chrX 137010812 137010812 TCGA-VN-A88R BND 49 27 AC068724.3 AL390879.1 chr2 154034631 154034631 chrX 14815871 14815871 TCGA-VN-A88R BND 11 28 GALNT13 * chr9 40920511 40920534 chrX 51841831 51841854 TCGA-VN-A88R BND 20 6 * MAGED1 chrX 102165285 102165285 chrX 102165369 102165369 TCGA-VN-A88R DEL 2 45 * * chrX 20733054 20733054 chrX 20733232 20733232 TCGA-VN-A88R DEL 20 7 * * chrX 30399180 30399180 chrX 30399271 30399271 TCGA-VN-A88R DEL 33 40 * * chrX 73464516 73464520 chrX 73464686 73464686 TCGA-VN-A88R DEL 9 36 * * chrX 79714853 79714858 chrX 79715110 79715110 TCGA-VN-A88R DEL 34 27 * * chrX 93343322 93343322 chrX 93343542 93343542 TCGA-VN-A88R DEL 35 46 * * chr11 43723607 43723610 chrX 7768474 7768477 TCGA-KK-A8IB BND 2 16 AC068205.2 * chr11 93428660 93428661 chrX 108784146 108784147 TCGA-KK-A8IB BND 42 40 DEUP1 * chr12 106209620 106210199 chrX 141252077 141252416 TCGA-KK-A8IB BND 31 14 * * chr19 31637024 31637024 chrX 147349044 147349044 TCGA-KK-A8IB BND 45 47 * * chr22 28669772 28669775 chrX 30441234 30441237 TCGA-KK-A8IB BND 38 15 TTC28 * chr3 26427391 26427391 chrX 83855987 83855987 TCGA-KK-A8IB BND 17 15 * * chr3 26686288 26686288 chrX 83631665 83631665 TCGA-KK-A8IB BND 28 3 LRRC3B * chr3 26694711 26694713 chrX 84166763 84166765 TCGA-KK-A8IB BND 35 14 LRRC3B RPS6KA6 chr3 26698969 26698972 chrX 83714623 83714626 TCGA-KK-A8IB BND 2 25 LRRC3B * chr4 161141717 161142417 chrX 83413443 83413881 TCGA-KK-A8IB BND 36 25 * * chr7 44992426 44992965 chrX 53721861 53722231 TCGA-KK-A8IB BND 22 36 * * chr7 44992590 44992592 chrX 80215135 80215147 TCGA-KK-A8IB BND 45 32 * * chrX 130272946 130272947 chrX 130273391 130273391 TCGA-KK-A8IB DEL 18 2 * * chrX 27020607 27020610 chrX 29298789 29298792 TCGA-KK-A8IB DEL 22 17 * IL1RAPL1 chrX 27066563 27066565 chrX 84945785 84945787 TCGA-KK-A8IB DUP 45 8 AC112493.1 * chrX 27435630 27435630 chrX 85048805 85048805 TCGA-KK-A8IB DEL 46 45 * APOOL chrX 27490235 27490235 chrX 84877886 84877886 TCGA-KK-A8IB INV 6 9 * * chrX 28242378 28242379 chrX 84872338 84872339 TCGA-KK-A8IB INV 5 49 * * chrX 31988136 31988137 chrX 32770436 32770437 TCGA-KK-A8IB INV 2 49 DMD DMD chrX 32402162 32402163 chrX 33552080 33552081 TCGA-KK-A8IB INV 7 5 DMD * chrX 64015472 64015472 chrX 69984880 69984880 TCGA-KK-A8IB DEL 32 10 * EDA chrX 83935099 83935102 chrX 84362813 84362816 TCGA-KK-A8IB INV 16 20 * HDX chrX 84811008 84811008 chrX 84811083 84811083 TCGA-KK-A8IB DEL 27 26 * * chrX 85054103 85054104 chrX 85414229 85414230 TCGA-KK-A8IB INV 5 23 APOOL * chrX 85082133 85082134 chrX 85420638 85420639 TCGA-KK-A8IB INV 1 3 APOOL * chr11 19618907 19618931 chrX 82104275 82104299 TCGA-ZG-A9ND BND 21 12 NAV2 * chr11 42610920 42610920 chrX 135386345 135386345 TCGA-ZG-A9ND BND 8 40 * * chr11 70218840 70219330 chrX 16182845 16183369 TCGA-ZG-A9ND BND 35 31 * * chr11 82789721 82789722 chrX 11935155 11935156 TCGA-ZG-A9ND BND 22 4 * * chr12 8793816 8793816 chrX 151556631 151556631 TCGA-ZG-A9ND BND 45 2 AC092490.1 * chr13 85765032 85765558 chrX 11934534 11934966 TCGA-ZG-A9ND BND 26 4 AL356413.1 * chr13 85765370 85765372 chrX 11935112 11935114 TCGA-ZG-A9ND BND 8 27 AL356413.1 * chr19 53831446 53831446 chrX 92273478 92273478 TCGA-ZG-A9ND BND 9 34 * PCDH11X chr1 112640364 112640368 chrX 78265527 78265532 TCGA-ZG-A9ND BND 3 49 CAPZA1 * chr1 246940020 246940020 chrX 30644280 30644280 TCGA-ZG-A9ND BND 26 50 * * chr20 39919165 39919179 chrX 112604901 112604915 TCGA-ZG-A9ND BND 2 13 * * chr2 33839557 33840038 chrX 119470657 119471059 TCGA-ZG-A9ND BND 3 28 LINC01320 SLC25A5 chr3 38513195 38514062 chrX 74438022 74438502 TCGA-ZG-A9ND BND 10 20 EXOG SLC16A2 chr4 48186723 48187167 chrX 40211075 40211463 TCGA-ZG-A9ND BND 19 32 TEC * chr6 47922799 47923436 chrX 11934535 11934927 TCGA-ZG-A9ND BND 34 32 PTCHD4 * chrX 17100437 17100439 chrX 56963033 56963035 TCGA-ZG-A9ND DUP 9 42 REPS2 SPIN3 chrX 25757262 25757276 chrX 25757262 25757276 TCGA-ZG-A9ND INS 30 9 * * chrX 32444577 32444578 chrX 32446100 32446101 TCGA-ZG-A9ND DEL 7 20 DMD DMD chrX 36906007 36906009 chrX 41950074 41950076 TCGA-ZG-A9ND DUP 38 42 * * chrX 66814192 66814192 chrX 67041887 67041887 TCGA-ZG-A9ND DUP 26 43 * * chr11 20571306 20571327 chrX 109867429 109867450 TCGA-KK-A7B0 BND 48 29 * * chr6 26840175 26840175 chrX 94646952 94646952 TCGA-KK-A7B0 BND 38 38 * * chrX 1013424 1013476 chrX 1013812 1013812 TCGA-KK-A7B0 DEL 27 48 * * chrX 353837 353868 chrX 353911 353911 TCGA-KK-A7B0 DEL 21 25 PPP2R3B PPP2R3B chrX 66870766 66870767 chrX 67047069 67047070 TCGA-KK-A7B0 DUP 5 32 * * chrX 86947677 86947678 chrX 86949410 86949411 TCGA-KK-A7B0 DEL 26 30 * * chr14 44417113 44417728 chrX 78215393 78215809 TCGA-ZG-A8QY BND 39 20 * * chr22 45831499 45831499 chrX 154549457 154549457 TCGA-ZG-A8QY BND 8 27 ATXN10 IKBKG chr22 50622894 50622894 chrX 154553963 154553963 TCGA-ZG-A8QY BND 27 16 ARSA IKBKG chr3 192046609 192046609 chrX 111066232 111066232 TCGA-ZG-A8QY BND 22 30 * PAK3 chr6 136162657 136163135 chrX 143497147 143498055 TCGA-ZG-A8QY BND 9 13 PDE7B AC239727.1 chrX 23128699 23128700 chrX 23181395 23181396 TCGA-ZG-A8QY DUP 22 13 PTCHD1-AS PTCHD1-AS chrX 37510994 37510998 chrX 37511121 37511121 TCGA-ZG-A8QY DEL 14 49 AF241726.1 AF241726.1 chrX 43865532 43865533 chrX 46436714 46436715 TCGA-ZG-A8QY DEL 32 3 MAOB * chrX 53725239 53725243 chrX 53986190 53986194 TCGA-ZG-A8QY DUP 36 17 * PHF8 chrX 66658412 66658414 chrX 66969440 66969442 TCGA-ZG-A8QY DUP 33 39 * * chrX 66903869 66903870 chrX 66946954 66946955 TCGA-ZG-A8QY DUP 48 18 * * chrX 89484780 89484781 chrX 89485032 89485032 TCGA-ZG-A8QY DEL 1 4 * * chr2 105128546 105128547 chrX 12069302 12069303 TCGA-EJ-A8FS BND 38 48 * * chr6 32491474 32492002 chrX 139341568 139342058 TCGA-EJ-A8FS BND 50 8 * * chr6 40840234 40840242 chrX 8180845 8180860 TCGA-EJ-A8FS BND 10 37 * AC079142.1 chr8 35387362 35387362 chrX 11713285 11713320 TCGA-EJ-A8FS BND 6 23 UNC5D AC004554.1 chrX 11714373 11714423 chrX 11784582 11784598 TCGA-EJ-A8FS DUP 23 1 AC004554.1 * chrX 11714577 11714586 chrX 11784582 11784598 TCGA-EJ-A8FS DEL 49 29 AC004554.1 * chrX 127202409 127202409 chrX 127202660 127202660 TCGA-EJ-A8FS DEL 12 9 * * chrX 134410664 134410664 chrX 134410965 134410965 TCGA-EJ-A8FS DEL 49 34 PHF6 PHF6 chrX 15266780 15266780 chrX 15267593 15267593 TCGA-EJ-A8FS DUP 2 37 ASB9 ASB9 chrX 66867954 66867954 chrX 66934587 66934587 TCGA-EJ-A8FS DUP 42 37 * * chrX 66926570 66926661 chrX 66947011 66947102 TCGA-EJ-A8FS INV 3 14 * * chr12 11556480 11556505 chrX 66474512 66474516 TCGA-ZG-A9L6 BND 27 31 AC007450.1 * chr12 11556480 11556505 chrX 66474477 66474480 TCGA-ZG-A9L6 BND 24 46 AC007450.1 * chr17 58560632 58560632 chrX 101193132 101193132 TCGA-ZG-A9L6 BND 25 23 TEX14 * chr20 3315363 3315847 chrX 66891613 66892442 TCGA-ZG-A9L6 BND 20 48 C20orf194 * chr2 149956912 149956915 chrX 105799784 105799787 TCGA-ZG-A9L6 BND 13 19 * * chr4 35494821 35495306 chrX 66891633 66892444 TCGA-ZG-A9L6 BND 3 3 RNU6-573P * chr8 5989410 5989411 chrX 11713229 11713230 TCGA-ZG-A9L6 BND 14 47 * AC004554.1 chr9 125268787 125268788 chrX 66766400 66766401 TCGA-ZG-A9L6 BND 40 39 GAPVD1 * chr9 125270695 125270697 chrX 66771329 66771331 TCGA-ZG-A9L6 BND 7 8 GAPVD1 * chrX 6532749 6532749 chrX 7844478 7844478 TCGA-ZG-A9L6 INV 4 41 * * chr14 34047146 34047802 chrX 106354321 106354770 TCGA-TK-A8OK BND 8 13 EGLN3 * chr18 38260682 38260682 chrX 11714310 11714322 TCGA-TK-A8OK BND 13 48 * AC004554.1 chr2 68212273 68212273 chrX 144158113 144158113 TCGA-TK-A8OK BND 39 23 AC017083.3 * chr3 84666158 84666158 chrX 11713285 11713320 TCGA-TK-A8OK BND 46 48 LINC00971 AC004554.1 chr4 29397659 29397659 chrX 11713285 11713320 TCGA-TK-A8OK BND 12 38 * AC004554.1 chr8 2845643 2845644 chrX 11714494 11714502 TCGA-TK-A8OK BND 31 39 * AC004554.1 chrX 102204437 102204438 chrX 102494365 102494366 TCGA-TK-A8OK DUP 33 32 * * chrX 1824114 1824128 chrX 1824460 1824460 TCGA-TK-A8OK DEL 14 26 * * chrX 19174897 19174915 chrX 19174952 19174952 TCGA-TK-A8OK DEL 34 33 * * chrX 23691525 23691525 chrX 24857639 24857639 TCGA-TK-A8OK DUP 41 1 * POLA1 chrX 66827146 66827151 chrX 67175592 67175597 TCGA-TK-A8OK DUP 28 22 * * chrX 70316379 70316383 chrX 103057456 103057460 TCGA-TK-A8OK DUP 27 11 KIF4A * chrX 72012615 72012615 chrX 72485018 72485018 TCGA-TK-A8OK DUP 2 31 NHSL2 HDAC8 chrX 72013840 72013841 chrX 72284319 72284320 TCGA-TK-A8OK INV 18 39 NHSL2 PIN4 chrX 72282755 72282755 chrX 72933766 72933766 TCGA-TK-A8OK DEL 37 36 PIN4 DMRTC1 chrX 73699661 73699661 chrX 102323523 102323523 TCGA-TK-A8OK DEL 42 31 * NXF2 chrX 57012424 57012432 chrX 86006849 86006857 TCGA-G9-6369 INV 3 6 * CHM chrX 66143149 66143153 chrX 68342799 68342803 TCGA-G9-6369 DUP 42 29 * OPHN1 chrX 66826255 66826255 chrX 66930198 66930198 TCGA-G9-6369 DUP 32 29 * * chr5 65934911 65934912 chrX 66770430 66770431 TCGA-VN-A88O BND 37 3 ERBIN * chrX 36827391 36827392 chrX 37511231 37511232 TCGA-VN-A88O INV 12 5 * AF241726.1 chrX 36833032 36833033 chrX 37513007 37513008 TCGA-VN-A88O INV 8 37 * AF241726.1 chrX 66408998 66408999 chrX 66435858 66435859 TCGA-VN-A88O DEL 12 17 * AL592049.1 chrX 66479262 66479262 chrX 66547161 66547161 TCGA-VN-A88O DUP 12 45 * * chrX 66530978 66530982 chrX 66538466 66538470 TCGA-VN-A88O INV 46 42 * * chrX 68841321 68841323 chrX 68843270 68843272 TCGA-VN-A88O INV 1 7 EFNB1 * chr13 93989153 93989154 chrX 14191272 14191273 TCGA-FC-A4JI BND 37 41 GPC6 * chr15 86069273 86069273 chrX 36148956 36148956 TCGA-FC-A4JI BND 26 28 * CFAP47 chr16 14902672 14902673 chrX 44918602 44918603 TCGA-FC-A4JI BND 44 23 * KDM6A chr16 15400084 15400085 chrX 68709219 68709220 TCGA-FC-A4JI BND 24 10 MPV17L STARD8 chr16 15401162 15401163 chrX 64416518 64416519 TCGA-FC-A4JI BND 18 18 MPV17L * chr16 26508016 26508016 chrX 46116530 46116530 TCGA-FC-A4JI BND 13 34 * * chr16 26841580 26841581 chrX 63773474 63773475 TCGA-FC-A4JI BND 19 9 * ARHGEF9 chr16 26876989 26876992 chrX 65392736 65392739 TCGA-FC-A4JI BND 12 18 * ZC3H12B chr16 27075915 27075916 chrX 68604896 68604897 TCGA-FC-A4JI BND 50 28 * * chr16 27380876 27380881 chrX 62574876 62574881 TCGA-FC-A4JI BND 41 32 * * chr16 28584057 28584059 chrX 65722847 65722856 TCGA-FC-A4JI BND 2 49 SGF29 MSN chr16 30972084 30972085 chrX 67679935 67679936 TCGA-FC-A4JI BND 5 29 SETD1A AR chr18 53312763 53312767 chrX 63776698 63776702 TCGA-FC-A4JI BND 50 40 DCC ARHGEF9 chr22 28669654 28669655 chrX 46005549 46005550 TCGA-FC-A4JI BND 49 49 TTC28 * chr3 116105673 116105674 chrX 144670010 144670011 TCGA-FC-A4JI BND 43 18 LSAMP * chr6 160235082 160235707 chrX 153013661 153014117 TCGA-FC-A4JI BND 31 32 SLC22A2 * chr6 62694374 62694375 chrX 67543865 67543866 TCGA-FC-A4JI BND 47 14 * AR chr6 85816555 85816557 chrX 66449245 66449247 TCGA-FC-A4JI BND 48 31 * * chrX 43942762 43942766 chrX 46602866 46602870 TCGA-FC-A4JI DUP 37 27 * SLC9A7 chrX 43980278 43980278 chrX 64428298 64428298 TCGA-FC-A4JI DEL 21 24 * * chrX 43981412 43981412 chrX 63413214 63413214 TCGA-FC-A4JI DUP 6 8 * LINC01278 chrX 44402060 44402061 chrX 44474992 44474993 TCGA-FC-A4JI DEL 39 46 * * chrX 44460998 44460998 chrX 67847881 67847881 TCGA-FC-A4JI INV 47 28 * * chrX 44722855 44722856 chrX 46708219 46708239 TCGA-FC-A4JI DUP 1 40 * SLC9A7 chrX 44802502 44802502 chrX 44885887 44885887 TCGA-FC-A4JI INV 13 26 * KDM6A chrX 44885372 44885372 chrX 62749207 62749207 TCGA-FC-A4JI DEL 13 48 KDM6A * chrX 45072729 45072732 chrX 45082878 45082881 TCGA-FC-A4JI DEL 21 16 KDM6A KDM6A chrX 45084883 45084884 chrX 68861499 68861500 TCGA-FC-A4JI INV 2 29 KDM6A * chrX 45245859 45245859 chrX 46458001 46458001 TCGA-FC-A4JI DEL 44 26 AC136489.1 KRBOX4 chrX 45246842 45246843 chrX 68023243 68023244 TCGA-FC-A4JI INV 8 21 AC136489.1 * chrX 45284621 45284623 chrX 68393494 68393496 TCGA-FC-A4JI DEL 10 10 AC136489.1 OPHN1 chrX 45284716 45284719 chrX 68069424 68069427 TCGA-FC-A4JI INV 1 45 AC136489.1 OPHN1 chrX 45376058 45376058 chrX 68493733 68493733 TCGA-FC-A4JI INV 34 6 * * chrX 45622249 45622252 chrX 64819027 64819030 TCGA-FC-A4JI DEL 37 12 LINC01204 * chrX 46071909 46071913 chrX 68935699 68935703 TCGA-FC-A4JI DEL 3 16 * * chrX 46243449 46243450 chrX 67599154 67599155 TCGA-FC-A4JI INV 50 3 * AR chrX 46553275 46553275 chrX 46554673 46554673 TCGA-FC-A4JI DEL 22 17 * Metazoa_SRP chrX 46603500 46603500 chrX 62902216 62902216 TCGA-FC-A4JI DUP 13 33 SLC9A7 * chrX 47071590 47071590 chrX 65115396 65115396 TCGA-FC-A4JI DUP 39 17 * * chrX 47074403 47074403 chrX 66896690 66896690 TCGA-FC-A4JI DUP 8 29 * * chrX 47164830 47164831 chrX 57811754 57811755 TCGA-FC-A4JI INV 6 22 RBM10 * chrX 47244787 47244788 chrX 68893222 68893238 TCGA-FC-A4JI INV 41 7 USP11 * chrX 47244881 47244882 chrX 68985813 68985814 TCGA-FC-A4JI DUP 11 35 USP11 * chrX 47301921 47301921 chrX 64166548 64166548 TCGA-FC-A4JI INV 34 19 * * chrX 57399977 57399977 chrX 65109968 65109968 TCGA-FC-A4JI INV 47 3 FAAH2 * chrX 57730900 57730900 chrX 66449245 66449247 TCGA-FC-A4JI INV 46 24 * * chrX 57766732 57766734 chrX 57768580 57768582 TCGA-FC-A4JI INV 22 9 MDH1P1 * chrX 57767414 57767414 chrX 64141888 64141888 TCGA-FC-A4JI INV 31 13 * * chrX 58187756 58187757 chrX 67778461 67778462 TCGA-FC-A4JI DEL 8 24 * * chrX 62553271 62553273 chrX 68251459 68251461 TCGA-FC-A4JI INV 25 7 * OPHN1 chrX 62664960 62664963 chrX 68978477 68978480 TCGA-FC-A4JI DUP 3 32 * * chrX 62719884 62719884 chrX 64725023 64725023 TCGA-FC-A4JI DUP 39 27 * * chrX 62748089 62748091 chrX 68086066 68086068 TCGA-FC-A4JI INV 30 27 * OPHN1 chrX 62903312 62903315 chrX 66517337 66517340 TCGA-FC-A4JI INV 39 23 * * chrX 63878083 63878083 chrX 67874242 67874242 TCGA-FC-A4JI INV 32 10 * * chrX 63904019 63904020 chrX 67830802 67830803 TCGA-FC-A4JI DUP 26 25 * * chrX 64451938 64451939 chrX 68701562 68701563 TCGA-FC-A4JI DEL 39 5 * STARD8 chrX 64504530 64504534 chrX 68462620 68462624 TCGA-FC-A4JI DUP 8 1 * * chrX 64815768 64815769 chrX 68022846 68022847 TCGA-FC-A4JI INV 25 35 * * chrX 65010148 65010148 chrX 65031505 65031505 TCGA-FC-A4JI DUP 31 4 ZC4H2 ZC4H2 chrX 65127559 65127559 chrX 66468144 66468144 TCGA-FC-A4JI INV 43 7 * * chrX 65158140 65158140 chrX 67831432 67831432 TCGA-FC-A4JI DEL 12 5 * * chrX 65722847 65722856 chrX 65723267 65723273 TCGA-FC-A4JI INV 46 47 MSN MSN chrX 66517337 66517340 chrX 73514941 73514944 TCGA-FC-A4JI DUP 6 17 * * chrX 67603524 67603524 chrX 67830601 67830601 TCGA-FC-A4JI INV 2 18 AR * chrX 67832358 67832358 chrX 68979084 68979084 TCGA-FC-A4JI DEL 40 17 * * chrX 68187779 68187780 chrX 68188078 68188078 TCGA-FC-A4JI DEL 21 48 OPHN1 OPHN1 chrX 68450939 68450939 chrX 68893222 68893238 TCGA-FC-A4JI DEL 12 37 * * chrX 68492991 68492992 chrX 69524794 69524795 TCGA-FC-A4JI INV 19 2 * FAM155B chrX 69113548 69113551 chrX 69114470 69114473 TCGA-FC-A4JI INV 22 43 * * chr10 17407110 17407110 chr10 20977831 20977831 TCGA-ZG-A8QY INS 20 33 ST8SIA6 NEBL chr10 18551626 18551626 chr10 19068760 19068760 TCGA-ZG-A8QY DEL 43 27 NSUN6 MALRD1 chr10 20988199 20988199 chr10 38124169 38124169 TCGA-ZG-A8QY INS 42 18 NEBL ZNF37A chr10 3928571 3928571 chr10 19057295 19057295 TCGA-ZG-A8QY INS 1 41 LINC02660 MALRD1 chr11 101493728 101493728 chr18 64206652 64206652 TCGA-ZG-A8QY BND 8 10 TRPC6 LINC01924 chr11 115502420 115502420 chr7 154579267 154579267 TCGA-ZG-A8QY BND 10 10 CADM1 DPP6 chr11 43888085 43888085 chr11 43888392 43888392 TCGA-ZG-A8QY DEL 20 14 ALKBH3 ALKBH3 chr11 87448597 87448597 chr11 87660538 87660538 TCGA-ZG-A8QY DEL 15 5 * * chr11 87466133 87466133 chr11 102575782 102575782 TCGA-ZG-A8QY INS 20 26 * * chr11 98242614 98242614 chr11 102667139 102667139 TCGA-ZG-A8QY DEL 45 28 * * chr11 98857117 98857117 chr11 101648905 101648905 TCGA-ZG-A8QY INS 1 16 * TRPC6 chr11 99401515 99401515 chr11 99970190 99970190 TCGA-ZG-A8QY DEL 12 42 CNTN5 CNTN5 chr11 99527129 99527129 chr11 99575052 99575052 TCGA-ZG-A8QY DEL 17 35 CNTN5 CNTN5 chr12 21470217 21470217 chr2 154127775 154127775 TCGA-ZG-A8QY BND 5 29 PYROXD1 GALNT13 chr12 21789655 21789655 chr2 153089707 153089707 TCGA-ZG-A8QY BND 28 21 * * chr16 30513065 30513065 chr16 30942152 30942152 TCGA-ZG-A8QY DEL 29 6 ITGAL FBXL19 chr16 78923443 78923443 chr16 79633731 79633731 TCGA-ZG-A8QY INS 29 5 WWOX * chr16 79629030 79629030 chr16 79629855 79629855 TCGA-ZG-A8QY DEL 46 23 * * chr1 170739448 170739448 chr1 170740019 170740019 TCGA-ZG-A8QY DEL 25 28 * * chr1 209398925 209398925 chr1 211809456 211809456 TCGA-ZG-A8QY INS 11 15 * LPGAT1 chr1 210669823 210669823 chr1 210670978 210670978 TCGA-ZG-A8QY DEL 12 22 HHAT HHAT chr1 88691338 88691338 chr1 88707246 88707246 TCGA-ZG-A8QY DEL 36 37 PKN2 PKN2 chr2 140932964 140932964 chr15 24882834 24882834 TCGA-ZG-A8QY BND 7 30 LRP1B SNRPN chr2 153065942 153065942 chr2 154506700 154506700 TCGA-ZG-A8QY DEL 42 23 * * chr2 184470758 184470758 chr12 20622866 20622866 TCGA-ZG-A8QY BND 8 39 * PDE3A chr2 198939266 198939266 chr2 198952977 198952977 TCGA-ZG-A8QY DEL 45 27 AC020718.1 AC020718.1 chr3 115530575 115530575 chr3 116045641 116045641 TCGA-ZG-A8QY INS 9 31 * LSAMP chr3 28615855 28615855 chr3 28616543 28616543 TCGA-ZG-A8QY DEL 19 37 AC098650.1 AC098650.1 chr4 108492152 108492165 chr8 50758637 50758650 TCGA-ZG-A8QY BND 17 38 * SNTG1 chr4 187417573 187417573 chr4 187418311 187418311 TCGA-ZG-A8QY DEL 28 50 * * chr5 60831494 60831494 chr5 61174177 61174177 TCGA-ZG-A8QY DEL 15 15 ELOVL7 SMIM15-AS1 chr5 9332368 9332368 chr5 9346245 9346245 TCGA-ZG-A8QY INS 34 22 SEMA5A SEMA5A chr6 102750867 102750867 chr6 102750976 102750976 TCGA-ZG-A8QY DEL 25 37 * * chr6 115614213 115614213 chr6 115615169 115615169 TCGA-ZG-A8QY DEL 3 48 * * chr6 121459689 121459689 chr6 121494006 121494006 TCGA-ZG-A8QY DEL 30 3 * * chr6 81880885 81880885 chr6 161709976 161709976 TCGA-ZG-A8QY DEL 22 38 LINC02542 PRKN chr6 82267064 82267064 chr6 121348826 121348826 TCGA-ZG-A8QY DEL 35 45 * * chr6 82267323 82267323 chr6 161709346 161709346 TCGA-ZG-A8QY INS 48 26 * PRKN chr6 82353742 82353742 chr6 121492200 121492200 TCGA-ZG-A8QY INS 12 42 * * chr6 83641528 83641528 chr6 83657328 83657328 TCGA-ZG-A8QY DEL 1 23 SNAP91 SNAP91 chr7 147170217 147170217 chr7 147171568 147171568 TCGA-ZG-A8QY DEL 3 2 CNTNAP2 CNTNAP2 chr7 147557991 147557991 chr7 148435547 148435547 TCGA-ZG-A8QY DEL 2 2 CNTNAP2 * chr7 158432098 158432098 chr7 159232319 159232319 TCGA-ZG-A8QY INS 2 33 PTPRN2 PIP5K1P2 chr8 135994815 135994815 chr8 136687167 136687167 TCGA-ZG-A8QY DEL 26 5 LINC02055 LINC02055 chr8 50777021 50777021 chr4 120474732 120474732 TCGA-ZG-A8QY BND 39 8 SNTG1 * chr9 116986107 116986107 chr9 117232756 117232756 TCGA-ZG-A8QY INS 46 15 ASTN2 ASTN2 chrX 51483381 51483381 chrX 51484117 51484117 TCGA-ZG-A8QY DEL 16 45 * * chr10 18108921 18108921 chr10 21550749 21550749 TCGA-CH-5737 INS 12 35 * MLLT10 chr10 18760381 18760381 chr10 20767805 20767805 TCGA-CH-5737 INS 18 6 * * chr10 19776271 19776271 chr10 19785442 19785442 TCGA-CH-5737 DEL 28 22 MALRD1 MALRD1 chr10 20322993 20322993 chr10 25336712 25336712 TCGA-CH-5737 DEL 17 42 * GPR158 chr10 20717101 20717101 chr10 26364113 26364113 TCGA-CH-5737 INS 36 22 * * chr10 21490772 21490772 chr10 57624704 57624704 TCGA-CH-5737 INS 42 29 * * chr10 21646419 21646419 chr10 25587432 25587432 TCGA-CH-5737 DEL 18 11 MLLT10 GPR158 chr10 21669311 21669311 chr10 25033475 25033475 TCGA-CH-5737 INS 26 11 MLLT10 AL512598.2 chr10 23579806 23579806 chr10 24830015 24830015 TCGA-CH-5737 DEL 33 31 * * chr10 24262804 24262804 chr10 25334944 25334944 TCGA-CH-5737 INS 46 14 KIAA1217 GPR158 chr10 79965544 79965544 chr10 79967655 79967655 TCGA-CH-5737 DEL 39 45 SFTPD SFTPD chr11 39989378 39989378 chr11 39990072 39990072 TCGA-CH-5737 DEL 10 28 * * chr11 90925532 90925532 chr11 99395887 99395887 TCGA-CH-5737 INS 42 25 * CNTN5 chr11 93309462 93309462 chr11 99429512 99429512 TCGA-CH-5737 DEL 28 15 * CNTN5 chr12 38014583 38014590 chr12 38044855 38044855 TCGA-CH-5737 DEL 43 7 * * chr13 57524836 57524836 chr13 60794411 60794411 TCGA-CH-5737 DEL 8 28 * * chr13 62639377 62639377 chr13 62640041 62640041 TCGA-CH-5737 DEL 27 8 * * chr13 62871058 62871058 chr13 67308143 67308143 TCGA-CH-5737 INS 48 24 * * chr13 63952856 63952856 chr13 65077138 65077138 TCGA-CH-5737 DEL 35 16 LINC00355 * chr13 66690173 66690173 chr13 81037457 81037457 TCGA-CH-5737 INS 13 48 PCDH9 * chr13 81594998 81594998 chr13 81595171 81595171 TCGA-CH-5737 DEL 23 16 * * chr1 158464515 158464515 chr1 159093408 159093408 TCGA-CH-5737 DEL 24 39 OR10K1 AIM2 chr1 188118687 188118687 chr1 188151676 188151676 TCGA-CH-5737 DEL 21 3 AL136372.2 * chr1 82349013 82349013 chr1 104118210 104118210 TCGA-CH-5737 INS 39 29 AL157944.1 AC092506.1 chr20 22505486 22505486 chr20 22505591 22505599 TCGA-CH-5737 DEL 41 50 * * chr21 21267005 21267005 chr21 21272663 21272663 TCGA-CH-5737 DEL 1 40 NCAM2 NCAM2 chr21 24468045 24468045 chr21 24470400 24470400 TCGA-CH-5737 DEL 19 40 LINC01684 LINC01684 chr2 126027699 126027699 chr2 126037197 126037197 TCGA-CH-5737 DEL 39 2 * * chr2 137975804 137975804 chr2 137980078 137980078 TCGA-CH-5737 DEL 4 38 HNMT HNMT chr2 140513288 140513288 chr2 140514114 140514114 TCGA-CH-5737 DEL 19 42 LRP1B LRP1B chr2 145054740 145054740 chr2 149019484 149019488 TCGA-CH-5737 DEL 1 10 TEX41 KIF5C chr2 154373273 154373273 chr2 183834924 183834924 TCGA-CH-5737 DEL 7 37 GALNT13 * chr2 162425364 162425364 chr2 212895811 212895811 TCGA-CH-5737 DEL 44 30 KCNH7 AC093865.1 chr2 162429448 162429448 chr2 213519787 213519787 TCGA-CH-5737 INS 11 1 KCNH7 SPAG16 chr2 194503755 194503755 chr2 194518930 194518930 TCGA-CH-5737 DEL 43 2 * * chr2 211880563 211880563 chr2 211880718 211880718 TCGA-CH-5737 DEL 37 41 ERBB4 ERBB4 chr2 55579701 55579703 chr2 57820724 57820724 TCGA-CH-5737 INS 7 18 PPP4R3B * chr2 55607882 55607882 chr2 57819568 57819568 TCGA-CH-5737 INS 23 46 PPP4R3B * chr2 58956781 58956781 chr2 84088766 84088766 TCGA-CH-5737 INS 7 48 LINC01122 * chr2 60777989 60777989 chr2 84600911 84600911 TCGA-CH-5737 INS 20 12 PAPOLG DNAH6 chr2 60814107 60814107 chr2 79403315 79403315 TCGA-CH-5737 INS 5 6 * CTNNA2 chr2 79526262 79526262 chr2 79527320 79527320 TCGA-CH-5737 DEL 16 13 CTNNA2 CTNNA2 chr2 80738811 80738811 chr2 80907770 80907770 TCGA-CH-5737 DEL 25 10 AC012355.1 * chr2 80744038 80744038 chr2 83176738 83176738 TCGA-CH-5737 INS 42 18 AC012355.1 * chr2 80903529 80903529 chr2 81813300 81813300 TCGA-CH-5737 DEL 49 49 * * chr3 117271385 117271385 chr3 119017813 119017813 TCGA-CH-5737 DEL 20 46 * IGSF11 chr3 122510662 122510662 chr3 124119801 124119801 TCGA-CH-5737 DEL 18 31 KPNA1 KALRN chr3 147073843 147073843 chr3 147088118 147088118 TCGA-CH-5737 DEL 27 18 AC092957.1 AC092957.1 chr3 81472890 81472890 chr3 86705264 86705264 TCGA-CH-5737 DEL 9 4 * * chr3 82152618 82152618 chr3 82155770 82155770 TCGA-CH-5737 DEL 49 30 LINC02008 LINC02008 chr3 97768998 97769001 chr3 114264857 114264857 TCGA-CH-5737 DEL 28 1 ARL6 * chr4 111696523 111696523 chr4 139357463 139357463 TCGA-CH-5737 DEL 38 25 * NAA15 chr4 171416401 171416401 chr4 171421957 171421957 TCGA-CH-5737 DEL 46 6 * * chr4 179694987 179694987 chr4 189052491 189052491 TCGA-CH-5737 DEL 47 25 * * chr4 180512438 180512438 chr4 180512759 180512759 TCGA-CH-5737 DEL 19 26 * * chr4 97530882 97530882 chr4 97532556 97532556 TCGA-CH-5737 DEL 22 5 STPG2 STPG2 chr5 15998119 15998119 chr5 16001583 16001583 TCGA-CH-5737 DEL 11 34 * * chr5 19847869 19847869 chr5 19850076 19850076 TCGA-CH-5737 DEL 4 47 CDH18 CDH18 chr5 31719036 31719036 chr5 102109981 102109981 TCGA-CH-5737 DEL 26 34 PDZD2 * chr5 96888483 96888483 chr5 96901701 96901701 TCGA-CH-5737 DEL 25 9 ERAP2 ERAP2 chr6 103417673 103417673 chr8 138668708 138668708 TCGA-CH-5737 BND 35 41 * COL22A1 chr6 116132159 116132159 chr6 152752756 152752756 TCGA-CH-5737 DEL 38 35 NT5DC1 VIP chr6 116557920 116557920 chr6 117191491 117191491 TCGA-CH-5737 DEL 35 16 CALHM4 * chr6 118576800 118576800 chr6 152578025 152578025 TCGA-CH-5737 INS 19 38 CEP85L SYNE1 chr6 120113970 120113970 chr6 120114284 120114284 TCGA-CH-5737 DEL 1 50 * * chr6 66326701 66326701 chr6 66334185 66334185 TCGA-CH-5737 DEL 39 3 * * chr6 71439399 71439399 chr8 5517004 5517004 TCGA-CH-5737 BND 39 40 * * chr6 73995229 73995229 chr6 73999613 73999613 TCGA-CH-5737 DEL 19 15 * * chr6 81915248 81915248 chr6 81924479 81924479 TCGA-CH-5737 DEL 30 46 LINC02542 LINC02542 chr7 53607930 53607930 chr7 53610167 53610167 TCGA-CH-5737 DEL 7 35 * * chr7 6095658 6095658 chr7 6134488 6134488 TCGA-CH-5737 INS 44 40 * USP42 chr8 105450168 105450168 chr8 106173926 106173926 TCGA-CH-5737 INS 50 8 ZFPM2 * chr8 105719613 105719613 chr8 107653067 107653067 TCGA-CH-5737 INS 9 50 ZFPM2 * chr8 107952533 107952533 chr8 108481467 108481467 TCGA-CH-5737 DEL 1 24 RSPO2 EMC2 chr8 119472556 119472556 chr6 64869331 64869331 TCGA-CH-5737 BND 23 36 * EYS chr8 31999588 31999588 chr8 32006719 32006719 TCGA-CH-5737 DEL 39 30 NRG1 NRG1 chr8 33042220 33042220 chr8 33514210 33514210 TCGA-CH-5737 DEL 41 13 AC090204.1 TTI2 chr8 33797090 33797090 chr8 33801288 33801288 TCGA-CH-5737 DEL 17 4 AF279873.3 AF279873.3 chr8 3832801 3832801 chr8 3834629 3834629 TCGA-CH-5737 DEL 15 14 CSMD1 CSMD1 chr9 138001303 138001303 chr9 138001358 138001358 TCGA-CH-5737 INS 37 33 CACNA1B CACNA1B chrX 25340687 25340687 chrX 31309096 31309096 TCGA-CH-5737 DEL 30 25 * DMD chrX 34283379 34283379 chrX 34305752 34305752 TCGA-CH-5737 DEL 12 25 AL592043.1 AL592043.1 chr11 132164294 132164294 chrX 104457320 104457320 TCGA-VP-A87J BND 25 47 NTM * chr11 26995151 26995151 chr5 57351743 57351743 TCGA-VP-A87J BND 11 32 FIBIN * chr11 49368301 49368301 chr11 123908789 123908789 TCGA-VP-A87J DEL 34 39 AC118942.1 OR8D4 chr12 34584220 34584220 chr12 34584389 34584389 TCGA-VP-A87J DEL 11 9 * * chr12 50664631 50664631 chr12 50664760 50664760 TCGA-VP-A87J DEL 15 42 DIP2B DIP2B chr16 59051538 59051538 chr16 64479852 64479852 TCGA-VP-A87J DEL 47 44 AC106793.1 AC092131.1 chr16 71992579 71992579 chr16 72746068 72746068 TCGA-VP-A87J DEL 39 25 PKD1L3 AC004943.2 chr2 214151213 214151213 chr2 214208139 214208139 TCGA-VP-A87J DEL 45 50 SPAG16 SPAG16 chr3 116763060 116763060 chr3 144147998 144147998 TCGA-VP-A87J INS 47 9 LSAMP * chr3 117324336 117324336 chr3 145225038 145225038 TCGA-VP-A87J DEL 49 22 * * chr3 145513148 145513148 chr3 145572532 145572532 TCGA-VP-A87J DEL 20 33 * * chr3 158564113 158564113 chr3 159874643 159874643 TCGA-VP-A87J DEL 50 1 AC106707.1 IQCJ-SCHIP1 chr3 191185323 191185323 chr3 191223036 191223036 TCGA-VP-A87J DEL 22 24 * OSTN chr3 80039285 80039285 chr3 81312464 81312464 TCGA-VP-A87J INS 17 1 * * chr3 81045384 81045384 chr3 81312544 81312544 TCGA-VP-A87J DEL 26 23 LINC02027 * chr4 113064261 113064261 chr4 113073062 113073062 TCGA-VP-A87J DEL 13 21 ANK2 ANK2 chr4 127231573 127231573 chr4 127234883 127234883 TCGA-VP-A87J DEL 21 42 AC093772.1 AC093772.1 chr4 130080672 130080672 chr4 130080954 130080954 TCGA-VP-A87J DEL 17 33 * * chr4 179618524 179618524 chr4 179946866 179946866 TCGA-VP-A87J DEL 50 28 * * chr4 187656874 187656874 chr4 189626267 189626267 TCGA-VP-A87J DEL 45 11 LINC02492 * chr4 23276919 23276919 chr4 23280828 23280828 TCGA-VP-A87J DEL 29 19 AC092440.1 AC092440.1 chr4 24144775 24144775 chr4 63859599 63859599 TCGA-VP-A87J INS 16 4 * * chr4 35061859 35061859 chr4 64412662 64412662 TCGA-VP-A87J DEL 47 42 * * chr4 44495089 44495089 chr4 46404216 46404216 TCGA-VP-A87J DEL 22 8 * GABRA2 chr4 68685834 68685834 chr4 153823584 153823584 TCGA-VP-A87J INS 12 23 * * chr4 91284520 91284520 chr4 92062498 92062498 TCGA-VP-A87J INS 2 35 CCSER1 * chr5 103892994 103892994 chr5 117124258 117124258 TCGA-VP-A87J DEL 27 50 * * chr5 107112879 107112879 chr5 119273332 119273332 TCGA-VP-A87J DEL 2 5 * TNFAIP8 chr5 50992699 50992699 chr5 84405720 84405720 TCGA-VP-A87J DEL 3 31 * EDIL3-DT chr5 50992905 50992905 chr5 83369863 83369863 TCGA-VP-A87J INS 49 43 * * chr5 81283389 81283389 chr5 88534409 88534409 TCGA-VP-A87J INS 6 45 CKMT2-AS1 LINC00461 chr5 88456564 88456564 chr4 33827894 33827894 TCGA-VP-A87J BND 2 38 AC091826.2 AC016687.3 chr6 117411590 117411590 chr6 164135528 164135528 TCGA-VP-A87J DEL 27 28 ROS1 * chr6 117910324 117910324 chr6 165520074 165520074 TCGA-VP-A87J DEL 34 11 SLC35F1 PDE10A chr6 117918586 117918586 chr6 163856340 163856340 TCGA-VP-A87J INS 49 42 SLC35F1 * chr7 10202448 10202448 chr7 10204430 10204430 TCGA-VP-A87J DEL 4 43 * * chr7 82623829 82623832 chr8 112239722 112239725 TCGA-VP-A87J BND 1 42 * CSMD3 chr7 83196451 83196451 chr7 86914394 86914394 TCGA-VP-A87J INS 19 16 * ELAPOR2 chr7 86573964 86573964 chr7 87091099 87091099 TCGA-VP-A87J INS 46 31 * * chr7 86587472 86587472 chr7 113067021 113067021 TCGA-VP-A87J DEL 49 44 * * chr8 112239722 112239725 chr7 82623829 82623832 TCGA-VP-A87J BND 39 22 CSMD3 * chr8 112323987 112323988 chr7 86924906 86924907 TCGA-VP-A87J BND 33 13 CSMD3 ELAPOR2 chr8 112635504 112635504 chr8 134961337 134961337 TCGA-VP-A87J INS 12 30 CSMD3 * chr8 132785301 132785301 chr7 116618668 116618668 TCGA-VP-A87J BND 29 7 PHF20L1 COMETT chr8 137136821 137136821 chr8 137140386 137140386 TCGA-VP-A87J DEL 24 34 * * chr8 48279058 48279058 chr8 51401521 51401521 TCGA-VP-A87J DEL 37 50 * PXDNL chr8 54640687 54640687 chr8 54644304 54644304 TCGA-VP-A87J DEL 7 48 RP1 RP1 chr8 78555257 78555257 chr15 22897381 22897381 TCGA-VP-A87J BND 13 17 PKIA CYFIP1 chr8 78707954 78707954 chr8 80327938 80327938 TCGA-VP-A87J DEL 16 39 ZC2HC1A AC034114.2 chr8 80169094 80169094 chr8 83530668 83530668 TCGA-VP-A87J DEL 50 7 TPD52 * chr8 98544842 98544842 chr8 98546391 98546391 TCGA-VP-A87J DEL 39 38 STK3 STK3 chr9 122569488 122569488 chr9 122569540 122569540 TCGA-VP-A87J INS 24 26 OR1L8 OR1L8 chr9 30345725 30345725 chr9 30347638 30347638 TCGA-VP-A87J DEL 32 50 * * chrX 100200780 100200780 chrX 100282793 100282793 TCGA-VP-A87J DEL 30 49 * * chr10 115246874 115246874 chrX 129536993 129536993 TCGA-EJ-5531 BND 28 10 ATRNL1 * chr10 63234237 63234237 chr10 63234706 63234706 TCGA-EJ-5531 INS 20 19 JMJD1C JMJD1C chr11 98268060 98268060 chr11 98272249 98272249 TCGA-EJ-5531 DEL 11 26 * * chr11 98771561 98771561 chr11 98782143 98782143 TCGA-EJ-5531 DEL 5 2 * * chr13 107208730 107208730 chr13 107302221 107302221 TCGA-EJ-5531 DEL 6 48 FAM155A FAM155A chr13 107581639 107581639 chr13 107876123 107876123 TCGA-EJ-5531 DEL 13 26 FAM155A * chr13 18683609 18683609 chr13 101077511 101077511 TCGA-EJ-5531 INS 26 16 * NALCN chr13 60985880 60985880 chr13 107873556 107873556 TCGA-EJ-5531 INS 21 1 * * chr13 80888159 80888159 chr6 78588491 78588491 TCGA-EJ-5531 BND 32 49 ARF4P4 * chr16 64148124 64148124 chr16 66376912 66376912 TCGA-EJ-5531 DEL 11 16 * CDH5 chr17 43084484 43084484 chr17 43085878 43085878 TCGA-EJ-5531 INS 29 12 BRCA1 BRCA1 chr17 43099551 43099551 chr17 43099998 43099998 TCGA-EJ-5531 INS 4 42 BRCA1 BRCA1 chr17 43125826 43125826 chr17 43126175 43126175 TCGA-EJ-5531 INS 9 21 BRCA1 BRCA1 chr1 101913742 101913742 chr1 101921323 101921323 TCGA-EJ-5531 DEL 21 47 OLFM3 OLFM3 chr1 195155646 195155646 chr1 195156410 195156410 TCGA-EJ-5531 DEL 48 39 * * chr1 236947632 236947632 chr1 239405546 239405546 TCGA-EJ-5531 INS 22 43 * CHRM3 chr1 237261265 237261265 chr1 238427378 238427378 TCGA-EJ-5531 DEL 49 15 RYR2 * chr1 237395095 237395095 chr1 239291876 239291876 TCGA-EJ-5531 DEL 1 33 RYR2 * chr2 143968788 143968788 chr2 147071245 147071245 TCGA-EJ-5531 DEL 37 37 GTDC1 * chr2 144005976 144005976 chr2 146831518 146831518 TCGA-EJ-5531 INS 18 31 GTDC1 * chr2 144929886 144929886 chr2 169172601 169172601 TCGA-EJ-5531 DEL 30 33 TEX41 LRP2 chr2 165799371 165799371 chr2 165823934 165823934 TCGA-EJ-5531 DEL 34 40 AC009495.3 AC009495.1 chr2 33965313 33965313 chr2 33997507 33997507 TCGA-EJ-5531 DEL 13 1 LINC01320 LINC01320 chr3 101163114 101163114 chr3 101205456 101205456 TCGA-EJ-5531 DEL 29 6 ACTR3P3 * chr4 19194706 19194706 chr4 20196234 20196234 TCGA-EJ-5531 DEL 34 27 LINC02438 * chr4 56865892 56865892 chr4 56866740 56866740 TCGA-EJ-5531 DEL 23 42 * * chr4 57867181 57867181 chr4 111518287 111518287 TCGA-EJ-5531 INS 32 29 * * chr5 120821117 120821117 chr5 120831644 120831644 TCGA-EJ-5531 DEL 40 3 * * chr5 28406453 28406453 chr5 28443509 28443509 TCGA-EJ-5531 DEL 36 39 * * chr5 28443466 28443466 chr5 92651283 92651283 TCGA-EJ-5531 DEL 25 37 * AC124854.1 chr5 4146433 4146433 chr5 4174944 4174944 TCGA-EJ-5531 DEL 27 38 * * chr5 4846376 4846376 chr5 19195958 19195958 TCGA-EJ-5531 DEL 26 28 AC106799.2 * chr5 4880262 4880262 chr5 19411215 19411215 TCGA-EJ-5531 INS 11 23 * * chr5 50525287 50525287 chr5 81194996 81194996 TCGA-EJ-5531 DEL 12 28 * RASGRF2 chr5 7802684 7802684 chr5 19173627 19173627 TCGA-EJ-5531 INS 45 49 ADCY2 * chr5 86395868 86395868 chr5 86400458 86400458 TCGA-EJ-5531 DEL 27 36 * * chr5 91949783 91949783 chr5 91970553 91970553 TCGA-EJ-5531 DEL 46 46 * * chr6 103546451 103546451 chr6 103604849 103604849 TCGA-EJ-5531 DEL 37 47 * * chr6 122240526 122240526 chr6 122268715 122268715 TCGA-EJ-5531 DEL 24 37 * * chr6 133833436 133833436 chr6 133833565 133833565 TCGA-EJ-5531 DEL 12 29 TARID TARID chr6 153331112 153331112 chr6 153945707 153945707 TCGA-EJ-5531 DEL 23 37 AL590867.1 * chr6 78536991 78536997 chr13 80663732 80663738 TCGA-EJ-5531 BND 10 28 * * chr6 80113405 80113405 chr6 80114632 80114632 TCGA-EJ-5531 DEL 25 1 BCKDHB BCKDHB chr6 80499110 80499110 chr6 80505957 80505957 TCGA-EJ-5531 DEL 17 13 * * chr6 86186200 86186200 chr6 120272583 120272583 TCGA-EJ-5531 DEL 33 36 * * chr7 13203012 13203012 chr7 13203151 13203151 TCGA-EJ-5531 DEL 28 45 AC011287.1 AC011287.1 chr7 34782678 34782679 chr9 99255452 99255453 TCGA-EJ-5531 BND 17 41 NPSR1 * chr7 35390261 35390261 chr7 35670593 35670593 TCGA-EJ-5531 INS 45 8 * HERPUD2 chr7 35390355 35390356 chr9 99523553 99523554 TCGA-EJ-5531 BND 31 4 * * chr7 35539042 35539046 chr9 101266287 101266291 TCGA-EJ-5531 BND 49 29 * PLPPR1 chr7 35595143 35595143 chr9 99524354 99524354 TCGA-EJ-5531 BND 35 44 * * chr7 35620820 35620820 chr9 101133157 101133157 TCGA-EJ-5531 BND 3 2 * PLPPR1 chr7 35662027 35662027 chr9 99807601 99807601 TCGA-EJ-5531 BND 44 35 HERPUD2 AL359710.1 chr8 111988509 111988509 chr8 111999952 111999952 TCGA-EJ-5531 DEL 21 46 * * chr8 12924022 12924022 chr8 13593538 13593538 TCGA-EJ-5531 DEL 49 1 * DLC1 chr8 15411689 15411689 chr8 15419527 15419527 TCGA-EJ-5531 DEL 37 4 * TUSC3 chr8 31481030 31481030 chr8 78063499 78063499 TCGA-EJ-5531 INS 2 9 * * chr8 31495241 31495241 chr8 76411974 76411974 TCGA-EJ-5531 INS 46 38 * LINC01111 chr8 75529855 75529855 chr8 75537696 75537696 TCGA-EJ-5531 DEL 49 26 HNF4G HNF4G chr8 90027867 90027867 chr8 90027944 90027944 TCGA-EJ-5531 DEL 34 19 DECR1 DECR1 chr9 100967333 100967333 chr9 104607961 104607961 TCGA-EJ-5531 DEL 50 19 * * chr9 101266287 101266291 chr7 35539042 35539046 TCGA-EJ-5531 BND 6 10 PLPPR1 * chr9 102723689 102723689 chr7 35677591 35677591 TCGA-EJ-5531 BND 39 2 * HERPUD2 chr9 104492599 104492599 chr7 35389923 35389923 TCGA-EJ-5531 BND 6 10 * * chr9 99255452 99255453 chr7 34782678 34782679 TCGA-EJ-5531 BND 36 25 * NPSR1 chr9 99382935 99382935 chr9 103401391 103401391 TCGA-EJ-5531 DEL 47 23 * AL390962.1 chr9 99523553 99523554 chr7 35390355 35390356 TCGA-EJ-5531 BND 31 39 * * chr9 99582208 99582208 chr7 35592098 35592098 TCGA-EJ-5531 BND 13 28 * * chr9 99759667 99759667 chr9 101513850 101513850 TCGA-EJ-5531 DEL 45 3 AL359710.1 PGAP4 chrX 34112569 34112569 chrX 34113592 34113592 TCGA-EJ-5531 DEL 14 7 * * chr10 12413514 12413514 chr12 128261932 128261932 TCGA-KK-A8IB BND 24 42 CAMK1D * chr10 87890650 87890650 chr10 89217367 89217367 TCGA-KK-A8IB DEL 36 25 PTEN LIPA chr11 113859052 113859052 chr11 115012705 115012705 TCGA-KK-A8IB DEL 33 1 USP28 * chr11 118223385 118223385 chr11 118254993 118254993 TCGA-KK-A8IB DEL 9 29 JAML MPZL2 chr11 70800668 70800668 chr19 10244890 10244890 TCGA-KK-A8IB BND 7 46 SHANK2 * chr12 33021032 33021032 chr12 33065942 33065942 TCGA-KK-A8IB DEL 30 31 * * chr12 44581422 44581422 chr12 44608157 44608157 TCGA-KK-A8IB INV 7 36 NELL2 NELL2 chr13 21249984 21249984 chr13 27030862 27030862 TCGA-KK-A8IB INV 34 5 * * chr13 21712303 21712303 chr13 32390013 32390013 TCGA-KK-A8IB DEL 36 18 * BRCA2 chr13 21919628 21919628 chr13 32380943 32380943 TCGA-KK-A8IB DUP 17 48 * BRCA2 chr13 21921291 21921291 chr13 32396642 32396642 TCGA-KK-A8IB DEL 42 11 * BRCA2 chr13 21922311 21922311 chr13 32391070 32391070 TCGA-KK-A8IB DUP 22 44 * BRCA2 chr13 21922478 21922478 chr13 27051280 27051280 TCGA-KK-A8IB DUP 1 42 * * chr13 21922642 21922642 chr13 32376639 32376639 TCGA-KK-A8IB INV 3 42 * BRCA2 chr13 27013870 27013870 chr13 32368406 32368406 TCGA-KK-A8IB INV 37 16 * BRCA2 chr13 27893289 27893289 chr13 32380612 32380612 TCGA-KK-A8IB INV 18 22 PLUT BRCA2 chr13 30162588 30162588 chr13 36087196 36087196 TCGA-KK-A8IB DUP 44 36 * DCLK1 chr13 32381074 32381074 chr13 32399158 32399158 TCGA-KK-A8IB INV 21 11 BRCA2 BRCA2 chr13 32386745 32386745 chr13 32434149 32434149 TCGA-KK-A8IB DEL 3 11 BRCA2 N4BP2L2 chr13 32387387 32387387 chr13 32389690 32389690 TCGA-KK-A8IB INV 12 37 BRCA2 BRCA2 chr13 32399858 32399858 chr13 36094682 36094682 TCGA-KK-A8IB DUP 16 9 BRCA2 DCLK1 chr13 32811945 32811945 chr13 36102710 36102710 TCGA-KK-A8IB INV 21 46 * DCLK1 chr13 32812196 32812196 chr13 32873404 32873404 TCGA-KK-A8IB DEL 13 26 * * chr13 37497807 37497807 chr13 37511439 37511439 TCGA-KK-A8IB DEL 34 35 * * chr13 38029593 38029593 chr13 38752267 38752267 TCGA-KK-A8IB INV 43 33 LINC02334 FREM2 chr13 38681204 38681204 chr13 41625644 41625644 TCGA-KK-A8IB INV 32 32 * VWA8 chr13 38746493 38746493 chr13 39374512 39374512 TCGA-KK-A8IB DEL 28 16 FREM2 LHFPL6 chr13 38752024 38752024 chr13 41528252 41528252 TCGA-KK-A8IB INV 42 46 FREM2 * chr13 41580375 41580375 chr13 41625172 41625172 TCGA-KK-A8IB INV 25 40 VWA8 VWA8 chr13 48304769 48304769 chr13 49283298 49283298 TCGA-KK-A8IB DEL 27 32 RB1 CDADC1 chr14 20639844 20639844 chr14 20657701 20657701 TCGA-KK-A8IB DEL 8 41 * * chr14 24166159 24166159 chr17 7675711 7675711 TCGA-KK-A8IB BND 37 25 AL136295.5 TP53 chr14 24166489 24166489 chr17 7675639 7675639 TCGA-KK-A8IB BND 30 27 AL136295.5 TP53 chr15 20534188 20534188 chr15 23130176 23130176 TCGA-KK-A8IB DUP 31 15 GOLGA6L6 GOLGA6L1 chr15 20535183 20535193 chr15 23129399 23129399 TCGA-KK-A8IB DEL 9 36 GOLGA6L6 GOLGA6L1 chr15 23129399 23129399 chr15 28560052 28560052 TCGA-KK-A8IB INV 42 41 GOLGA6L1 AC138749.1 chr15 23130176 23130176 chr15 28561450 28561459 TCGA-KK-A8IB INV 30 19 GOLGA6L1 * chr16 19045 19045 chrX 156020888 156020888 TCGA-KK-A8IB BND 34 21 WASH4P AJ271736.1 chr16 31960841 31960841 chr16 33950839 33950839 TCGA-KK-A8IB DEL 38 35 AC034105.1 IGHV3OR16-16 chr16 48544014 48544014 chr16 51692413 51692413 TCGA-KK-A8IB INV 45 6 N4BP1 * chr17 1418934 1418934 chr22 25439867 25439867 TCGA-KK-A8IB BND 9 17 * * chr17 1420316 1420316 chr22 25438571 25438571 TCGA-KK-A8IB BND 50 32 * IGLVIVOR22-1 chr17 7683837 7683837 chr12 114670097 114670097 TCGA-KK-A8IB BND 46 14 TP53 * chr17 82631267 82631267 chr17 82631600 82631600 TCGA-KK-A8IB INS 22 24 FOXK2 FOXK2 chr19 1501349 1501349 chr19 44679860 44679860 TCGA-KK-A8IB INV 46 16 * AC243964.3 chr19 29265858 29265858 chr19 29267912 29267912 TCGA-KK-A8IB INV 3 6 * * chr19 42060494 42060494 chr19 44713581 44713581 TCGA-KK-A8IB DUP 10 4 GRIK5 AC243964.3 chr1 21405268 21405268 chr1 22169429 22169429 TCGA-KK-A8IB DUP 40 22 * * chr1 47481478 47481478 chr1 48997496 48997496 TCGA-KK-A8IB INS 10 6 * AGBL4 chr20 24335106 24335106 chr20 57032112 57032112 TCGA-KK-A8IB INV 48 7 * * chr20 36396348 36396348 chr20 58688595 58688595 TCGA-KK-A8IB INV 5 44 DLGAP4 NPEPL1 chr21 38452361 38452361 chr21 41496711 41496711 TCGA-KK-A8IB DEL 22 47 ERG TMPRSS2 chr21 38508211 38508211 chr21 41475973 41475973 TCGA-KK-A8IB DEL 35 14 ERG TMPRSS2 chr2 125361466 125361466 chr2 127266911 127266911 TCGA-KK-A8IB DEL 27 44 * ERCC3 chr2 152750200 152750200 chr2 152887542 152887542 TCGA-KK-A8IB DEL 19 19 ARL6IP6 * chr2 161957316 161957316 chr2 162130585 162130585 TCGA-KK-A8IB DEL 37 42 SLC4A10 * chr2 180895623 180895623 chr14 37574528 37574528 TCGA-KK-A8IB BND 30 15 SCHLAP1 AL121790.1 chr2 183654861 183654861 chr2 185653745 185653745 TCGA-KK-A8IB INS 1 48 * * chr2 65000029 65000029 chr2 83589649 83589649 TCGA-KK-A8IB DEL 22 23 SLC1A4 * chr2 6868211 6868211 chr2 195727001 195727001 TCGA-KK-A8IB INV 19 5 RSAD2 SLC39A10 chr2 80450210 80450210 chr2 140416290 140416290 TCGA-KK-A8IB INS 22 37 CTNNA2 LRP1B chr3 107420451 107420451 chr3 165258993 165258993 TCGA-KK-A8IB DEL 3 43 AC063944.1 LINC01322 chr3 108796436 108796436 chr3 110624980 110624980 TCGA-KK-A8IB INS 28 42 * * chr3 110275034 110275034 chr3 110280556 110280556 TCGA-KK-A8IB DEL 11 27 * * chr3 118524994 118524994 chr3 119624610 119624610 TCGA-KK-A8IB INS 19 22 AC068633.1 PLA1A chr3 123552434 123552434 chr3 151926981 151926981 TCGA-KK-A8IB DEL 45 37 HACD2 AADACL2-AS1 chr3 21363218 21363218 chr3 80701882 80701882 TCGA-KK-A8IB DEL 34 1 * * chr3 71663720 71663720 chr3 84415707 84415707 TCGA-KK-A8IB DEL 28 41 AC097634.4 * chr3 86802638 86802638 chr3 103490866 103490866 TCGA-KK-A8IB INV 44 29 * * chr4 107086750 107086750 chr17 8067828 8067828 TCGA-KK-A8IB BND 32 14 DKK2 ALOXE3P1 chr4 115159156 115159156 chr4 116895246 116895246 TCGA-KK-A8IB DEL 15 49 * * chr5 101601443 101601443 chr5 138251771 138251771 TCGA-KK-A8IB DUP 21 50 * * chr5 101716619 101716619 chr5 105017565 105017565 TCGA-KK-A8IB DUP 16 24 * AC099520.1 chr5 101717504 101717504 chr5 104991811 104991811 TCGA-KK-A8IB DEL 27 34 * AC099520.1 chr5 101781960 101781960 chr5 138277157 138277157 TCGA-KK-A8IB INV 41 44 * * chr5 102049453 102049453 chr5 102833284 102833284 TCGA-KK-A8IB DEL 45 11 * PAM chr5 102058588 102058588 chr5 102501897 102501897 TCGA-KK-A8IB INV 44 33 * AC094108.1 chr5 102072303 102072303 chr5 137845588 137845588 TCGA-KK-A8IB INV 27 5 * AC106791.1 chr5 103333406 103333406 chr5 104129085 104129085 TCGA-KK-A8IB INV 44 18 * * chr5 103406012 103406012 chr5 135757274 135757274 TCGA-KK-A8IB INV 34 27 * SLC25A48 chr5 103935628 103935628 chr5 133876349 133876349 TCGA-KK-A8IB INV 13 35 * * chr5 104106423 104106423 chr5 104998020 104998020 TCGA-KK-A8IB INV 37 35 * AC099520.1 chr5 104308927 104308927 chr5 104525914 104525914 TCGA-KK-A8IB DEL 41 19 * AC099520.1 chr5 104463978 104463978 chr14 20729343 20729343 TCGA-KK-A8IB BND 30 14 AC099520.1 * chr5 104864871 104864871 chr5 132996700 132996700 TCGA-KK-A8IB DUP 23 44 AC099520.1 * chr5 105196229 105196229 chr5 138707228 138707228 TCGA-KK-A8IB INV 37 4 AC099520.1 CTNNA1 chr5 105403899 105403899 chr5 138118518 138118518 TCGA-KK-A8IB INV 15 44 * NME5 chr5 114963002 114963002 chr14 20737471 20737471 TCGA-KK-A8IB BND 6 31 * * chr5 124307757 124307757 chr12 26505142 26505142 TCGA-KK-A8IB BND 16 30 LINC01170 ITPR2 chr5 133213629 133213629 chr14 20655737 20655737 TCGA-KK-A8IB BND 41 23 AC010307.2 * chr5 133229185 133229185 chr14 20713338 20713338 TCGA-KK-A8IB BND 23 25 FSTL4 * chr5 133234232 133234232 chr5 135777495 135777495 TCGA-KK-A8IB INV 20 9 FSTL4 SLC25A48 chr5 136376663 136376663 chr5 138161906 138161906 TCGA-KK-A8IB INV 49 42 AC063980.1 BRD8 chr5 155391654 155391654 chr17 1482388 1482388 TCGA-KK-A8IB BND 28 10 * MYO1C chr5 173117812 173117812 chr2 239175315 239175315 TCGA-KK-A8IB BND 34 28 CREBRF HDAC4 chr5 179885319 179885319 chr5 179886465 179886465 TCGA-KK-A8IB INV 12 43 TBC1D9B TBC1D9B chr5 58695471 58695471 chr5 59118187 59118187 TCGA-KK-A8IB DUP 42 42 RAB3C PDE4D chr5 60075610 60075610 chr5 60104091 60104091 TCGA-KK-A8IB DEL 24 12 PDE4D PDE4D chr5 92153953 92153953 chr5 94959801 94959801 TCGA-KK-A8IB DEL 43 6 AC114316.1 MCTP1 chr6 153624876 153624876 chr6 153625407 153625407 TCGA-KK-A8IB DEL 34 1 * * chr6 16441530 16441530 chr13 44002905 44002905 TCGA-KK-A8IB BND 13 28 ATXN1 AL512506.3 chr6 167169810 167169810 chr6 167386947 167386947 TCGA-KK-A8IB INV 34 37 TCP10L2 * chr6 16726590 16726590 chr13 43220089 43220089 TCGA-KK-A8IB BND 9 11 ATXN1 ENOX1 chr6 20798790 20798790 chr7 149969297 149969297 TCGA-KK-A8IB BND 45 7 CDKAL1 * chr6 32482938 32482982 chr6 32590581 32590598 TCGA-KK-A8IB DUP 26 30 * HLA-DRB1 chr7 140348804 140348804 chr7 151077340 151077340 TCGA-KK-A8IB INV 30 12 SLC37A3 FASTK chr7 141191931 141191931 chr7 151277036 151277036 TCGA-KK-A8IB DUP 25 1 TMEM178B SMARCD3 chr7 142160927 142160927 chr7 145709730 145709730 TCGA-KK-A8IB DEL 36 39 MGAM2 * chr7 143269913 143269913 chr7 143270119 143270119 TCGA-KK-A8IB INV 41 38 GSTK1 GSTK1 chr7 143355878 143355878 chr7 151025411 151025411 TCGA-KK-A8IB INV 13 17 FAM131B ATG9B chr7 143567200 143567200 chr7 151045333 151045333 TCGA-KK-A8IB DUP 27 33 * ABCB8 chr7 145759290 145759290 chr7 145877337 145877337 TCGA-KK-A8IB INV 15 20 * * chr7 145766103 145766103 chr7 146723479 146723479 TCGA-KK-A8IB DUP 21 3 * CNTNAP2 chr7 145770976 145770976 chr13 40562574 40562574 TCGA-KK-A8IB BND 37 37 * FOXO1 chr7 147697974 147697974 chr7 153242414 153242414 TCGA-KK-A8IB DUP 50 38 CNTNAP2 * chr7 148116534 148116534 chr7 149188739 149188739 TCGA-KK-A8IB DUP 49 44 CNTNAP2 * chr7 148116777 148116777 chr7 151306993 151306993 TCGA-KK-A8IB DEL 40 20 CNTNAP2 * chr7 148800291 148800291 chr7 149188616 149188616 TCGA-KK-A8IB DEL 13 46 CUL1 * chr7 149020857 149020857 chr7 149164867 149164867 TCGA-KK-A8IB DUP 9 17 PDIA4 ZNF398 chr7 149209472 149209472 chr7 158660918 158660918 TCGA-KK-A8IB INV 29 28 ZNF282 NCAPG2 chr7 149982944 149982944 chr7 151106146 151106146 TCGA-KK-A8IB INV 9 9 * AGAP3 chr7 152716213 152716213 chr7 153826493 153826493 TCGA-KK-A8IB DUP 30 44 * * chr7 157201270 157201270 chr13 42175292 42175292 TCGA-KK-A8IB BND 48 7 UBE3C DGKH chr7 158243057 158243057 chr7 158498793 158498793 TCGA-KK-A8IB DEL 5 26 PTPRN2 PTPRN2 chr7 158452438 158452438 chr13 42064522 42064522 TCGA-KK-A8IB BND 10 34 PTPRN2 DGKH chr7 48901466 48901466 chr7 49535577 49535577 TCGA-KK-A8IB DEL 5 15 * * chr7 49440811 49440811 chr7 139067414 139067414 TCGA-KK-A8IB INV 35 24 * ZC3HAV1 chr7 66477071 66477071 chr7 66589389 66589389 TCGA-KK-A8IB DUP 12 12 LINC00174 AC006001.3 chr8 105169182 105169182 chr8 105169496 105169511 TCGA-KK-A8IB DEL 27 26 ZFPM2 ZFPM2 chr8 130875421 130875421 chr8 130875715 130875715 TCGA-KK-A8IB INV 26 24 ADCY8 ADCY8 chr8 77500255 77500255 chr8 77511280 77511280 TCGA-KK-A8IB DEL 31 31 AC062004.1 AC062004.1 chr9 105041678 105041678 chr9 105041792 105041792 TCGA-KK-A8IB DEL 3 24 * * chr9 14143169 14143169 chr13 41528599 41528599 TCGA-KK-A8IB BND 18 42 NFIB * chr9 9132188 9132188 chr9 9260352 9260352 TCGA-KK-A8IB DEL 15 41 PTPRD PTPRD chrX 109712912 109712912 chr12 39258914 39258914 TCGA-KK-A8IB BND 23 11 ACSL4 * chrX 17761828 17761828 chrX 69797701 69797701 TCGA-KK-A8IB DUP 28 42 * EDA chrX 17805062 17805062 chrX 18040557 18040557 TCGA-KK-A8IB DUP 46 2 RAI2 LINC01456 chrX 17931592 17931592 chrX 21383729 21383729 TCGA-KK-A8IB DEL 4 44 * CNKSR2 chrX 18178535 18178535 chrX 55760143 55760143 TCGA-KK-A8IB DEL 8 12 BEND2 * chrX 18830073 18830073 chrX 18830498 18830498 TCGA-KK-A8IB INV 30 24 * * chrX 19023093 19023093 chrX 56538579 56538579 TCGA-KK-A8IB DEL 6 11 ADGRG2 * chrX 19044258 19044258 chrX 19044593 19044593 TCGA-KK-A8IB INV 30 24 ADGRG2 ADGRG2 chrX 20223732 20223732 chrX 20223843 20223843 TCGA-KK-A8IB INV 48 10 RPS6KA3 RPS6KA3 chrX 20253805 20253805 chrX 20253924 20253924 TCGA-KK-A8IB INV 37 3 RPS6KA3 RPS6KA3 chrX 20379534 20379534 chrX 20379702 20379702 TCGA-KK-A8IB INV 40 7 * * chrX 20773977 20773977 chrX 65828557 65828557 TCGA-KK-A8IB DEL 4 37 AL807742.1 * chrX 21534652 21534652 chrX 64723072 64723072 TCGA-KK-A8IB DEL 33 35 CNKSR2 * chrX 21773752 21773752 chrX 65742568 65742568 TCGA-KK-A8IB INV 45 5 * * chrX 23421508 23421508 chrX 64722334 64722334 TCGA-KK-A8IB DUP 33 19 * * chrX 24264136 24264136 chrX 24264355 24264355 TCGA-KK-A8IB INV 37 10 * * chrX 24554536 24554536 chrX 65543989 65543989 TCGA-KK-A8IB DEL 47 31 * * chrX 56537516 56537516 chrX 56725212 56725212 TCGA-KK-A8IB DEL 22 14 * * chrX 56742049 56742049 chrX 68839431 68839431 TCGA-KK-A8IB INV 47 13 NBDY EFNB1 chrX 62570199 62570199 chrX 69745498 69745498 TCGA-KK-A8IB INV 37 10 * EDA chrX 63832394 63832394 chrX 63832548 63832548 TCGA-KK-A8IB INV 21 32 * * chrX 63837713 63837713 chrX 63838014 63838014 TCGA-KK-A8IB INV 10 37 * * chrX 64260926 64260926 chrX 64261066 64261066 TCGA-KK-A8IB INV 14 25 * * chrX 65027602 65027602 chrX 68624072 68624072 TCGA-KK-A8IB DUP 6 8 ZC4H2 * chrX 65446202 65446202 chrX 65446412 65446412 TCGA-KK-A8IB INV 48 46 ZC3H12B ZC3H12B chrX 65825967 65825967 chrX 69239035 69239035 TCGA-KK-A8IB DEL 32 12 * * chrX 67080269 67080269 chrX 67080314 67080314 TCGA-KK-A8IB INV 1 40 * * chrX 69185630 69185630 chrX 69185851 69185851 TCGA-KK-A8IB INV 30 8 LINC00269 LINC00269 chrX 69319296 69319296 chrX 69319448 69319448 TCGA-KK-A8IB INV 48 25 * * chr10 48525369 48525369 chr8 42387045 42387045 TCGA-CH-5788 BND 35 6 ARHGAP22 * chr10 59217682 59217682 chr10 89600102 89600102 TCGA-CH-5788 DEL 30 14 PHYHIPL PANK1 chr10 75237292 75237292 chr8 42392034 42392034 TCGA-CH-5788 BND 39 35 COMTD1 VDAC3 chr10 92442764 92442764 chr8 42384876 42384882 TCGA-CH-5788 BND 46 11 * * chr15 74124785 74124785 chr15 74159315 74159315 TCGA-CH-5788 DEL 27 41 ISLR2 AC010931.2 chr21 38476855 38476855 chr8 42384876 42384882 TCGA-CH-5788 BND 43 17 ERG * chr2 16507415 16507425 chr3 183399921 183399921 TCGA-CH-5788 BND 34 10 * MCF2L2 chr3 115960754 115960754 chr3 115978516 115978516 TCGA-CH-5788 DEL 45 7 LSAMP LSAMP chr3 141192878 141192878 chr3 183395493 183395493 TCGA-CH-5788 INS 3 27 * MCF2L2 chr3 152066533 152066533 chr2 16507415 16507425 TCGA-CH-5788 BND 36 42 * * chr6 10408804 10408804 chr3 52153303 52153303 TCGA-CH-5788 BND 18 45 TFAP2A POC1A chr8 38174647 38174647 chr21 41499680 41499680 TCGA-CH-5788 BND 43 28 LSM1 TMPRSS2 chr8 42383909 42383909 chr10 92436296 92436296 TCGA-CH-5788 BND 28 40 * * chr8 42384876 42384882 chr21 38476855 38476855 TCGA-CH-5788 BND 24 16 * ERG chr8 42410175 42410175 chr10 48525529 48525529 TCGA-CH-5788 BND 47 29 * ARHGAP22 chrX 152242031 152242031 chr18 15095249 15095249 TCGA-CH-5788 BND 26 22 GABRA3 AP005242.1 chr11 104358181 104358181 chr11 105783967 105783967 TCGA-J4-A6G3 DEL 14 37 * GRIA4 chr11 16252837 16252837 chr11 16295250 16295250 TCGA-J4-A6G3 DEL 29 27 SOX6 SOX6 chr11 18920419 18920419 chr11 18964827 18964827 TCGA-J4-A6G3 DUP 10 39 * * chr11 22279157 22279157 chr11 23144070 23144070 TCGA-J4-A6G3 INV 6 20 ANO5 * chr11 30026591 30026591 chr11 30813757 30813757 TCGA-J4-A6G3 DEL 25 17 * * chr11 36054823 36054823 chr20 37450241 37450241 TCGA-J4-A6G3 BND 41 22 LDLRAD3 * chr11 36126985 36126985 chr11 102017795 102017795 TCGA-J4-A6G3 INV 36 24 LDLRAD3 * chr11 36496508 36496508 chr11 106896579 106896579 TCGA-J4-A6G3 INV 38 17 TRAF6 GUCY1A2 chr11 78641407 78641407 chr11 78641602 78641602 TCGA-J4-A6G3 DEL 37 1 * * chr11 80635310 80635310 chr11 80901558 80901558 TCGA-J4-A6G3 DEL 18 43 * * chr12 100189637 100189637 chr12 101327787 101327787 TCGA-J4-A6G3 DUP 37 5 MIR1827 UTP20 chr12 12676775 12676775 chr12 12793256 12793256 TCGA-J4-A6G3 DEL 21 36 GPR19 APOLD1 chr12 132876997 132876997 chr12 132934093 132934093 TCGA-J4-A6G3 DUP 2 3 CHFR CHFR chr12 60485295 60485295 chr12 61271764 61271764 TCGA-J4-A6G3 DEL 25 49 * * chr12 9478695 9478695 chr12 9583161 9583161 TCGA-J4-A6G3 INV 11 48 AC092821.3 AC092821.3 chr13 38160492 38160492 chr13 81117740 81117740 TCGA-J4-A6G3 DEL 48 6 * * chr14 105568756 105568757 chr14 105688969 105688969 TCGA-J4-A6G3 INV 34 2 * * chr14 37782022 37782022 chr14 38794531 38794531 TCGA-J4-A6G3 DUP 39 14 TTC6 LINC00639 chr14 54795618 54795618 chr2 25776568 25776568 TCGA-J4-A6G3 BND 34 41 * ASXL2 chr16 13850479 13850479 chr16 13850583 13850583 TCGA-J4-A6G3 DEL 31 9 * * chr16 55736856 55736856 chr16 55816034 55816034 TCGA-J4-A6G3 DEL 23 7 CES1P2 CES1 chr16 62311602 62311602 chr16 62341095 62341095 TCGA-J4-A6G3 INV 12 10 * AC009161.2 chr16 72582893 72582893 chr16 72700900 72700900 TCGA-J4-A6G3 DUP 38 49 LINC01572 AC004943.2 chr17 43544748 43544748 chr17 59668239 59668239 TCGA-J4-A6G3 DEL 28 2 DHX8 CLTC chr17 45584874 45584874 chr17 64919427 64919427 TCGA-J4-A6G3 DEL 28 26 DND1P1 LRRC37A3 chr17 56792298 56792298 chr17 66799304 66799304 TCGA-J4-A6G3 DUP 35 17 C17orf67 PRKCA chr17 56792730 56792746 chr17 66798870 66798909 TCGA-J4-A6G3 DUP 31 45 C17orf67 PRKCA chr17 56792730 56792746 chr17 66799365 66799383 TCGA-J4-A6G3 DUP 13 36 C17orf67 PRKCA chr17 56793274 56793274 chr17 66798870 66798909 TCGA-J4-A6G3 INV 28 50 C17orf67 PRKCA chr17 72545776 72545776 chr10 87869800 87869800 TCGA-J4-A6G3 BND 43 46 LINC00511 PTEN chr17 7684767 7684767 chr3 48574901 48574901 TCGA-J4-A6G3 BND 28 40 TP53 COL7A1 chr18 5193227 5193227 chr18 5874988 5874988 TCGA-J4-A6G3 DEL 32 7 AKAIN1 MIR3976HG chr18 77252862 77252862 chr21 43337054 43337054 TCGA-J4-A6G3 BND 49 29 GALR1 * chr19 10758245 10758245 chr19 54181757 54181757 TCGA-J4-A6G3 INV 4 5 DNM2 MBOAT7 chr19 48669513 48669513 chr21 46090943 46090943 TCGA-J4-A6G3 BND 13 48 SEC1P * chr1 120318216 120318216 chr1 148930605 148930605 TCGA-J4-A6G3 DEL 50 34 AC244669.2 PDE4DIP chr1 121624031 121624031 chr1 121737248 121737248 TCGA-J4-A6G3 DUP 20 8 * * chr1 169241740 169241740 chr1 169274646 169274646 TCGA-J4-A6G3 INV 34 41 NME7 NME7 chr1 191329471 191329471 chr1 248322238 248322238 TCGA-J4-A6G3 INV 25 50 * * chr1 191926298 191926298 chr1 248345331 248345331 TCGA-J4-A6G3 DEL 40 25 LINC02770 * chr1 191930195 191930195 chr1 191931652 191931652 TCGA-J4-A6G3 INV 42 33 LINC02770 LINC02770 chr1 205669726 205669726 chr21 38499298 38499298 TCGA-J4-A6G3 BND 27 20 SLC45A3 ERG chr1 72299316 72299316 chr1 72375311 72375311 TCGA-J4-A6G3 INV 17 49 * * chr1 72300317 72300317 chr1 72403263 72403263 TCGA-J4-A6G3 INV 36 27 RPL31P12 * chr20 15334663 15334663 chr20 15440428 15440428 TCGA-J4-A6G3 DEL 41 28 MACROD2 MACROD2 chr20 15617742 15617742 chr20 15843047 15843047 TCGA-J4-A6G3 DEL 44 46 MACROD2 MACROD2 chr21 31784744 31784750 chr21 41806400 41806400 TCGA-J4-A6G3 DUP 26 39 * PRDM15 chr21 38471127 38471127 chr21 41499400 41499400 TCGA-J4-A6G3 DEL 6 39 ERG TMPRSS2 chr2 114173532 114173532 chr2 210710540 210710540 TCGA-J4-A6G3 INV 20 6 * * chr2 114352921 114352921 chr2 210697601 210697601 TCGA-J4-A6G3 DUP 49 10 * * chr2 115998937 115998937 chr2 211553224 211553224 TCGA-J4-A6G3 INV 42 5 * ERBB4 chr2 126737147 126737147 chr2 134979813 134979813 TCGA-J4-A6G3 DEL 30 31 * MAP3K19 chr2 131219430 131219430 chr2 133512598 133512598 TCGA-J4-A6G3 INV 12 22 PLEKHB2 NCKAP5 chr2 133463464 133463464 chr2 189441109 189441109 TCGA-J4-A6G3 DEL 22 34 NCKAP5 WDR75 chr2 133636371 133636371 chr11 23793096 23793096 TCGA-J4-A6G3 BND 13 20 * LINC02726 chr2 133924313 133924313 chr2 133999705 133999705 TCGA-J4-A6G3 DEL 44 45 * * chr2 133965027 133965027 chr2 189872329 189872329 TCGA-J4-A6G3 DEL 10 45 * PMS1 chr2 134011039 134011039 chr2 211273753 211273753 TCGA-J4-A6G3 DEL 40 19 * * chr2 134057038 134057038 chr2 190154860 190154860 TCGA-J4-A6G3 INV 2 48 * C2orf88 chr2 134265987 134265987 chr2 211500519 211500519 TCGA-J4-A6G3 INV 45 13 MGAT5 ERBB4 chr2 134587206 134587206 chr2 147944191 147944191 TCGA-J4-A6G3 INV 6 20 TMEM163 ORC4 chr2 134623625 134623625 chr2 136219894 136219894 TCGA-J4-A6G3 INV 9 4 TMEM163 * chr2 134630194 134630194 chr11 22323091 22323091 TCGA-J4-A6G3 BND 37 39 TMEM163 AC104009.1 chr2 135117473 135117473 chr6 64295504 64295504 TCGA-J4-A6G3 BND 17 17 RAB3GAP1 EYS chr2 135730085 135730085 chr2 137994244 137994244 TCGA-J4-A6G3 INV 38 3 * HNMT chr2 135824743 135824743 chr2 136287558 136287558 TCGA-J4-A6G3 DEL 4 11 LCT * chr2 137997277 137997277 chr2 189838597 189838597 TCGA-J4-A6G3 INV 36 32 HNMT PMS1 chr2 139515585 139515585 chr2 142994775 142994775 TCGA-J4-A6G3 DEL 44 31 * KYNU chr2 153381093 153381093 chr2 154121658 154121658 TCGA-J4-A6G3 DEL 47 18 * GALNT13 chr2 154564773 154564773 chr2 162872475 162872475 TCGA-J4-A6G3 INV 18 12 * * chr2 184942465 184942465 chr2 186291664 186291664 TCGA-J4-A6G3 DEL 7 36 * * chr2 185661352 185661352 chr2 185894272 185894272 TCGA-J4-A6G3 DEL 1 20 U8 * chr2 185671073 185671073 chr2 186053781 186053781 TCGA-J4-A6G3 DUP 45 44 * LINC01473 chr2 185891330 185891330 chr2 186755974 186755974 TCGA-J4-A6G3 DEL 14 3 * FAM171B chr2 198280356 198280356 chr2 199639061 199639061 TCGA-J4-A6G3 INV 22 29 PLCL1 LINC01877 chr2 211250623 211250623 chr11 23769740 23769740 TCGA-J4-A6G3 BND 10 2 * LINC02726 chr2 232760410 232760410 chr18 57583152 57583152 TCGA-J4-A6G3 BND 45 34 GIGYF2 FECH chr2 238870151 238870151 chr9 89371903 89371904 TCGA-J4-A6G3 BND 49 49 TWIST2 SEMA4D chr2 33293881 33293881 chr2 34294975 34294975 TCGA-J4-A6G3 DEL 15 9 LTBP1 LINC01320 chr2 34612281 34612281 chr2 37003713 37003713 TCGA-J4-A6G3 DUP 47 12 LINC01320 HEATR5B chr2 37010720 37010720 chr2 122865668 122865668 TCGA-J4-A6G3 INV 49 45 HEATR5B * chr2 52682907 52682907 chr2 126880405 126880405 TCGA-J4-A6G3 INV 33 49 * * chr2 56291198 56291198 chr2 56299616 56299616 TCGA-J4-A6G3 DEL 22 19 AC007744.1 AC007744.1 chr2 80039273 80039273 chr2 84585040 84585040 TCGA-J4-A6G3 DEL 41 19 CTNNA2 DNAH6 chr3 102466168 102466168 chr3 110901192 110901192 TCGA-J4-A6G3 DEL 15 11 ZPLD1 NECTIN3-AS1 chr3 102471876 102471876 chr3 108983167 108983167 TCGA-J4-A6G3 INV 13 27 ZPLD1 MORC1 chr3 103692674 103692674 chr3 108955615 108955615 TCGA-J4-A6G3 INV 6 31 * * chr3 103710507 103710507 chr3 110874738 110874738 TCGA-J4-A6G3 DUP 41 30 * * chr3 108724852 108724852 chr3 111264486 111264486 TCGA-J4-A6G3 DEL 13 8 * NECTIN3 chr3 113345509 113345509 chr3 116310678 116310678 TCGA-J4-A6G3 DEL 28 35 CFAP44 LSAMP chr3 113849774 113849774 chr3 113939798 113939798 TCGA-J4-A6G3 DEL 11 19 GRAMD1C GRAMD1C chr3 148828016 148828016 chr3 149498953 149498953 TCGA-J4-A6G3 DEL 4 42 CPB1 TM4SF4 chr3 165237919 165237919 chr3 166168009 166168009 TCGA-J4-A6G3 INV 22 25 LINC01322 * chr3 17523585 17523585 chr3 20268573 20268573 TCGA-J4-A6G3 DEL 20 32 TBC1D5 SGO1-AS1 chr3 191359643 191359643 chr3 191709939 191709939 TCGA-J4-A6G3 INV 15 23 CCDC50 * chr3 37527720 37527720 chr3 81002769 81002769 TCGA-J4-A6G3 DEL 23 37 ITGA9 LINC02027 chr3 78067127 78067127 chr3 79693238 79693238 TCGA-J4-A6G3 INV 12 18 * ROBO1 chr3 78067957 78067957 chr3 81650818 81650818 TCGA-J4-A6G3 INV 36 43 * GBE1 chr3 79693661 79693661 chr5 44106872 44106872 TCGA-J4-A6G3 BND 15 5 ROBO1 * chr3 80510542 80510542 chr3 81646981 81646981 TCGA-J4-A6G3 INV 31 29 * GBE1 chr3 80512150 80512150 chr5 44109776 44109776 TCGA-J4-A6G3 BND 45 15 * * chr3 85959337 85959337 chr3 88645743 88645743 TCGA-J4-A6G3 DEL 24 44 CADM2 * chr4 127269965 127269965 chr4 127358211 127358211 TCGA-J4-A6G3 DEL 39 49 AC093772.1 AC093772.1 chr4 127641547 127641547 chr4 153843860 153843860 TCGA-J4-A6G3 INV 27 31 INTU * chr4 128171283 128171283 chr4 157722866 157722866 TCGA-J4-A6G3 INV 45 44 LARP1B * chr4 128171725 128171725 chr4 153398084 153398084 TCGA-J4-A6G3 DEL 45 14 LARP1B MND1 chr4 128197676 128197676 chr4 129142388 129142388 TCGA-J4-A6G3 INV 32 18 LARP1B * chr4 128616691 128616691 chr4 156490368 156490368 TCGA-J4-A6G3 DUP 17 30 * * chr4 129169720 129169720 chr4 157807057 157807057 TCGA-J4-A6G3 INV 37 50 * * chr4 129282339 129282339 chr4 156114665 156114665 TCGA-J4-A6G3 INV 49 1 * * chr4 129358302 129358302 chr4 156593890 156593890 TCGA-J4-A6G3 DUP 8 8 * * chr4 129430670 129430670 chr4 153369637 153369637 TCGA-J4-A6G3 INV 33 31 * MND1 chr4 129634609 129634609 chr4 157504442 157504442 TCGA-J4-A6G3 DUP 46 35 * * chr4 129955736 129955736 chr4 157071393 157071393 TCGA-J4-A6G3 DEL 6 3 * * chr4 129976483 129976483 chr4 154879709 154879709 TCGA-J4-A6G3 DUP 22 16 * * chr4 129976563 129976563 chr4 156259435 156259435 TCGA-J4-A6G3 DUP 16 44 * * chr4 130083372 130083372 chr4 157565327 157565327 TCGA-J4-A6G3 DEL 36 28 * * chr4 130200974 130200974 chr4 130391869 130391869 TCGA-J4-A6G3 INV 14 5 * * chr4 130377472 130377472 chr4 156177062 156177062 TCGA-J4-A6G3 DEL 38 28 LINC02479 * chr4 153314945 153314945 chr4 158396116 158396116 TCGA-J4-A6G3 INV 10 19 TRIM2 RXFP1 chr4 153315931 153315931 chr4 158272721 158272721 TCGA-J4-A6G3 DEL 15 40 TRIM2 AIDAP2 chr4 153395250 153395250 chr4 155666241 155666241 TCGA-J4-A6G3 DEL 15 31 MND1 GUCY1A1 chr4 153406245 153406245 chr4 157722999 157722999 TCGA-J4-A6G3 INV 23 50 MND1 * chr4 153757149 153757149 chr4 157188507 157188507 TCGA-J4-A6G3 INV 33 1 RNF175 * chr4 153979849 153979849 chr4 156329864 156329864 TCGA-J4-A6G3 DEL 17 18 * * chr4 154803016 154803016 chr4 156535575 156535575 TCGA-J4-A6G3 DEL 17 19 RBM46 * chr4 154878754 154878754 chr4 156594853 156594853 TCGA-J4-A6G3 DUP 3 7 * * chr4 154895400 154895400 chr4 157274536 157274536 TCGA-J4-A6G3 DUP 33 12 * GRIA2 chr4 156752652 156752652 chr4 158320593 158320593 TCGA-J4-A6G3 DUP 15 29 * RXFP1 chr4 157058858 157058858 chr4 157780752 157780752 TCGA-J4-A6G3 DEL 15 37 * * chr4 157296309 157296309 chr4 158273058 158273058 TCGA-J4-A6G3 INV 29 41 GRIA2 AIDAP2 chr4 157393495 157393495 chr4 157730076 157730076 TCGA-J4-A6G3 DEL 31 22 * * chr4 17058675 17058675 chr4 62782356 62782356 TCGA-J4-A6G3 DEL 45 38 AC106894.1 * chr4 174291611 174291611 chr4 176410694 176410694 TCGA-J4-A6G3 DEL 11 5 CEP44 * chr4 178818747 178818747 chr4 181609586 181609586 TCGA-J4-A6G3 DEL 42 16 * * chr4 18008059 18008059 chr4 46518604 46518604 TCGA-J4-A6G3 DEL 17 34 LCORL * chr4 185870681 185870681 chr13 80361362 80361362 TCGA-J4-A6G3 BND 4 8 SORBS2 * chr4 186076137 186076137 chr13 80414216 80414216 TCGA-J4-A6G3 BND 21 34 TLR3 * chr4 187030285 187030285 chr4 187060639 187060639 TCGA-J4-A6G3 DEL 8 17 * AC110772.2 chr4 189939573 189939573 chr13 80428941 80428941 TCGA-J4-A6G3 BND 24 7 FRG1-DT * chr4 63827891 63827891 chr4 63876663 63876663 TCGA-J4-A6G3 INV 32 25 * * chr4 6511643 6511643 chr21 41805988 41805997 TCGA-J4-A6G3 BND 7 48 PPP2R2C PRDM15 chr4 91187981 91187981 chr4 99576017 99576017 TCGA-J4-A6G3 DEL 7 6 CCSER1 MTTP chr5 11001450 11001450 chr5 11001594 11001594 TCGA-J4-A6G3 INV 16 32 CTNND2 CTNND2 chr5 11075520 11075520 chr5 11160131 11160131 TCGA-J4-A6G3 DUP 3 1 CTNND2 CTNND2 chr5 118218629 118218629 chr5 123667672 123667672 TCGA-J4-A6G3 INS 1 29 LINC02147 * chr5 137850715 137850715 chr5 137883008 137883008 TCGA-J4-A6G3 DUP 9 14 AC106791.1 MYOT chr5 29358801 29358801 chr5 30421987 30421987 TCGA-J4-A6G3 INV 40 29 * * chr5 45222988 45222988 chr5 104186237 104186237 TCGA-J4-A6G3 DEL 1 2 * * chr5 45248057 45248057 chr5 123665849 123665849 TCGA-J4-A6G3 INS 18 1 * * chr5 58233742 58233742 chr5 59068287 59068287 TCGA-J4-A6G3 DUP 44 49 * PDE4D chr5 7942200 7942200 chr5 11160131 11160131 TCGA-J4-A6G3 DUP 27 24 * CTNND2 chr5 85743637 85743637 chr5 101748887 101748887 TCGA-J4-A6G3 DEL 23 46 * * chr6 103661154 103661154 chr6 103680042 103680042 TCGA-J4-A6G3 DEL 38 38 * * chr6 114990157 114990157 chr6 115316324 115316324 TCGA-J4-A6G3 DEL 34 18 * * chr6 120203292 120203293 chr7 63947079 63947080 TCGA-J4-A6G3 BND 17 7 * * chr6 120622231 120622231 chr6 121385019 121385019 TCGA-J4-A6G3 DEL 49 33 * * chr6 154429374 154429374 chr9 75001963 75001963 TCGA-J4-A6G3 BND 44 30 CNKSR3 CARNMT1 chr6 296057 296058 chr16 33529128 33529128 TCGA-J4-A6G3 BND 11 8 DUSP22 * chr6 31389262 31389262 chr6 31513647 31513647 TCGA-J4-A6G3 DUP 27 10 * * chr6 8522615 8522615 chrX 8374887 8374887 TCGA-J4-A6G3 BND 31 35 AL355499.2 * chr6 96727684 96727684 chr6 96900059 96900059 TCGA-J4-A6G3 DEL 20 32 * * chr7 103425059 103425059 chr7 115042192 115042192 TCGA-J4-A6G3 INS 38 4 SLC26A5 * chr7 10352896 10352896 chr7 10353289 10353289 TCGA-J4-A6G3 DEL 37 5 * * chr7 11099741 11099741 chr7 97129343 97129343 TCGA-J4-A6G3 INS 26 23 PHF14 SDHAF3 chr7 11412410 11412410 chr7 36999084 36999084 TCGA-J4-A6G3 INS 16 35 AC004160.1 ELMO1 chr7 11589052 11589052 chr7 111192410 111192410 TCGA-J4-A6G3 DEL 38 42 THSD7A IMMP2L chr7 146075783 146075783 chr7 146451898 146451898 TCGA-J4-A6G3 DUP 38 1 * CNTNAP2 chr7 146282115 146282115 chr7 153302146 153302146 TCGA-J4-A6G3 INS 33 45 CNTNAP2 * chr7 147449897 147449897 chr7 147482941 147482941 TCGA-J4-A6G3 DUP 10 20 CNTNAP2 CNTNAP2 chr7 157461300 157461300 chr15 85897066 85897066 TCGA-J4-A6G3 BND 28 11 * * chr7 18219556 18219556 chr7 87876253 87876253 TCGA-J4-A6G3 INS 14 39 HDAC9 SLC25A40 chr7 34396117 34396117 chr7 53477360 53477360 TCGA-J4-A6G3 DEL 39 10 NPSR1-AS1 * chr7 34396499 34396499 chr7 131802954 131802954 TCGA-J4-A6G3 INS 12 2 NPSR1-AS1 * chr7 36999545 36999545 chr7 44927540 44927540 TCGA-J4-A6G3 INS 5 45 ELMO1 * chr7 38058053 38058053 chr7 80209118 80209118 TCGA-J4-A6G3 DEL 38 5 * GNAI1 chr7 41820472 41820472 chr7 132188477 132188477 TCGA-J4-A6G3 INS 18 36 * PLXNA4 chr7 47122824 47122824 chr7 109370155 109370155 TCGA-J4-A6G3 INS 17 32 * * chr7 51060361 51060361 chr7 127342976 127342976 TCGA-J4-A6G3 INS 9 27 COBL * chr7 52746964 52746964 chr7 151443552 151443552 TCGA-J4-A6G3 INS 45 39 * * chr7 52897833 52897833 chr7 140005271 140005271 TCGA-J4-A6G3 DEL 20 28 SGO1P2 TBXAS1 chr7 64714412 64714412 chr7 64714716 64714716 TCGA-J4-A6G3 DEL 25 35 * * chr7 7503711 7503711 chr7 14026615 14026615 TCGA-J4-A6G3 DEL 11 8 COL28A1 * chr7 75537031 75537031 chr7 122356392 122356392 TCGA-J4-A6G3 DEL 41 40 HIP1 CADPS2 chr7 77618839 77618839 chr7 77619163 77619163 TCGA-J4-A6G3 INS 32 2 PTPN12 PTPN12 chr7 80839563 80839563 chr7 93968472 93968472 TCGA-J4-A6G3 DEL 30 49 SEMA3C BET1 chr7 8572563 8572563 chr7 17596544 17596544 TCGA-J4-A6G3 DEL 8 29 NXPH1 * chr7 8937764 8937764 chr7 87188505 87188505 TCGA-J4-A6G3 INS 13 6 AC009500.1 DMTF1 chr7 9260662 9260662 chr7 87189641 87189641 TCGA-J4-A6G3 DEL 3 1 * DMTF1 chr7 96457496 96457496 chr7 118535441 118535441 TCGA-J4-A6G3 DEL 50 22 * * chr8 112733803 112733803 chr8 115065577 115065577 TCGA-J4-A6G3 DEL 44 40 CSMD3 * chr8 142255388 142255388 chrX 3524808 3524808 TCGA-J4-A6G3 BND 9 47 TSNARE1 * chr8 143981815 143981815 chr8 144016502 144016502 TCGA-J4-A6G3 DUP 18 10 PARP10 SPATC1 chr8 2298206 2298206 chr8 3464862 3464862 TCGA-J4-A6G3 DUP 12 6 * CSMD1 chr8 2838013 2838013 chr8 14060710 14060710 TCGA-J4-A6G3 INV 39 14 * * chr8 3805634 3805634 chr8 14716928 14716928 TCGA-J4-A6G3 INV 40 19 CSMD1 SGCZ chr8 50272696 50272696 chr18 64310201 64310201 TCGA-J4-A6G3 BND 28 2 SNTG1 LINC01924 chr8 71222828 71222828 chr8 71232904 71232904 TCGA-J4-A6G3 DEL 29 47 AC015687.1 EYA1 chr8 71233979 71233979 chr8 71334978 71334978 TCGA-J4-A6G3 DEL 14 8 EYA1 EYA1 chr8 74826820 74826820 chr8 76408213 76408213 TCGA-J4-A6G3 DEL 26 23 AC011632.1 LINC01111 chr8 83256011 83256011 chr8 91584973 91584973 TCGA-J4-A6G3 INV 25 32 * AC103409.1 chr8 84837204 84837204 chr8 109397230 109397230 TCGA-J4-A6G3 DUP 44 30 RALYL PKHD1L1 chr8 86267389 86267389 chr8 91600555 91600555 TCGA-J4-A6G3 INV 20 22 SLC7A13 AC103409.1 chr8 86500255 86500255 chr8 91263622 91263622 TCGA-J4-A6G3 INV 24 15 RMDN1 SLC26A7 chr8 88295247 88295247 chr8 88968241 88968241 TCGA-J4-A6G3 INV 29 35 MMP16 * chr8 88508647 88508647 chr8 90045142 90045142 TCGA-J4-A6G3 DEL 32 2 AC090578.1 DECR1 chr8 88511078 88511078 chr8 90816930 90816930 TCGA-J4-A6G3 DUP 45 29 AC090578.1 NECAB1 chr8 90255161 90255161 chr8 91232155 91232155 TCGA-J4-A6G3 DUP 18 40 LINC00534 SLC26A7 chr8 90820264 90820264 chr8 94548415 94548415 TCGA-J4-A6G3 INV 25 19 NECAB1 VIRMA chr8 91121078 91121078 chr8 109411196 109411196 TCGA-J4-A6G3 DEL 46 17 LRRC69 PKHD1L1 chr8 91163116 91163116 chr8 94734563 94734563 TCGA-J4-A6G3 DUP 34 22 LRRC69 DPY19L4 chr9 133307393 133307393 chr9 134586930 134586930 TCGA-J4-A6G3 INV 14 50 * * chr9 24476804 24476804 chr9 24618855 24618855 TCGA-J4-A6G3 INV 22 2 * * chr9 28011397 28011397 chr9 28109501 28109501 TCGA-J4-A6G3 INV 14 7 LINGO2 LINGO2 chr9 28085578 28085578 chr9 30639383 30639383 TCGA-J4-A6G3 DEL 39 45 LINGO2 * chr9 30674470 30674470 chr7 88462054 88462054 TCGA-J4-A6G3 BND 14 43 * * chrX 1105429 1105429 chrX 1105460 1105460 TCGA-J4-A6G3 INV 33 43 * * chrX 12893228 12893228 chrX 141804496 141804496 TCGA-J4-A6G3 DEL 13 47 * * chrX 5943158 5943158 chrX 6014839 6014839 TCGA-J4-A6G3 DEL 16 15 NLGN4X NLGN4X chrX 5978589 5978589 chrX 93040934 93040934 TCGA-J4-A6G3 DEL 47 30 NLGN4X * chrX 73328646 73328646 chrX 77839421 77839421 TCGA-J4-A6G3 DEL 50 13 * MAGT1 chrX 77691189 77691189 chrX 118298760 118298760 TCGA-J4-A6G3 DEL 35 34 ATRX * chrX 8095087 8095087 chrX 16995284 16995284 TCGA-J4-A6G3 INV 2 10 AC079142.1 REPS2 chr10 59238335 59238335 chr10 92944043 92944043 TCGA-EJ-A8FS DEL 5 33 PHYHIPL EXOC6 chr10 81979833 81979833 chr10 105593177 105593177 TCGA-EJ-A8FS DEL 48 5 NRG3 * chr10 87912778 87912778 chr10 89740289 89740289 TCGA-EJ-A8FS DEL 4 10 PTEN KIF20B chr10 9329392 9329392 chr20 8754106 8754132 TCGA-EJ-A8FS BND 45 32 * PLCB1 chr11 102863516 102863516 chr11 104096062 104096062 TCGA-EJ-A8FS DEL 36 1 MMP12 PDGFD chr11 103422783 103422783 chr11 107316648 107316648 TCGA-EJ-A8FS DEL 14 2 DYNC2H1 AP000766.1 chr11 104078567 104078567 chr11 110791593 110791593 TCGA-EJ-A8FS DEL 10 17 PDGFD * chr11 108241625 108241625 chr11 108310360 108310360 TCGA-EJ-A8FS DEL 21 42 ATM ATM chr11 109017543 109017543 chr11 109731828 109731828 TCGA-EJ-A8FS INS 26 7 AP003123.1 * chr11 109498444 109498444 chr11 109770276 109770276 TCGA-EJ-A8FS DEL 23 6 AP003049.2 LINC02715 chr11 109519193 109519193 chr11 110785744 110785744 TCGA-EJ-A8FS INS 15 50 AP003049.2 * chr11 48506459 48506459 chr11 87645705 87645705 TCGA-EJ-A8FS DUP 2 3 * * chr11 92005131 92005131 chr11 101774579 101774579 TCGA-EJ-A8FS INS 12 50 * TRPC6 chr11 92396114 92396114 chr11 105502493 105502493 TCGA-EJ-A8FS DEL 46 45 FAT3 CARD18 chr11 92603482 92603482 chr11 103435439 103435439 TCGA-EJ-A8FS DEL 35 3 FAT3 DYNC2H1 chr11 93481051 93481051 chr11 107267034 107267034 TCGA-EJ-A8FS INS 50 15 SMCO4 * chr11 9671851 9671851 chr11 10049753 10049753 TCGA-EJ-A8FS DUP 40 39 SWAP70 SBF2 chr11 97754116 97754116 chr11 99546503 99546503 TCGA-EJ-A8FS INS 35 6 * CNTN5 chr11 98194169 98194169 chr11 105493522 105493522 TCGA-EJ-A8FS INS 42 27 * CARD18 chr12 109342807 109342809 chr12 113113705 113113706 TCGA-EJ-A8FS DEL 48 35 * RASAL1 chr12 113015136 113015156 chr14 60478427 60478440 TCGA-EJ-A8FS BND 40 25 AC004551.1 C14orf39 chr12 116982530 116982530 chr14 61295694 61295709 TCGA-EJ-A8FS BND 45 24 FBXW8 PRKCH chr12 121233790 121233790 chr12 121690283 121690283 TCGA-EJ-A8FS INV 1 9 P2RX4 * chr12 121689914 121689914 chr18 80172353 80172353 TCGA-EJ-A8FS BND 29 40 * PARD6G chr12 131395565 131395565 chr12 132464246 132464274 TCGA-EJ-A8FS INV 21 42 * * chr12 131395619 131395619 chr12 132349485 132349485 TCGA-EJ-A8FS INV 32 28 * * chr12 131396135 131396135 chr12 132464364 132464364 TCGA-EJ-A8FS INV 33 36 * * chr12 67847618 67847618 chr12 67902756 67902756 TCGA-EJ-A8FS INV 5 26 * * chr12 79546246 79546246 chr12 79761784 79761784 TCGA-EJ-A8FS DEL 27 8 AC027288.1 AC073569.2 chr13 21530574 21530574 chr16 86642630 86642630 TCGA-EJ-A8FS BND 43 32 FNTAP2 * chr13 36326180 36326180 chr13 86542814 86542814 TCGA-EJ-A8FS DEL 8 33 SPART * chr13 89719230 89719230 chr13 89741133 89741133 TCGA-EJ-A8FS DEL 12 5 * * chr13 90572007 90572007 chr13 90690375 90690375 TCGA-EJ-A8FS DEL 4 29 * * chr14 101463956 101463956 chr18 78548581 78548581 TCGA-EJ-A8FS BND 29 33 * * chr14 102069477 102069477 chr14 103073828 103073828 TCGA-EJ-A8FS DEL 17 4 * * chr14 37589820 37589837 chr7 13974160 13974160 TCGA-EJ-A8FS BND 30 50 * ETV1 chr14 60478427 60478440 chr14 61284058 61284058 TCGA-EJ-A8FS DUP 22 26 C14orf39 PRKCH chr14 60479038 60479038 chr14 61291036 61291036 TCGA-EJ-A8FS INV 24 26 C14orf39 PRKCH chr14 61198762 61198762 chr14 61291143 61291143 TCGA-EJ-A8FS INV 9 31 PRKCH PRKCH chr14 61286629 61286629 chr14 61295694 61295709 TCGA-EJ-A8FS INV 5 43 PRKCH PRKCH chr14 61288248 61288248 chr14 61295040 61295040 TCGA-EJ-A8FS INV 9 37 PRKCH PRKCH chr15 30631719 30631719 chr15 32621146 32621146 TCGA-EJ-A8FS DEL 29 28 ARHGAP11B ARHGAP11A chr15 67919950 67919950 chr19 11666034 11666034 TCGA-EJ-A8FS BND 43 25 * AC008543.1 chr16 64219783 64219783 chr16 64383008 64383008 TCGA-EJ-A8FS DEL 20 37 * AC092131.1 chr16 64850543 64850543 chr16 64881596 64881596 TCGA-EJ-A8FS DEL 1 7 * * chr16 72767880 72767880 chr16 72819645 72819645 TCGA-EJ-A8FS DEL 34 15 AC004943.2 ZFHX3 chr16 86419352 86419352 chr16 89069466 89069466 TCGA-EJ-A8FS DUP 30 40 * * chr16 88929330 88929331 chr17 59829641 59829642 TCGA-EJ-A8FS BND 15 14 CBFA2T3 VMP1 chr17 19901107 19901107 chr17 63545711 63545711 TCGA-EJ-A8FS INV 32 39 * KCNH6 chr17 83098301 83098301 chr17 83162279 83162279 TCGA-EJ-A8FS DUP 28 13 AC130371.2 AC139099.2 chr18 48002553 48002553 chr18 76728238 76728245 TCGA-EJ-A8FS INV 21 36 * * chr18 48002582 48002582 chr21 38489896 38489896 TCGA-EJ-A8FS BND 30 47 * ERG chr1 120963996 120963996 chr1 143737614 143737614 TCGA-EJ-A8FS INV 13 34 LINC00623 AC239800.2 chr1 172092262 172092262 chr1 174383486 174383490 TCGA-EJ-A8FS DEL 7 26 DNM3 RABGAP1L chr1 174670947 174670947 chr10 89244601 89244601 TCGA-EJ-A8FS BND 25 9 RABGAP1L LIPA chr1 174690869 174690869 chr10 87741191 87741192 TCGA-EJ-A8FS BND 32 18 RABGAP1L PAPSS2 chr1 19317810 19317810 chr12 121234065 121234065 TCGA-EJ-A8FS BND 45 12 SLC66A1 P2RX4 chr1 195629951 195629951 chr1 195682978 195682978 TCGA-EJ-A8FS DEL 2 10 * * chr1 19653541 19653541 chr12 122264556 122264556 TCGA-EJ-A8FS BND 36 11 NBL1 VPS33A chr1 201143633 201143633 chr1 201378453 201378453 TCGA-EJ-A8FS DEL 14 35 TMEM9 TNNT2 chr1 236407483 236407483 chr1 236451544 236451544 TCGA-EJ-A8FS DEL 5 43 EDARADD EDARADD chr1 40995168 40995168 chr1 42758376 42758376 TCGA-EJ-A8FS DEL 42 24 CTPS1 P3H1 chr1 46513801 46513801 chr2 47308692 47308692 TCGA-EJ-A8FS BND 24 4 DMBX1 EPCAM-DT chr1 81461933 81461933 chr2 75849313 75849313 TCGA-EJ-A8FS BND 37 16 ADGRL2 * chr1 8322036 8322036 chr1 203603932 203603932 TCGA-EJ-A8FS INV 22 46 SLC45A1 * chr1 83477187 83477187 chr1 85695472 85695472 TCGA-EJ-A8FS DUP 15 44 * ZNHIT6 chr1 84081346 84081346 chr1 86176619 86176619 TCGA-EJ-A8FS DEL 11 16 PRKACB * chr1 97154876 97154877 chr1 97267764 97267764 TCGA-EJ-A8FS DEL 37 46 DPYD DPYD chr20 13766239 13766239 chr20 14742530 14742530 TCGA-EJ-A8FS DUP 18 23 ESF1 MACROD2 chr21 10427096 10427096 chr21 31784913 31784938 TCGA-EJ-A8FS DUP 38 28 BAGE2 * chr21 38475438 38475438 chr21 41502578 41502578 TCGA-EJ-A8FS DEL 16 1 ERG TMPRSS2 chr21 38489036 38489036 chr21 41495437 41495437 TCGA-EJ-A8FS DEL 50 35 ERG TMPRSS2 chr21 38504053 38504053 chr21 41495709 41495709 TCGA-EJ-A8FS DEL 48 25 ERG TMPRSS2 chr2 13840414 13840414 chr2 46383074 46383075 TCGA-EJ-A8FS DEL 20 2 LINC00276 EPAS1 chr2 15307737 15307738 chr2 46477581 46477581 TCGA-EJ-A8FS DUP 41 6 NBAS AC016912.2 chr2 155275637 155275637 chr2 155291812 155291812 TCGA-EJ-A8FS DEL 8 41 * * chr2 206721346 206721346 chr4 107858944 107858944 TCGA-EJ-A8FS BND 12 18 * SGMS2 chr2 212418010 212418014 chr9 25118696 25118700 TCGA-EJ-A8FS BND 11 46 ERBB4 * chr2 212431048 212431048 chr9 26812611 26812611 TCGA-EJ-A8FS BND 22 39 ERBB4 * chr2 212553082 212553084 chr9 26692945 26692947 TCGA-EJ-A8FS BND 8 16 * * chr2 225018532 225018532 chr2 225018648 225018648 TCGA-EJ-A8FS DEL 2 17 DOCK10 DOCK10 chr2 239095584 239095584 chr2 239251359 239251359 TCGA-EJ-A8FS DEL 14 44 HDAC4 HDAC4 chr2 241989502 241989502 chr9 134685621 134685621 TCGA-EJ-A8FS BND 41 30 LINC01237 COL5A1 chr2 34470762 34470762 chr2 34511501 34511501 TCGA-EJ-A8FS DEL 27 34 LINC01320 LINC01320 chr2 40999371 40999374 chr2 41017911 41017911 TCGA-EJ-A8FS INV 12 36 * * chr2 41017470 41017470 chr2 42082831 42082831 TCGA-EJ-A8FS DUP 25 10 * * chr2 41343536 41343536 chr2 42086627 42086627 TCGA-EJ-A8FS DEL 41 17 * * chr2 44525888 44525888 chr2 44974519 44974519 TCGA-EJ-A8FS DUP 43 1 CAMKMT * chr2 44833522 44833522 chr2 99838627 99838627 TCGA-EJ-A8FS DUP 29 24 * AFF3 chr2 75856977 75856995 chr2 128194994 128194994 TCGA-EJ-A8FS INV 26 7 * UGGT1 chr2 79605997 79605997 chr2 79610358 79610358 TCGA-EJ-A8FS DEL 24 42 CTNNA2 CTNNA2 chr2 81101245 81101245 chr2 81846667 81846667 TCGA-EJ-A8FS DEL 19 38 * * chr2 81235819 81235819 chr2 81260901 81260901 TCGA-EJ-A8FS DEL 39 39 * * chr2 81768142 81768145 chr4 117928402 117928405 TCGA-EJ-A8FS BND 7 19 * * chr3 100846093 100846093 chr6 62535881 62535881 TCGA-EJ-A8FS BND 42 22 ABI3BP * chr3 101159494 101159494 chr6 106825845 106825845 TCGA-EJ-A8FS BND 37 50 * * chr3 10118679 10118679 chr3 10212743 10212743 TCGA-EJ-A8FS DUP 7 13 BRK1 IRAK2 chr3 132349962 132349962 chr8 127734991 127734991 TCGA-EJ-A8FS BND 43 25 ACP3 CASC11 chr3 83832747 83832747 chr3 83892367 83892367 TCGA-EJ-A8FS INS 42 42 * * chr3 86386149 86386149 chr3 87125774 87125775 TCGA-EJ-A8FS INS 7 24 * LINC00506 chr3 86553109 86553109 chr3 87025896 87025896 TCGA-EJ-A8FS INS 21 24 * * chr4 102007045 102007045 chr4 102007184 102007184 TCGA-EJ-A8FS DEL 30 2 BANK1 BANK1 chr4 106188049 106188049 chr2 210013294 210013294 TCGA-EJ-A8FS BND 17 33 TBCK RPE chr4 106772262 106772266 chr2 214323665 214323669 TCGA-EJ-A8FS BND 7 18 * SPAG16 chr4 106840905 106840905 chr2 206039570 206039570 TCGA-EJ-A8FS BND 4 2 * INO80D chr4 114794439 114794439 chr4 114819996 114819996 TCGA-EJ-A8FS DEL 30 13 * * chr4 115834217 115834217 chr4 116427335 116427335 TCGA-EJ-A8FS DEL 7 5 * CUL4AP1 chr4 117025677 117025677 chr4 117056755 117056755 TCGA-EJ-A8FS DEL 26 31 * * chr4 117399461 117399461 chr2 81184980 81184980 TCGA-EJ-A8FS BND 43 25 * * chr4 126876618 126876618 chr4 175499461 175499461 TCGA-EJ-A8FS DEL 27 38 * * chr4 166755340 166755340 chr4 166762368 166762368 TCGA-EJ-A8FS INS 30 6 SPOCK3 SPOCK3 chr4 49486965 49486965 chr4 49568688 49568688 TCGA-EJ-A8FS INV 19 47 AC119751.3 * chr4 63828479 63828479 chr4 63875976 63875976 TCGA-EJ-A8FS INV 33 34 * * chr4 7695586 7695586 chr9 132520060 132520060 TCGA-EJ-A8FS BND 49 43 SORCS2 CFAP77 chr5 111437060 111437060 chr5 112363128 112363128 TCGA-EJ-A8FS INS 5 32 CAMK4 EPB41L4A chr5 111654314 111654314 chr5 112369349 112369349 TCGA-EJ-A8FS DEL 2 3 STARD4-AS1 EPB41L4A chr5 170400208 170400208 chr5 170400658 170400658 TCGA-EJ-A8FS DEL 33 22 KCNIP1 KCNIP1 chr5 17208490 17208490 chr10 9329568 9329568 TCGA-EJ-A8FS BND 13 47 BASP1 * chr5 17208607 17208611 chr20 8754106 8754132 TCGA-EJ-A8FS BND 34 27 BASP1 PLCB1 chr5 18812636 18812636 chr5 18818372 18818372 TCGA-EJ-A8FS DEL 5 46 * * chr5 20810382 20810382 chr5 34393667 34393667 TCGA-EJ-A8FS DUP 12 24 LINC02241 * chr5 60229847 60229847 chr5 60924927 60924927 TCGA-EJ-A8FS INS 2 15 PDE4D ERCC8 chr6 100142079 100142079 chr6 102988286 102988286 TCGA-EJ-A8FS DEL 27 18 * * chr6 104000472 104000472 chr6 104831440 104831440 TCGA-EJ-A8FS DEL 21 11 * HACE1 chr6 105432612 105432612 chr3 101586716 101586716 TCGA-EJ-A8FS BND 13 30 * PCNP chr6 106684682 106684682 chr3 100386836 100386836 TCGA-EJ-A8FS BND 34 15 * TOMM70 chr6 110904246 110904246 chr20 35864218 35864218 TCGA-EJ-A8FS BND 27 32 * PHF20 chr6 110904246 110904246 chr6 111349320 111349320 TCGA-EJ-A8FS DUP 41 21 * REV3L chr6 111349320 111349320 chr20 35864109 35864109 TCGA-EJ-A8FS BND 46 25 REV3L PHF20 chr6 112640042 112640042 chr17 19504348 19504348 TCGA-EJ-A8FS BND 30 25 * SLC47A1 chr6 112733037 112733037 chr21 30046697 30046697 TCGA-EJ-A8FS BND 41 2 * * chr6 122041141 122041141 chr6 154979168 154979168 TCGA-EJ-A8FS DEL 8 17 * TIAM2 chr6 143762856 143762856 chr7 150737614 150737615 TCGA-EJ-A8FS BND 19 20 PHACTR2 GIMAP5 chr6 143764848 143764848 chr6 144423558 144423561 TCGA-EJ-A8FS DUP 12 41 PHACTR2 UTRN chr6 143765038 143765038 chr6 144423558 144423561 TCGA-EJ-A8FS DEL 28 49 PHACTR2 UTRN chr6 143765351 143765351 chr6 144423737 144423737 TCGA-EJ-A8FS INV 29 42 PHACTR2 UTRN chr6 144423379 144423379 chr20 35872408 35872409 TCGA-EJ-A8FS BND 26 46 UTRN PHF20 chr6 160456622 160456622 chr6 160535638 160535638 TCGA-EJ-A8FS DUP 1 22 LPAL2 LPA chr6 17920445 17920446 chr8 75377199 75377199 TCGA-EJ-A8FS BND 40 21 KIF13A * chr6 18114032 18114032 chr14 61305288 61305288 TCGA-EJ-A8FS BND 38 9 * PRKCH chr6 18687171 18687171 chr12 112649240 112649240 TCGA-EJ-A8FS BND 6 7 * RPH3A chr6 32480473 32480473 chr6 32621001 32621001 TCGA-EJ-A8FS DUP 15 34 * * chr6 32486351 32486351 chr6 32572341 32572341 TCGA-EJ-A8FS DUP 17 15 * * chr6 62516961 62516961 chr6 102365417 102365417 TCGA-EJ-A8FS DEL 45 8 * * chr6 62535881 62535881 chr3 100846093 100846093 TCGA-EJ-A8FS BND 6 33 * ABI3BP chr6 99585233 99585233 chr6 105754956 105754956 TCGA-EJ-A8FS INS 13 36 * AL591518.1 chr7 156703909 156703909 chr14 61281227 61281227 TCGA-EJ-A8FS BND 12 47 LMBR1 PRKCH chr7 156704053 156704053 chr14 61287458 61287458 TCGA-EJ-A8FS BND 4 41 LMBR1 PRKCH chr7 156821112 156821112 chr12 109342807 109342809 TCGA-EJ-A8FS BND 47 20 LMBR1 * chr7 156821299 156821299 chr12 113113705 113113706 TCGA-EJ-A8FS BND 24 26 LMBR1 RASAL1 chr7 38413460 38413461 chr7 41945384 41945384 TCGA-EJ-A8FS DEL 6 29 AMPH * chr7 52999399 52999399 chr7 53000890 53000890 TCGA-EJ-A8FS DEL 11 31 * * chr8 127299713 127299732 chr8 127742732 127742739 TCGA-EJ-A8FS DUP 18 39 PCAT1 * chr8 22280762 22280763 chr8 25130329 25130329 TCGA-EJ-A8FS DEL 29 42 PIWIL2 * chr8 37350408 37350408 chr8 37350513 37350513 TCGA-EJ-A8FS INV 45 49 * * chr8 47837720 47837720 chr8 47932598 47932599 TCGA-EJ-A8FS DEL 30 22 PRKDC PRKDC chr8 50411943 50411943 chr8 51196119 51196119 TCGA-EJ-A8FS INS 23 36 SNTG1 * chr8 50541353 50541353 chr8 59916817 59916817 TCGA-EJ-A8FS DEL 8 5 SNTG1 * chr8 581478 581478 chr8 3216323 3216323 TCGA-EJ-A8FS DUP 43 24 * CSMD1 chr8 66625529 66625529 chr14 61281508 61281508 TCGA-EJ-A8FS BND 26 11 * PRKCH chr8 72815990 72815990 chr14 61287137 61287137 TCGA-EJ-A8FS BND 12 50 KCNB2 PRKCH chr9 113797053 113797053 chr15 34793311 34793311 TCGA-EJ-A8FS BND 49 22 * ACTC1 chr9 113797099 113797099 chr15 34816959 34816959 TCGA-EJ-A8FS BND 10 4 * * chr9 123397937 123397938 chr9 123485527 123485527 TCGA-EJ-A8FS DEL 42 45 DENND1A DENND1A chr9 131817781 131817781 chr9 131975573 131975573 TCGA-EJ-A8FS DEL 41 16 AL160271.2 MED27 chr9 133745627 133745627 chr19 17216436 17216436 TCGA-EJ-A8FS BND 8 44 * USE1 chr9 24452383 24452383 chr9 26178132 26178132 TCGA-EJ-A8FS DEL 46 46 * * chr9 24532261 24532261 chr9 26538452 26538452 TCGA-EJ-A8FS INS 50 45 * * chr9 24851474 24851474 chr9 24892529 24892529 TCGA-EJ-A8FS DEL 31 43 * * chr9 25078369 25078369 chr11 24331066 24331066 TCGA-EJ-A8FS BND 28 25 * * chr9 26692945 26692947 chr2 212553082 212553084 TCGA-EJ-A8FS BND 3 37 * * chr9 41757375 41757375 chr9 67619369 67619372 TCGA-EJ-A8FS DEL 33 25 * * chr9 41781071 41781081 chr9 61993220 61993220 TCGA-EJ-A8FS DEL 6 10 * * chr9 42564019 42564019 chr9 42566150 42566150 TCGA-EJ-A8FS INV 50 8 * * chr9 61532966 61532966 chr9 61991964 61991972 TCGA-EJ-A8FS INV 50 7 * * chr9 61533807 61533807 chr9 61993011 61993011 TCGA-EJ-A8FS INV 10 39 * * chrX 107109214 107109225 chrX 107823249 107823249 TCGA-EJ-A8FS DEL 26 14 RBM41 * chrX 142079604 142079605 chrX 143735773 143735777 TCGA-EJ-A8FS DUP 24 49 * * chrX 314656 314656 chrX 320691 320691 TCGA-EJ-A8FS DEL 22 35 GTPBP6 LINC00685 chrX 43525530 43525530 chrX 46859638 46859638 TCGA-EJ-A8FS DEL 14 29 * RP2 chrX 66771727 66771728 chrX 66990410 66990410 TCGA-EJ-A8FS DUP 40 34 * * chrX 66771727 66771728 chrX 67076308 67076308 TCGA-EJ-A8FS DUP 24 8 * * chr11 103648165 103648165 chr11 104759024 104759024 TCGA-2A-A8VO INS 49 37 * * chr11 104098345 104098345 chr11 106629421 106629421 TCGA-2A-A8VO INS 49 15 PDGFD * chr11 104877080 104877080 chr11 104905824 104905824 TCGA-2A-A8VO DEL 1 34 * CASP4LP chr11 106750545 106750545 chr11 109105636 109105636 TCGA-2A-A8VO DEL 18 31 GUCY1A2 * chr11 109728510 109728510 chr11 123895252 123895252 TCGA-2A-A8VO DEL 16 26 * * chr11 38097443 38097443 chr11 38112217 38112217 TCGA-2A-A8VO DEL 10 17 * * chr11 40024137 40024137 chr11 106762622 106762622 TCGA-2A-A8VO DEL 17 25 * GUCY1A2 chr11 40052913 40052913 chr11 106103297 106103297 TCGA-2A-A8VO INS 36 4 * AP001001.1 chr11 56519705 56519705 chr11 98087376 98087376 TCGA-2A-A8VO DEL 43 13 * * chr11 92209272 92209272 chr11 92210483 92210483 TCGA-2A-A8VO DEL 7 45 * * chr11 98084066 98084066 chr11 98421104 98421104 TCGA-2A-A8VO DEL 14 31 * * chr13 46540486 46540486 chr5 23267965 23267965 TCGA-2A-A8VO BND 12 44 * * chr14 74672059 74672059 chr14 74672426 74672426 TCGA-2A-A8VO INS 21 10 AREL1 AREL1 chr18 29357239 29357239 chr18 29357649 29357649 TCGA-2A-A8VO DEL 17 8 AC074237.1 AC074237.1 chr19 23411055 23411055 chr19 23430061 23430061 TCGA-2A-A8VO DEL 26 44 LINC01224 * chr1 173280579 173280579 chr1 173854446 173854446 TCGA-2A-A8VO DEL 24 46 * DARS2 chr1 196293854 196293854 chr1 196303672 196303672 TCGA-2A-A8VO DEL 37 22 KCNT2 KCNT2 chr1 220623104 220623104 chr1 220623969 220623969 TCGA-2A-A8VO DEL 45 28 MARK1 MARK1 chr1 68160248 68160248 chr1 68160430 68160430 TCGA-2A-A8VO INS 50 48 GNG12-AS1 GNG12-AS1 chr1 88378656 88378656 chr1 89598092 89598092 TCGA-2A-A8VO DEL 8 5 PKN2-AS1 LRRC8C-DT chr22 39629830 39629830 chr22 39630607 39630607 TCGA-2A-A8VO DEL 48 13 CACNA1I CACNA1I chr2 103465134 103465134 chr2 140549409 140549409 TCGA-2A-A8VO DEL 11 34 * LRP1B chr2 153344461 153344461 chr2 153477528 153477528 TCGA-2A-A8VO DEL 3 16 LINC01850 AC012501.2 chr2 185300982 185300982 chr2 185312140 185312140 TCGA-2A-A8VO DEL 31 30 * * chr2 186452567 186452567 chr1 147764833 147764833 TCGA-2A-A8VO BND 23 21 * GJA5 chr2 211794628 211794628 chr4 177755268 177755268 TCGA-2A-A8VO BND 3 22 ERBB4 LINC01098 chr2 35012894 35012894 chr2 35013266 35013266 TCGA-2A-A8VO DEL 19 49 AC012593.1 AC012593.1 chr3 165210008 165210008 chr3 165212090 165212090 TCGA-2A-A8VO DEL 21 22 LINC01322 LINC01322 chr4 134052461 134052461 chr4 170048431 170048431 TCGA-2A-A8VO INS 48 46 * * chr4 135524159 135524159 chr4 137846232 137846232 TCGA-2A-A8VO INS 37 46 * * chr4 135819374 135819374 chr4 135886542 135886542 TCGA-2A-A8VO DEL 19 39 * LINC00613 chr4 156511961 156511961 chr4 178965424 178965424 TCGA-2A-A8VO INS 6 43 * * chr4 157241568 157241568 chr4 157265311 157265311 TCGA-2A-A8VO DEL 43 50 GRIA2 GRIA2 chr4 157515434 157515434 chr4 159145422 159145422 TCGA-2A-A8VO DEL 47 15 * RAPGEF2 chr4 170429266 170429266 chr4 171596967 171596967 TCGA-2A-A8VO INS 20 24 * * chr4 170440707 170440707 chr4 171858030 171858030 TCGA-2A-A8VO INS 45 9 * GALNTL6 chr5 21745247 21745247 chr5 21788415 21788415 TCGA-2A-A8VO DEL 8 44 AC091946.1 CDH12 chr5 23259487 23259487 chr13 84245303 84245303 TCGA-2A-A8VO BND 12 24 * * chr5 23386814 23386814 chr13 46905157 46905157 TCGA-2A-A8VO BND 48 37 * * chr5 91415054 91415054 chr5 91415225 91415225 TCGA-2A-A8VO DEL 45 39 ARRDC3-AS1 ARRDC3-AS1 chr6 52786163 52786163 chr6 52826658 52826658 TCGA-2A-A8VO INS 5 10 * * chr6 60581542 60581542 chrX 95780449 95780449 TCGA-2A-A8VO BND 18 32 * * chr6 60601218 60601218 chrX 95339020 95339020 TCGA-2A-A8VO BND 43 28 * * chr6 74861919 74861919 chr6 74863797 74863797 TCGA-2A-A8VO DEL 39 22 * * chr6 79977716 79977716 chr6 79985918 79985918 TCGA-2A-A8VO DEL 22 41 * * chr6 81175575 81175575 chr6 81180524 81180524 TCGA-2A-A8VO DEL 30 31 * * chr6 85971191 85971191 chr6 92569347 92569347 TCGA-2A-A8VO DEL 14 10 * * chr6 86149716 86149716 chr6 86176750 86176750 TCGA-2A-A8VO DEL 11 45 * * chr6 91678277 91678277 chr6 92786797 92786797 TCGA-2A-A8VO INS 50 35 CASC6 * chr6 93132455 93132455 chr6 115043330 115043330 TCGA-2A-A8VO DEL 49 26 * * chr7 152257723 152257723 chr7 155169715 155169715 TCGA-2A-A8VO INS 34 48 KMT2C * chr7 153172240 153172240 chr7 155271911 155271911 TCGA-2A-A8VO DEL 43 18 * * chr7 153333172 153333172 chr7 154281226 154281226 TCGA-2A-A8VO INS 17 50 * DPP6 chr7 57561870 57561870 chr18 27942144 27942144 TCGA-2A-A8VO BND 27 26 * * chr8 114187697 114187699 chr8 114189738 114189738 TCGA-2A-A8VO DEL 26 36 * * chr8 50398561 50398561 chr8 50741656 50741656 TCGA-2A-A8VO DEL 7 26 SNTG1 SNTG1 chr8 55108829 55108829 chr8 55114540 55114540 TCGA-2A-A8VO DEL 10 35 XKR4 XKR4 chr8 60016544 60016544 chr8 60045370 60045370 TCGA-2A-A8VO DEL 12 19 * * chr8 63900685 63900685 chr8 91141410 91141410 TCGA-2A-A8VO DEL 15 22 LINC01414 LRRC69 chr9 12727562 12727562 chr9 12735249 12735249 TCGA-2A-A8VO DEL 49 26 LURAP1L-AS1 LURAP1L-AS1 chrX 33228965 33228965 chrX 33230049 33230049 TCGA-2A-A8VO DEL 35 14 DMD DMD chr10 51430321 51430321 chr10 51439220 51439220 TCGA-V1-A9ZK DEL 26 38 PRKG1 PRKG1 chr10 53451227 53451227 chr10 53451572 53451572 TCGA-V1-A9ZK DEL 36 45 * * chr11 5086154 5086154 chr6 70142716 70142716 TCGA-V1-A9ZK BND 9 25 * COL19A1 chr11 6163719 6163723 chr6 64650545 64650549 TCGA-V1-A9ZK BND 2 20 AC022762.1 EYS chr12 128517156 128517156 chr6 161947831 161947831 TCGA-V1-A9ZK BND 43 22 TMEM132C PRKN chr12 85462537 85462537 chr12 87714850 87714850 TCGA-V1-A9ZK DEL 5 14 * * chr12 87714287 87714287 chr6 60480630 60480630 TCGA-V1-A9ZK BND 34 13 * AC244258.1 chr16 58607291 58607291 chr16 59044265 59044265 TCGA-V1-A9ZK DEL 43 18 CNOT1 AC106793.1 chr16 59056564 59056564 chr16 88432888 88432888 TCGA-V1-A9ZK DEL 23 18 AC106793.1 ZNF469 chr16 60882344 60882344 chr16 66689930 66689930 TCGA-V1-A9ZK INS 47 21 * CMTM4 chr16 61305733 61305733 chr16 65625718 65625718 TCGA-V1-A9ZK DEL 34 50 * AC092138.2 chr16 66457691 66457691 chr16 88086043 88086043 TCGA-V1-A9ZK INS 47 48 BEAN1 AC134312.4 chr18 58569073 58569073 chr10 37059294 37059294 TCGA-V1-A9ZK BND 41 29 ALPK2 * chr1 158213259 158213259 chr1 158225270 158225270 TCGA-V1-A9ZK DEL 6 16 * * chr1 165267522 165267522 chr1 166506445 166506445 TCGA-V1-A9ZK DEL 44 5 LMX1A * chr1 165323716 165323716 chr1 169910502 169910502 TCGA-V1-A9ZK INS 27 26 LMX1A * chr1 165451249 165451249 chr1 170830918 170830918 TCGA-V1-A9ZK DEL 25 30 * * chr1 166947378 166947378 chr1 170601833 170601833 TCGA-V1-A9ZK DEL 30 48 ILDR2 AL023495.1 chr1 169609844 169609844 chr1 170828818 170828818 TCGA-V1-A9ZK INS 14 13 SELP * chr1 172285521 172285521 chr1 172376820 172376820 TCGA-V1-A9ZK INS 17 2 DNM3 DNM3 chr1 172331101 172331101 chr1 172689696 172689696 TCGA-V1-A9ZK DEL 3 36 DNM3 * chr1 186116360 186116360 chr1 186144695 186144695 TCGA-V1-A9ZK DEL 13 50 HMCN1 HMCN1 chr1 190797304 190797304 chr1 190908678 190908678 TCGA-V1-A9ZK DEL 15 37 LINC01720 AL138927.1 chr1 192129522 192129522 chr1 200540097 200540097 TCGA-V1-A9ZK DEL 31 20 * * chr1 194760520 194760520 chr1 200783426 200783426 TCGA-V1-A9ZK INS 14 15 * CAMSAP2 chr1 195184961 195184961 chr1 195259865 195259865 TCGA-V1-A9ZK DEL 19 43 * * chr1 195419608 195419608 chr1 195429106 195429111 TCGA-V1-A9ZK DEL 18 9 * * chr1 198544962 198544962 chr1 200792764 200792765 TCGA-V1-A9ZK DEL 47 1 * CAMSAP2 chr21 18396464 18396464 chr21 18486493 18486493 TCGA-V1-A9ZK DEL 13 10 TMPRSS15 TMPRSS15 chr21 19041344 19041344 chr21 19063304 19063304 TCGA-V1-A9ZK DEL 3 18 * * chr2 19756739 19756739 chr2 25775318 25775318 TCGA-V1-A9ZK DEL 39 24 * ASXL2 chr2 211738952 211738952 chr2 212793118 212793118 TCGA-V1-A9ZK DEL 15 12 ERBB4 AC093865.1 chr2 212666610 212666610 chr2 215753528 215753528 TCGA-V1-A9ZK DEL 50 17 AC093865.1 LINC00607 chr2 212727669 212727673 chr2 215005383 215005383 TCGA-V1-A9ZK DEL 23 25 AC093865.1 ABCA12 chr2 80387028 80387028 chr2 80389377 80389377 TCGA-V1-A9ZK DEL 20 8 CTNNA2 CTNNA2 chr2 84231908 84231908 chr2 84233086 84233086 TCGA-V1-A9ZK DEL 41 47 * * chr3 100810157 100810157 chr3 100811276 100811276 TCGA-V1-A9ZK DEL 33 15 ABI3BP ABI3BP chr3 115331828 115331828 chr3 115340418 115340418 TCGA-V1-A9ZK DEL 18 33 * * chr3 115572467 115572467 chr3 115820982 115820982 TCGA-V1-A9ZK DEL 44 44 * LSAMP chr3 165039777 165039777 chr3 165040444 165040444 TCGA-V1-A9ZK DEL 14 34 SI SI chr3 35437695 35437695 chr3 35437819 35437819 TCGA-V1-A9ZK DEL 31 44 * * chr3 35926174 35926174 chr3 35955753 35955753 TCGA-V1-A9ZK DEL 49 34 * * chr3 59105656 59105656 chr3 59823795 59823795 TCGA-V1-A9ZK INS 43 7 AC126121.3 FHIT chr4 106106938 106106938 chr4 106111286 106111286 TCGA-V1-A9ZK DEL 2 50 TBCK TBCK chr4 107742459 107742459 chr4 108658110 108658110 TCGA-V1-A9ZK INS 15 24 * OSTC chr4 107940523 107940523 chr4 130834800 130834800 TCGA-V1-A9ZK DEL 38 40 CYP2U1-AS1 * chr4 108695156 108695156 chr4 130793448 130793448 TCGA-V1-A9ZK INS 41 5 * * chr4 133179572 133179572 chr4 133242109 133242109 TCGA-V1-A9ZK DEL 3 11 PCDH10 * chr4 139416880 139416880 chr4 161994580 161994580 TCGA-V1-A9ZK DEL 6 35 NAA15 FSTL5 chr4 139440693 139440693 chr4 159899005 159899005 TCGA-V1-A9ZK INS 12 6 AC097376.3 * chr4 158553027 158553027 chr4 160097905 160097905 TCGA-V1-A9ZK DEL 10 34 RXFP1 * chr4 159927900 159927900 chr4 160845593 160845593 TCGA-V1-A9ZK INS 23 41 * * chr4 161380204 161380204 chr4 161425112 161425112 TCGA-V1-A9ZK INS 19 22 AC104793.1 FSTL5 chr4 161434797 161434797 chr4 162547609 162547609 TCGA-V1-A9ZK INS 4 5 FSTL5 * chr4 89363354 89363354 chr4 90418673 90418673 TCGA-V1-A9ZK INS 33 13 * CCSER1 chr5 103068018 103068018 chr5 104177684 104177684 TCGA-V1-A9ZK DEL 48 23 * * chr5 103880805 103880805 chr5 109648787 109648787 TCGA-V1-A9ZK DEL 8 21 AC008505.1 * chr5 2187488 2187488 chr5 4941331 4941331 TCGA-V1-A9ZK DEL 17 8 * * chr5 25421992 25421992 chr5 25423209 25423209 TCGA-V1-A9ZK DEL 25 16 AC022140.1 AC022140.1 chr5 26894587 26894587 chr5 29423427 29423427 TCGA-V1-A9ZK DEL 42 21 CDH9 * chr5 40839752 40839752 chr5 40852561 40852561 TCGA-V1-A9ZK DEL 19 44 CARD6 CARD6 chr5 52449419 52449419 chr5 80930558 80930559 TCGA-V1-A9ZK DEL 37 47 * * chr6 123147971 123147971 chr6 125709346 125709346 TCGA-V1-A9ZK INS 44 30 * AL365259.1 chr6 123320339 123320339 chr6 125245369 125245369 TCGA-V1-A9ZK DEL 1 32 TRDN TPD52L1 chr6 123355748 123355748 chr6 145947631 145947631 TCGA-V1-A9ZK INS 45 14 TRDN SHPRH chr6 124798071 124798071 chr6 152428133 152428133 TCGA-V1-A9ZK DEL 5 5 NKAIN2 SYNE1 chr6 124879261 124879261 chr6 153770374 153770374 TCGA-V1-A9ZK INS 20 19 * * chr6 125232405 125232405 chr6 125382147 125382147 TCGA-V1-A9ZK DEL 24 40 TPD52L1 AL450332.1 chr6 125355535 125355535 chr6 153792947 153792947 TCGA-V1-A9ZK DEL 14 36 * * chr6 126413098 126413098 chr6 126416983 126416983 TCGA-V1-A9ZK DEL 38 1 * * chr6 126984005 126984005 chr6 126995045 126995045 TCGA-V1-A9ZK DEL 21 36 * * chr6 133833436 133833436 chr6 133833516 133833516 TCGA-V1-A9ZK DEL 9 29 TARID TARID chr6 151515970 151515970 chr6 151580631 151580631 TCGA-V1-A9ZK DEL 19 8 CCDC170 CCDC170 chr6 161947831 161947831 chr12 128517156 128517156 TCGA-V1-A9ZK BND 39 50 PRKN TMEM132C chr6 60475631 60475631 chr6 60767333 60767333 TCGA-V1-A9ZK INS 21 16 AC244258.1 * chr6 60766282 60766283 chr12 128567800 128567801 TCGA-V1-A9ZK BND 40 13 * TMEM132C chr6 60972019 60972019 chr6 61007280 61007280 TCGA-V1-A9ZK DEL 8 45 * * chr6 64650545 64650549 chr11 6163719 6163723 TCGA-V1-A9ZK BND 16 15 EYS AC022762.1 chr6 64768005 64768005 chr11 6854850 6854850 TCGA-V1-A9ZK BND 20 28 EYS AC087280.2 chr6 64894863 64894863 chr6 153432220 153432220 TCGA-V1-A9ZK INS 26 7 EYS * chr6 65742929 65742929 chr11 6207425 6207425 TCGA-V1-A9ZK BND 41 34 * C11orf42 chr6 75652451 75652451 chr6 95406880 95406880 TCGA-V1-A9ZK DEL 42 21 SENP6 * chr6 96511491 96511491 chr6 125488682 125488682 TCGA-V1-A9ZK DEL 50 44 UFL1-AS1 * chr7 112653587 112653587 chr7 113335849 113335849 TCGA-V1-A9ZK DEL 49 39 AC002463.1 * chr7 114193505 114193505 chr7 115192534 115192534 TCGA-V1-A9ZK DEL 29 21 FOXP2 LINC01392 chr7 12117478 12117478 chr7 12117689 12117689 TCGA-V1-A9ZK INS 14 3 * * chr7 122320274 122320274 chr7 124913996 124913996 TCGA-V1-A9ZK DEL 5 35 CADPS2 POT1 chr7 123859886 123859886 chr7 126572561 126572561 TCGA-V1-A9ZK INS 3 49 HYAL4 GRM8 chr7 124221252 124221252 chr7 128181887 128181887 TCGA-V1-A9ZK DEL 50 50 AC006148.1 * chr7 124242787 124242787 chr7 126885373 126885373 TCGA-V1-A9ZK DEL 4 38 AC006148.1 GRM8 chr7 145452456 145452456 chr7 147038031 147038031 TCGA-V1-A9ZK INS 43 25 * CNTNAP2 chr7 53736344 53736344 chr7 120087999 120087999 TCGA-V1-A9ZK INS 21 3 LINC01446 * chr7 54530394 54530394 chr7 55653205 55653205 TCGA-V1-A9ZK DEL 49 41 * * chr7 75086154 75086154 chr7 121832467 121832467 TCGA-V1-A9ZK DEL 5 37 * * chr7 82890937 82890937 chr7 82926054 82926054 TCGA-V1-A9ZK DEL 30 15 PCLO PCLO chr8 113339298 113339298 chr8 113341478 113341478 TCGA-V1-A9ZK DEL 26 23 CSMD3 CSMD3 chr8 135070421 135070421 chr8 137820362 137820363 TCGA-V1-A9ZK DEL 47 5 * AC046195.1 chr8 135146804 135146804 chr8 135458638 135458638 TCGA-V1-A9ZK INS 10 50 * KHDRBS3 chr8 135923718 135923718 chr8 135941544 135941544 TCGA-V1-A9ZK DEL 25 14 LINC02055 LINC02055 chr8 138674904 138674904 chr8 138692897 138692897 TCGA-V1-A9ZK DEL 4 11 COL22A1 COL22A1 chr8 24925010 24925010 chr8 24957951 24957951 TCGA-V1-A9ZK DEL 49 20 * NEFL chr8 3305621 3305621 chr8 3511696 3511696 TCGA-V1-A9ZK DEL 37 7 CSMD1 CSMD1 chr8 3912533 3912533 chr8 3947133 3947133 TCGA-V1-A9ZK DEL 36 46 CSMD1 CSMD1 chr8 4359201 4359201 chr8 137746461 137746461 TCGA-V1-A9ZK INS 14 41 CSMD1 * chr8 49621954 49621954 chr8 134551726 134551726 TCGA-V1-A9ZK INS 20 12 * ZFAT chr8 49715837 49715837 chr8 137297363 137297363 TCGA-V1-A9ZK INS 21 49 * * chr8 76467733 76467733 chr8 76467869 76467869 TCGA-V1-A9ZK DEL 10 20 LINC01111 LINC01111 chrX 137908700 137908700 chrX 142362002 142362002 TCGA-V1-A9ZK DEL 18 35 Z96074.1 * chrX 139782813 139782813 chrX 140081863 140081865 TCGA-V1-A9ZK DEL 13 16 ATP11C * chr10 100294842 100294842 chr10 100390552 100390552 TCGA-KK-A8IK DUP 9 10 PKD2L1 OLMALINC chr10 108840193 108840193 chr10 108840593 108840593 TCGA-KK-A8IK DEL 35 38 * * chr10 22384290 22384290 chr10 22512092 22512092 TCGA-KK-A8IK DUP 41 4 SPAG6 * chr10 5585259 5585259 chr10 5916780 5916780 TCGA-KK-A8IK INV 23 36 * FBH1 chr10 61956813 61956813 chr10 62827355 62827355 TCGA-KK-A8IK DUP 32 29 ARID5B EGR2 chr10 71828846 71828846 chr10 72193134 72193134 TCGA-KK-A8IK DUP 40 12 PSAP ASCC1 chr10 7378060 7378060 chr10 7382648 7382648 TCGA-KK-A8IK DEL 9 41 SFMBT2 SFMBT2 chr10 7575519 7575519 chr10 7767156 7767156 TCGA-KK-A8IK DEL 11 37 ITIH5 KIN chr10 7768853 7768858 chr2 126239726 126239731 TCGA-KK-A8IK BND 27 47 KIN * chr10 8290016 8290016 chr10 11626166 11626166 TCGA-KK-A8IK INV 30 20 * * chr10 87208133 87208133 chr10 88344844 88344844 TCGA-KK-A8IK DEL 2 16 NUTM2A-AS1 RNLS chr11 101695214 101695214 chr11 101703699 101703699 TCGA-KK-A8IK INS 41 2 TRPC6 TRPC6 chr11 101999682 101999682 chr13 107891774 107891774 TCGA-KK-A8IK BND 5 30 CEP126 * chr11 102539155 102539155 chr11 102539361 102539361 TCGA-KK-A8IK INV 42 17 * * chr11 102540324 102540324 chr17 8063764 8063764 TCGA-KK-A8IK BND 8 8 * ALOXE3P1 chr11 104131582 104131582 chr11 132861448 132861448 TCGA-KK-A8IK DEL 47 37 PDGFD OPCML chr11 22144890 22144895 chr6 79657064 79657069 TCGA-KK-A8IK BND 42 2 ANO5 SH3BGRL2 chr11 22742833 22742833 chr11 22745968 22745968 TCGA-KK-A8IK DEL 26 45 GAS2 GAS2 chr11 2580590 2580590 chr11 5294291 5294291 TCGA-KK-A8IK DUP 3 25 KCNQ1 HBG2 chr11 29416138 29416138 chr11 29658604 29658604 TCGA-KK-A8IK DEL 14 31 LINC02755 * chr11 40938160 40938160 chr11 41225334 41225334 TCGA-KK-A8IK DEL 34 7 LRRC4C LRRC4C chr11 62013235 62013235 chr11 66252764 66252764 TCGA-KK-A8IK INV 48 25 AP003733.1 * chr11 63315233 63315233 chr11 95293090 95293090 TCGA-KK-A8IK INV 18 32 SLC22A10 * chr11 63352732 63352732 chr11 63383495 63383495 TCGA-KK-A8IK DUP 5 47 SLC22A10 SLC22A9 chr11 79321170 79321170 chr11 82267798 82267798 TCGA-KK-A8IK DEL 2 41 TENM4 MIR4300HG chr11 81647998 81647998 chr11 94925797 94925810 TCGA-KK-A8IK DEL 3 43 * AP002383.2 chr11 82236063 82236063 chr11 86730429 86730429 TCGA-KK-A8IK INV 1 13 MIR4300HG AP003059.2 chr11 82353765 82353765 chr11 82359105 82359105 TCGA-KK-A8IK DEL 34 40 MIR4300HG MIR4300HG chr11 82614433 82614434 chr18 44182678 44182679 TCGA-KK-A8IK BND 1 47 MIR4300HG * chr11 87354535 87354535 chr11 88492697 88492697 TCGA-KK-A8IK DEL 25 6 * * chr11 87652948 87652948 chr11 87698456 87698456 TCGA-KK-A8IK DEL 26 37 * * chr11 88446758 88446758 chr11 88478520 88478520 TCGA-KK-A8IK DUP 20 13 * * chr11 92875083 92875083 chr17 17914798 17914801 TCGA-KK-A8IK BND 13 19 FAT3 TOM1L2 chr11 94551533 94551533 chr11 94551768 94551768 TCGA-KK-A8IK INV 14 31 PIWIL4 PIWIL4 chr11 94921590 94921590 chr17 17618659 17618659 TCGA-KK-A8IK BND 7 19 AP002383.2 * chr11 94925797 94925810 chr17 17914798 17914801 TCGA-KK-A8IK BND 40 32 AP002383.2 TOM1L2 chr11 95053309 95053309 chr17 17160641 17160641 TCGA-KK-A8IK BND 25 22 * MPRIP chr11 96503138 96503138 chr11 96969955 96969955 TCGA-KK-A8IK DEL 44 28 JRKL * chr11 99361188 99361188 chr17 9976015 9976015 TCGA-KK-A8IK BND 27 23 CNTN5 GAS7 chr12 131303674 131303674 chr12 131656599 131656599 TCGA-KK-A8IK INV 37 42 * * chr12 131304601 131304601 chr12 131656498 131656498 TCGA-KK-A8IK DEL 49 35 * * chr12 13870283 13870283 chr12 13882781 13882781 TCGA-KK-A8IK DEL 9 44 GRIN2B GRIN2B chr12 43927536 43927536 chr12 43930293 43930293 TCGA-KK-A8IK DEL 12 12 TMEM117 TMEM117 chr12 58327782 58327782 chr12 58336564 58336564 TCGA-KK-A8IK INS 18 20 * * chr12 60655303 60655303 chr5 45297500 45297500 TCGA-KK-A8IK BND 20 46 * HCN1 chr12 60892963 60892965 chr5 46242885 46242887 TCGA-KK-A8IK BND 35 46 * * chr12 61807021 61807021 chr12 61817180 61817180 TCGA-KK-A8IK DEL 34 17 TAFA2 TAFA2 chr12 86847291 86847291 chr12 86859394 86859394 TCGA-KK-A8IK INV 14 20 * * chr13 108740166 108740166 chr8 72322114 72322114 TCGA-KK-A8IK BND 49 15 MYO16 * chr13 38624623 38624623 chr13 38671082 38671082 TCGA-KK-A8IK DEL 49 43 * * chr13 53430624 53430624 chr7 40656087 40656087 TCGA-KK-A8IK BND 32 38 * SUGCT chr13 55833373 55833373 chr7 40737884 40737884 TCGA-KK-A8IK BND 23 8 * SUGCT chr13 58315579 58315579 chr13 58324313 58324313 TCGA-KK-A8IK DEL 45 18 * * chr13 58752115 58752115 chr7 49172566 49172566 TCGA-KK-A8IK BND 49 3 DNAJA1P1 * chr13 81392239 81392239 chr5 113376691 113376691 TCGA-KK-A8IK BND 46 21 * MCC chr13 81438779 81438779 chr5 112634695 112634695 TCGA-KK-A8IK BND 25 9 * * chr13 86089230 86089230 chr13 86536686 86536686 TCGA-KK-A8IK INS 7 48 AL354994.1 * chr13 87616100 87616102 chr5 113754091 113754093 TCGA-KK-A8IK BND 36 18 MIR4500HG * chr13 87649097 87649097 chr5 112806313 112806313 TCGA-KK-A8IK BND 31 36 MIR4500HG APC chr13 98101167 98101167 chr13 98251784 98251784 TCGA-KK-A8IK DUP 25 21 * FARP1 chr13 98101850 98101850 chr13 98137055 98137055 TCGA-KK-A8IK INV 34 43 * * chr14 21213560 21213560 chr14 25028675 25028675 TCGA-KK-A8IK DUP 6 1 HNRNPC STXBP6 chr14 36622152 36622152 chr14 37169800 37169800 TCGA-KK-A8IK DEL 6 24 AL132857.1 SLC25A21 chr14 37223407 37223407 chr14 38609263 38609263 TCGA-KK-A8IK DEL 8 48 MIPOL1 * chr14 37531916 37531916 chr14 37599513 37599513 TCGA-KK-A8IK DUP 35 1 MIPOL1 TTC6 chr14 41051392 41051393 chr14 41062831 41062831 TCGA-KK-A8IK DEL 41 8 * * chr14 98540525 98540525 chr14 98762208 98762208 TCGA-KK-A8IK DUP 36 25 * * chr15 20102983 20102983 chr15 21111929 21111929 TCGA-KK-A8IK DEL 21 46 * * chr15 20104862 20104862 chr15 21111358 21111358 TCGA-KK-A8IK DUP 26 43 * * chr15 20106355 20106355 chr15 21110047 21110047 TCGA-KK-A8IK DEL 37 4 * * chr15 20535183 20535193 chr15 28561450 28561459 TCGA-KK-A8IK INV 5 44 GOLGA6L6 * chr15 20535812 20535812 chr15 28559746 28559746 TCGA-KK-A8IK DEL 23 39 GOLGA6L6 AC138749.1 chr15 23129912 23129912 chr15 28561163 28561163 TCGA-KK-A8IK INV 42 7 GOLGA6L1 AC138749.1 chr16 24468735 24468735 chr16 24850097 24850097 TCGA-KK-A8IK DUP 36 18 * SLC5A11 chr16 29197215 29197215 chr16 88164135 88164135 TCGA-KK-A8IK DUP 50 49 AC009093.8 * chr16 29298561 29298561 chr16 88273162 88273162 TCGA-KK-A8IK DUP 36 15 AC009093.10 AC138512.1 chr16 62187846 62187846 chr16 62618959 62618959 TCGA-KK-A8IK DEL 46 35 RNU6-21P * chr17 14418498 14418498 chr17 14418912 14418912 TCGA-KK-A8IK INV 13 31 AC022816.1 AC022816.1 chr17 14987630 14987630 chr17 14987979 14987979 TCGA-KK-A8IK INV 41 22 * * chr17 15633734 15633734 chr17 15634025 15634025 TCGA-KK-A8IK INV 14 7 AC005324.2 AC005324.2 chr17 16011032 16011032 chr17 16179854 16179854 TCGA-KK-A8IK DUP 35 21 TTC19 NCOR1 chr17 16159244 16159244 chr17 16159838 16159838 TCGA-KK-A8IK INV 28 31 NCOR1 NCOR1 chr17 16279795 16279795 chr17 22305247 22305247 TCGA-KK-A8IK DEL 49 1 PIGL * chr17 16880165 16880165 chr17 16880641 16880641 TCGA-KK-A8IK INV 3 22 * * chr17 17018592 17018592 chr17 17018857 17018857 TCGA-KK-A8IK INV 18 2 * * chr17 17213328 17213328 chr17 17213575 17213575 TCGA-KK-A8IK INV 8 14 MPRIP MPRIP chr17 17359574 17359574 chr17 17359776 17359776 TCGA-KK-A8IK INV 5 13 * * chr17 19976191 19976191 chr17 19976726 19976726 TCGA-KK-A8IK INV 26 46 AKAP10 AKAP10 chr17 20559658 20559658 chr17 20559941 20559941 TCGA-KK-A8IK INV 2 21 AC015818.3 AC015818.3 chr17 31567278 31567278 chr17 37018448 37018448 TCGA-KK-A8IK INV 21 33 * AATF chr17 31567379 31567379 chr17 31828252 31828252 TCGA-KK-A8IK INV 35 7 * * chr17 31877463 31877463 chr17 31942739 31942739 TCGA-KK-A8IK DEL 32 47 UTP6 SUZ12 chr17 7457985 7457995 chr17 42131890 42131890 TCGA-KK-A8IK INV 20 15 * AC099811.2 chr17 7457985 7457995 chr17 38320587 38320587 TCGA-KK-A8IK DUP 37 18 * MRPL45 chr17 7573256 7573256 chr17 38321135 38321135 TCGA-KK-A8IK DEL 13 35 EIF4A1 MRPL45 chr17 7574396 7574396 chr17 42131961 42131961 TCGA-KK-A8IK INV 44 30 EIF4A1 AC099811.2 chr17 76296537 76296537 chr17 76894843 76894843 TCGA-KK-A8IK DUP 24 26 QRICH2 MGAT5B chr17 8836896 8836896 chr17 8837401 8837401 TCGA-KK-A8IK INV 21 5 PIK3R6 PIK3R6 chr18 43947314 43947317 chr11 82648810 82648813 TCGA-KK-A8IK BND 37 38 * MIR4300HG chr18 51123539 51123545 chr6 119593091 119593097 TCGA-KK-A8IK BND 33 21 * * chr18 56413142 56413142 chr6 100992173 100992173 TCGA-KK-A8IK BND 30 25 * * chr18 56452207 56452209 chr6 101145257 101145259 TCGA-KK-A8IK BND 33 29 * * chr18 63024243 63024243 chr18 65545760 65545760 TCGA-KK-A8IK INS 43 35 * * chr18 63852076 63852076 chr18 65966282 65966282 TCGA-KK-A8IK INS 39 26 * * chr18 64450541 64450541 chr18 65578858 65578858 TCGA-KK-A8IK DEL 8 18 * * chr18 64507188 64507193 chr6 96022698 96022703 TCGA-KK-A8IK BND 10 17 * FUT9 chr18 64567671 64567671 chr18 65436997 65436997 TCGA-KK-A8IK INS 22 10 * LINC01916 chr18 65456132 65456133 chr6 96052475 96052476 TCGA-KK-A8IK BND 9 41 * FUT9 chr18 67680220 67680220 chr18 67693635 67693635 TCGA-KK-A8IK DEL 14 14 AC114689.3 AC114689.3 chr1 114817495 114817495 chr1 114865372 114865372 TCGA-KK-A8IK DEL 22 43 * SYCP1 chr1 155978246 155978246 chr1 156980954 156980954 TCGA-KK-A8IK DUP 30 1 ARHGEF2 ARHGEF11 chr1 171286720 171286720 chr1 171305601 171305601 TCGA-KK-A8IK DEL 4 40 * * chr1 186418880 186418882 chr9 11255062 11255064 TCGA-KK-A8IK BND 3 24 ODR4 * chr1 186758640 186758645 chr9 10989812 10989817 TCGA-KK-A8IK BND 47 29 * * chr1 186994109 186994109 chr1 188721214 188721214 TCGA-KK-A8IK INS 17 41 * * chr1 188771833 188771833 chr9 15973226 15973226 TCGA-KK-A8IK BND 36 28 * CCDC171 chr1 191240679 191240679 chr1 196862388 196862388 TCGA-KK-A8IK INS 14 32 * BX248415.1 chr1 191933455 191933455 chr1 193141461 193141461 TCGA-KK-A8IK INV 42 4 LINC02770 CDC73 chr1 192410214 192410214 chr1 193141599 193141599 TCGA-KK-A8IK DEL 23 42 AL390957.1 CDC73 chr1 192721116 192721116 chr1 192724264 192724264 TCGA-KK-A8IK DEL 43 1 AL390957.1 AL390957.1 chr1 192961402 192961404 chr6 80022689 80022691 TCGA-KK-A8IK BND 44 39 * TTK chr1 194599544 194599544 chr6 81987162 81987162 TCGA-KK-A8IK BND 14 11 * * chr1 215092770 215092770 chr1 241192084 241192084 TCGA-KK-A8IK DEL 18 3 KCNK2 RGS7 chr1 66838678 66838678 chr1 67076326 67076326 TCGA-KK-A8IK DUP 49 14 DNAI4 * chr1 68285862 68285862 chr1 68364737 68364737 TCGA-KK-A8IK DUP 1 10 * * chr20 15084038 15084038 chr1 169470680 169470680 TCGA-KK-A8IK BND 23 41 MACROD2 SLC19A2 chr20 15146921 15146921 chr1 169514816 169514816 TCGA-KK-A8IK BND 42 29 MACROD2 F5 chr20 31401516 31401516 chr20 31595154 31595154 TCGA-KK-A8IK INV 13 40 * * chr20 50140139 50140139 chr20 50198588 50198588 TCGA-KK-A8IK DEL 7 32 PEDS1-UBE2V1 * chr20 60167531 60167531 chr20 60183550 60183550 TCGA-KK-A8IK DEL 23 19 MIR646HG MIR646HG chr20 61850353 61850353 chr20 61887198 61887198 TCGA-KK-A8IK DEL 42 41 CDH4 CDH4 chr2 125345918 125345918 chr10 7594813 7594813 TCGA-KK-A8IK BND 47 25 * ITIH5 chr2 126239726 126239731 chr10 7768853 7768858 TCGA-KK-A8IK BND 12 41 * KIN chr2 131675207 131675207 chr11 96464362 96464362 TCGA-KK-A8IK BND 27 5 * JRKL chr2 135503589 135503589 chr2 135533127 135533127 TCGA-KK-A8IK DEL 36 34 ZRANB3 R3HDM1 chr2 139477158 139477158 chr2 141878266 141878266 TCGA-KK-A8IK DUP 48 29 AC016710.1 LRP1B chr2 140082835 140082835 chr2 142973676 142973676 TCGA-KK-A8IK DEL 34 39 * KYNU chr2 140084528 140084529 chr4 138367648 138367649 TCGA-KK-A8IK BND 42 14 * LINC00499 chr2 144195664 144195664 chr2 144199026 144199026 TCGA-KK-A8IK DEL 38 5 GTDC1 GTDC1 chr2 193824702 193824702 chr2 193834041 193834041 TCGA-KK-A8IK INS 27 7 * * chr2 208647029 208647030 chr2 208652898 208652898 TCGA-KK-A8IK DEL 7 26 PTH2R PTH2R chr2 232123997 232123997 chr2 232313085 232313085 TCGA-KK-A8IK INV 17 28 DIS3L2 DIS3L2 chr2 232125879 232125879 chr17 13190863 13190863 TCGA-KK-A8IK BND 30 46 DIS3L2 * chr2 232310420 232310420 chr2 232313441 232313441 TCGA-KK-A8IK INV 19 41 DIS3L2 DIS3L2 chr2 240100945 240100945 chr2 240132502 240132502 TCGA-KK-A8IK DUP 34 13 * COPS9 chr2 34920282 34920282 chr2 34920401 34920401 TCGA-KK-A8IK DEL 36 1 AC012593.1 AC012593.1 chr2 40303176 40303176 chr2 83942846 83942846 TCGA-KK-A8IK INV 50 30 SLC8A1 * chr2 49268729 49268729 chr2 49288955 49288955 TCGA-KK-A8IK DEL 22 49 AC009975.1 AC009975.1 chr2 56678238 56678242 chr4 109457622 109457626 TCGA-KK-A8IK BND 36 39 * SEC24B chr2 56998104 56998104 chr2 57018573 57018573 TCGA-KK-A8IK DEL 21 5 * * chr2 57461460 57461465 chr4 129735231 129735236 TCGA-KK-A8IK BND 8 49 * LINC02466 chr2 57554642 57554642 chr11 66564689 66564689 TCGA-KK-A8IK BND 4 1 * CTSF chr2 57683030 57683033 chr4 135499366 135499370 TCGA-KK-A8IK BND 33 35 * * chr3 100579357 100579357 chr3 101083366 101083366 TCGA-KK-A8IK DUP 48 12 * * chr3 103483439 103483439 chr3 103721708 103721708 TCGA-KK-A8IK DUP 49 29 * * chr3 106789170 106789170 chr3 163799885 163799885 TCGA-KK-A8IK INS 21 45 * * chr3 108382062 108382062 chr3 160587323 160587323 TCGA-KK-A8IK DEL 11 7 MYH15 * chr3 108957151 108957151 chr3 161040590 161040590 TCGA-KK-A8IK INS 40 43 * PPM1L chr3 113024562 113024562 chr3 113032773 113032773 TCGA-KK-A8IK INS 24 48 AC078785.1 AC078785.1 chr3 133518705 133518705 chr3 133555665 133555665 TCGA-KK-A8IK DEL 39 3 * * chr3 141665791 141665791 chr21 36497210 36497210 TCGA-KK-A8IK BND 4 40 LINC02618 CLDN14 chr3 145224940 145224940 chr3 146754864 146754864 TCGA-KK-A8IK INS 20 11 * * chr3 151737914 151737914 chr17 55981097 55981097 TCGA-KK-A8IK BND 15 33 AADACL2 ANKFN1 chr3 151749573 151749573 chr15 92659583 92659583 TCGA-KK-A8IK BND 17 19 AADACL2 FAM174B chr3 162307403 162307403 chr3 162327191 162327191 TCGA-KK-A8IK DEL 49 4 * * chr3 166447728 166447728 chr3 166451169 166451169 TCGA-KK-A8IK DEL 32 33 * * chr3 166524209 166524209 chr3 166528683 166528683 TCGA-KK-A8IK DEL 16 27 * * chr3 178948390 178948390 chr17 13190362 13190362 TCGA-KK-A8IK BND 15 8 * * chr3 179097634 179097634 chr17 13191835 13191835 TCGA-KK-A8IK BND 25 19 Y_RNA * chr3 186575394 186575394 chr20 24208523 24208523 TCGA-KK-A8IK BND 5 23 DNAJB11 LINC01721 chr3 195941315 195941315 chr3 196000979 196000979 TCGA-KK-A8IK DEL 26 10 AC124944.2 * chr3 46751412 46751412 chr3 46810535 46810535 TCGA-KK-A8IK DEL 36 33 AC109583.1 AC109583.1 chr3 79403610 79403610 chr3 79419357 79419357 TCGA-KK-A8IK DEL 31 27 ROBO1 ROBO1 chr3 80149747 80149747 chr3 83371648 83371648 TCGA-KK-A8IK DEL 19 26 * * chr3 80750025 80750025 chr3 158068297 158068297 TCGA-KK-A8IK INS 4 8 * AC079943.2 chr3 81510934 81510934 chr3 82067885 82067885 TCGA-KK-A8IK DEL 5 36 GBE1 LINC02008 chr3 81540175 81540175 chr3 82649336 82649336 TCGA-KK-A8IK INS 2 35 GBE1 * chr3 81826010 81826010 chr3 158086224 158086224 TCGA-KK-A8IK DEL 37 30 * AC079943.2 chr3 82359277 82359277 chr3 94425367 94425367 TCGA-KK-A8IK INS 2 1 LINC02008 * chr3 89127438 89127438 chr3 89548734 89548734 TCGA-KK-A8IK DEL 46 18 EPHA3 * chr3 89173570 89173570 chr3 89761266 89761266 TCGA-KK-A8IK INS 24 28 EPHA3 * chr3 89547856 89547856 chr3 89792377 89792377 TCGA-KK-A8IK DEL 50 16 * * chr3 97794114 97794122 chr3 97801431 97801431 TCGA-KK-A8IK DEL 3 42 ARL6 AC110491.3 chr4 108798319 108798319 chr4 110374276 110374276 TCGA-KK-A8IK DEL 42 15 * ENPEP chr4 108886865 108886865 chr4 111269517 111269517 TCGA-KK-A8IK INS 40 10 COL25A1 * chr4 109329119 109329119 chr4 109721128 109721128 TCGA-KK-A8IK DEL 3 16 * PLA2G12A chr4 109455553 109455553 chr4 111188038 111188038 TCGA-KK-A8IK INS 4 43 SEC24B * chr4 109457622 109457626 chr2 56678238 56678242 TCGA-KK-A8IK BND 24 48 SEC24B * chr4 109707519 109707519 chr4 109820356 109820356 TCGA-KK-A8IK INS 17 33 * GAR1 chr4 109771932 109771932 chr4 111186494 111186494 TCGA-KK-A8IK INS 1 49 CFI * chr4 110168289 110168289 chr2 56868445 56868445 TCGA-KK-A8IK BND 15 4 ELOVL6 * chr4 110291685 110291685 chr4 110639124 110639124 TCGA-KK-A8IK DEL 49 4 ZBED1P1 PITX2 chr4 111035416 111035416 chr4 111050381 111050381 TCGA-KK-A8IK DEL 4 24 * * chr4 111499752 111499752 chr4 111504148 111504148 TCGA-KK-A8IK DEL 47 13 * * chr4 112433960 112433960 chr4 125885849 125885849 TCGA-KK-A8IK INS 28 27 ALPK1 * chr4 116695597 116695597 chr4 116697101 116697101 TCGA-KK-A8IK DEL 45 44 * * chr4 117572156 117572156 chr4 136219026 136219026 TCGA-KK-A8IK DEL 21 22 LINC01378 AC018680.1 chr4 125497073 125497073 chr4 125565012 125565012 TCGA-KK-A8IK DEL 8 26 * * chr4 127552504 127552504 chr4 127558768 127558768 TCGA-KK-A8IK DEL 1 30 * * chr4 128343749 128343749 chr4 128403436 128403436 TCGA-KK-A8IK DEL 15 37 LINC02615 LINC02615 chr4 129098232 129098232 chr4 133559503 133559503 TCGA-KK-A8IK DEL 34 28 C4orf33 * chr4 132769846 132769847 chr2 57482846 57482847 TCGA-KK-A8IK BND 42 36 * * chr4 133169510 133169511 chr2 57570103 57570104 TCGA-KK-A8IK BND 27 19 PCDH10 * chr4 133542185 133542185 chr4 135414852 135414852 TCGA-KK-A8IK DEL 34 26 * * chr4 133940141 133940141 chr4 133944089 133944089 TCGA-KK-A8IK DEL 1 43 AC079380.1 AC079380.1 chr4 134652126 134652126 chr4 134657372 134657380 TCGA-KK-A8IK DEL 39 25 * * chr4 135381990 135381990 chr2 57605669 57605669 TCGA-KK-A8IK BND 4 35 * * chr4 135499366 135499370 chr2 57683030 57683033 TCGA-KK-A8IK BND 42 49 * * chr4 136017553 136017553 chr4 136029169 136029169 TCGA-KK-A8IK DEL 15 2 * * chr4 138293984 138293984 chr2 142281589 142281589 TCGA-KK-A8IK BND 39 9 * * chr4 138367648 138367649 chr2 140084528 140084529 TCGA-KK-A8IK BND 46 4 LINC00499 * chr4 14266005 14266005 chr4 14318004 14318004 TCGA-KK-A8IK DEL 47 35 * * chr4 154455514 154455516 chr2 104800576 104800579 TCGA-KK-A8IK BND 43 35 DCHS2 * chr4 172685875 172685875 chr4 172852521 172852521 TCGA-KK-A8IK DEL 22 33 GALNTL6 GALNTL6 chr4 173337778 173337778 chr4 173412576 173412576 TCGA-KK-A8IK DEL 19 4 * * chr4 20352586 20352586 chr4 30495203 30495203 TCGA-KK-A8IK DEL 9 25 SLIT2 * chr4 28813331 28813331 chr4 38289824 38289824 TCGA-KK-A8IK INS 24 15 * * chr4 30490839 30490839 chr4 38290486 38290486 TCGA-KK-A8IK DEL 25 31 * * chr4 44712532 44712532 chr4 44713138 44713138 TCGA-KK-A8IK DEL 25 3 GNPDA2 GNPDA2 chr4 46588433 46588433 chr4 46652470 46652470 TCGA-KK-A8IK DEL 37 22 * * chr4 46653707 46653720 chr4 57024606 57024606 TCGA-KK-A8IK DEL 23 49 * POLR2B chr4 46653707 46653720 chr4 57111442 57111442 TCGA-KK-A8IK INS 50 10 * IGFBP7 chr4 46694250 46694250 chr4 47782655 47782655 TCGA-KK-A8IK DEL 9 7 * CORIN chr4 47192915 47192915 chr4 57032066 57032066 TCGA-KK-A8IK DEL 10 25 GABRB1 IGFBP7 chr4 47772475 47772475 chr4 47801979 47801979 TCGA-KK-A8IK DEL 44 47 CORIN CORIN chr4 57020473 57020473 chr4 57043438 57043438 TCGA-KK-A8IK INS 26 23 POLR2B IGFBP7 chr4 57029765 57029765 chr4 98744441 98744441 TCGA-KK-A8IK DEL 21 26 POLR2B * chr4 57034038 57034038 chr4 98756818 98756818 TCGA-KK-A8IK DEL 7 35 IGFBP7 * chr4 57145307 57145307 chr4 98714049 98714049 TCGA-KK-A8IK INS 13 24 IGFBP7-AS1 AC114811.1 chr4 57253633 57253633 chr4 57839658 57839658 TCGA-KK-A8IK INS 20 15 * * chr4 57872539 57872539 chr4 98217785 98217787 TCGA-KK-A8IK DEL 39 46 * * chr4 62346753 62346753 chr4 67274282 67274282 TCGA-KK-A8IK DEL 11 10 * * chr4 62513165 62513165 chr4 63909904 63909904 TCGA-KK-A8IK INS 18 37 * * chr4 62851765 62851765 chr4 63951586 63951586 TCGA-KK-A8IK DEL 22 39 * * chr5 107467129 107467129 chr5 107467581 107467581 TCGA-KK-A8IK DEL 39 36 EFNA5 EFNA5 chr5 112574993 112574993 chr13 87671909 87671909 TCGA-KK-A8IK BND 20 32 * MIR4500HG chr5 112634695 112634695 chr13 81438779 81438779 TCGA-KK-A8IK BND 40 27 * * chr5 113711791 113711792 chr13 86287842 86287843 TCGA-KK-A8IK BND 15 35 * * chr5 113754091 113754093 chr13 87616100 87616102 TCGA-KK-A8IK BND 37 13 * MIR4500HG chr5 114989578 114989578 chr5 114999310 114999310 TCGA-KK-A8IK INS 39 23 * * chr5 11837 11837 chrX 156029886 156029886 TCGA-KK-A8IK BND 40 6 * * chr5 119850145 119850145 chr10 132332374 132332374 TCGA-KK-A8IK BND 46 46 * STK32C chr5 120567580 120567580 chr5 136882954 136882954 TCGA-KK-A8IK INV 5 45 PRR16 * chr5 123442186 123442186 chr5 134389899 134389899 TCGA-KK-A8IK INV 24 48 * UBE2B chr5 128217455 128217455 chr5 140918822 140918822 TCGA-KK-A8IK INV 27 36 * PCDHA1 chr5 130282616 130282616 chr10 128258189 128258189 TCGA-KK-A8IK BND 1 33 * LINC01163 chr5 134994480 134994480 chr5 135105990 135105990 TCGA-KK-A8IK DUP 20 13 PCBD2 C5orf66 chr5 142145973 142145973 chr5 142795788 142795788 TCGA-KK-A8IK INV 19 2 NDFIP1 ARHGAP26 chr5 143513776 143513776 chr10 85246487 85246487 TCGA-KK-A8IK BND 41 9 AC016598.1 * chr5 152695069 152695071 chr7 41767400 41767402 TCGA-KK-A8IK BND 4 9 LINC01470 INHBA-AS1 chr5 153116019 153116022 chr7 41736212 41736215 TCGA-KK-A8IK BND 12 33 LINC01470 INHBA-AS1 chr5 153250391 153250394 chr7 41181878 41181881 TCGA-KK-A8IK BND 14 47 * * chr5 153762631 153762632 chr7 41188238 41188239 TCGA-KK-A8IK BND 4 29 GRIA1 * chr5 2653040 2653040 chr5 96297150 96297150 TCGA-KK-A8IK INV 45 28 * AC104123.1 chr5 27205659 27205659 chr5 90786001 90786001 TCGA-KK-A8IK INV 26 31 * ADGRV1 chr5 27784855 27784855 chr5 150384256 150384256 TCGA-KK-A8IK INV 46 32 * TCOF1 chr5 4045021 4045021 chr5 4286154 4286154 TCGA-KK-A8IK DEL 34 31 * * chr5 44677115 44677115 chr5 44743171 44743171 TCGA-KK-A8IK DEL 44 4 * * chr5 60322274 60322274 chr5 61255460 61255464 TCGA-KK-A8IK INS 9 6 PDE4D LINC02057 chr5 691756 691756 chr5 783261 783261 TCGA-KK-A8IK INV 12 2 TPPP * chr6 101006558 101006558 chr8 118295069 118295069 TCGA-KK-A8IK BND 4 45 * SAMD12 chr6 101145257 101145259 chr18 56452207 56452209 TCGA-KK-A8IK BND 11 46 * * chr6 119593091 119593097 chr18 51123539 51123545 TCGA-KK-A8IK BND 22 10 * * chr6 119922834 119922834 chr18 54114888 54114888 TCGA-KK-A8IK BND 50 50 * * chr6 125985540 125985540 chr6 127475203 127475203 TCGA-KK-A8IK DEL 2 3 TRMT11 AL096711.2 chr6 126272727 126272727 chr6 126986003 126986003 TCGA-KK-A8IK DEL 7 28 * * chr6 127029260 127029267 chr1 196492022 196492029 TCGA-KK-A8IK BND 25 23 * KCNT2 chr6 143357852 143357852 chr6 144347637 144347641 TCGA-KK-A8IK INV 49 35 * UTRN chr6 143358062 143358062 chr6 144347637 144347641 TCGA-KK-A8IK DUP 35 3 * UTRN chr6 143358220 143358220 chr6 144347350 144347356 TCGA-KK-A8IK DUP 48 2 * UTRN chr6 143362764 143362764 chr17 76894529 76894529 TCGA-KK-A8IK BND 46 7 * MGAT5B chr6 143362764 143362764 chr6 144348301 144348301 TCGA-KK-A8IK DUP 23 34 * UTRN chr6 144347350 144347356 chr17 76297958 76297958 TCGA-KK-A8IK BND 12 17 UTRN QRICH2 chr6 149593491 149593491 chr6 153060827 153060827 TCGA-KK-A8IK DUP 47 20 RPS18P9 RGS17 chr6 153563939 153563939 chr6 153579572 153579572 TCGA-KK-A8IK DEL 36 41 * * chr6 160206719 160206719 chr6 160217065 160217065 TCGA-KK-A8IK DEL 26 49 SLC22A2 SLC22A2 chr6 162591008 162591008 chr6 164873065 164873065 TCGA-KK-A8IK DEL 8 13 PRKN * chr6 167169469 167169469 chr6 167388746 167388746 TCGA-KK-A8IK INV 7 16 TCP10L2 * chr6 34089316 34089316 chr6 37811111 37811111 TCGA-KK-A8IK DUP 39 15 GRM4 * chr6 62232260 62232260 chr6 87358334 87358334 TCGA-KK-A8IK DEL 37 38 KHDRBS2 SMIM8 chr6 62876690 62876690 chr6 63364332 63364332 TCGA-KK-A8IK DEL 41 25 * * chr6 65466093 65466093 chr6 65652790 65652790 TCGA-KK-A8IK INS 9 37 EYS EYS chr6 65595767 65595767 chr6 65926746 65926746 TCGA-KK-A8IK INS 39 22 EYS * chr6 68405478 68405478 chr6 126006452 126006452 TCGA-KK-A8IK DEL 50 29 * TRMT11 chr6 74814767 74814767 chr6 77589638 77589638 TCGA-KK-A8IK DUP 43 27 * * chr6 76278428 76278428 chr11 21977512 21977512 TCGA-KK-A8IK BND 39 30 * ANO5 chr6 77697760 77697760 chr6 77752299 77752299 TCGA-KK-A8IK DEL 3 8 MEI4 MEI4 chr6 79877576 79877577 chr6 79978413 79978413 TCGA-KK-A8IK DEL 36 26 * * chr6 80022689 80022691 chr1 192961402 192961404 TCGA-KK-A8IK BND 30 9 TTK * chr6 80609776 80609776 chr6 81340109 81340109 TCGA-KK-A8IK INS 31 11 * * chr6 85068966 85068966 chr11 23105161 23105161 TCGA-KK-A8IK BND 39 36 * * chr6 96022698 96022703 chr18 64507188 64507193 TCGA-KK-A8IK BND 4 48 FUT9 * chr6 96052475 96052476 chr18 65456132 65456133 TCGA-KK-A8IK BND 26 35 FUT9 * chr7 103182092 103182092 chr7 106160813 106160813 TCGA-KK-A8IK DUP 38 32 DPY19L2P2 * chr7 12418535 12418535 chr7 13733252 13733252 TCGA-KK-A8IK DEL 33 11 * AC011287.1 chr7 15114529 15114529 chr7 15133679 15133679 TCGA-KK-A8IK DEL 28 28 * * chr7 153507348 153507348 chr7 154933728 154933728 TCGA-KK-A8IK DEL 39 25 * PAXIP1-AS2 chr7 18491859 18491859 chr7 21402133 21402133 TCGA-KK-A8IK DEL 7 19 HDAC9 AC005094.1 chr7 19114367 19114367 chr10 8713208 8713208 TCGA-KK-A8IK BND 36 14 TWIST1 * chr7 20228738 20228738 chr11 61449181 61449181 TCGA-KK-A8IK BND 38 24 * AP003108.2 chr7 31460589 31460589 chr9 28246566 28246566 TCGA-KK-A8IK BND 6 9 * LINGO2 chr7 33511251 33511251 chr9 28030772 28030772 TCGA-KK-A8IK BND 13 44 BBS9 LINGO2 chr7 41181878 41181881 chr5 153250391 153250394 TCGA-KK-A8IK BND 21 11 * * chr7 41736212 41736215 chr5 153116019 153116022 TCGA-KK-A8IK BND 38 34 INHBA-AS1 LINC01470 chr7 41767400 41767402 chr5 152695069 152695071 TCGA-KK-A8IK BND 24 6 INHBA-AS1 LINC01470 chr7 47769406 47769406 chr7 47784577 47784577 TCGA-KK-A8IK DEL 9 16 PKD1L1 PKD1L1 chr7 49208116 49208116 chr7 49392835 49392835 TCGA-KK-A8IK DEL 1 49 * * chr7 49445902 49445902 chr7 49469404 49469404 TCGA-KK-A8IK DEL 19 26 * * chr7 49838546 49838546 chr7 49872410 49872410 TCGA-KK-A8IK DEL 2 26 VWC2 VWC2 chr7 51073578 51073578 chr7 51141325 51141325 TCGA-KK-A8IK DEL 26 23 COBL COBL chr7 51178402 51178402 chr7 56800762 56800762 TCGA-KK-A8IK DEL 47 34 COBL * chr7 52433562 52433562 chr7 57857924 57857924 TCGA-KK-A8IK INS 36 20 * * chr7 54457863 54457863 chr7 54481410 54481410 TCGA-KK-A8IK DEL 18 26 * * chr7 83346363 83346363 chr7 85633866 85633866 TCGA-KK-A8IK DEL 13 14 * * chr7 84215296 84215296 chr7 125108113 125108113 TCGA-KK-A8IK INS 14 10 SEMA3A POT1-AS1 chr8 105169182 105169182 chr8 105169496 105169511 TCGA-KK-A8IK DEL 6 36 ZFPM2 ZFPM2 chr8 116074542 116074542 chr8 116779011 116779011 TCGA-KK-A8IK DEL 17 16 LINC00536 UTP23 chr8 116768226 116768226 chr8 118415516 118415516 TCGA-KK-A8IK DEL 33 37 EIF3H SAMD12 chr8 117403520 117403522 chr6 100998265 100998268 TCGA-KK-A8IK BND 11 47 * * chr8 127072114 127072114 chr8 127198110 127198110 TCGA-KK-A8IK DUP 37 22 PCAT1 PCAT1 chr8 137761352 137761352 chr8 137831611 137831611 TCGA-KK-A8IK DEL 37 24 * AC046195.1 chr8 145075469 145075469 chrX 156019850 156019850 TCGA-KK-A8IK BND 5 25 * AJ271736.1 chr8 48343387 48343387 chr8 63412783 63412783 TCGA-KK-A8IK INS 40 42 * AC011124.1 chr8 80190605 80190605 chr8 82642026 82642026 TCGA-KK-A8IK DUP 32 29 TPD52 AC060765.1 chr8 89085883 89085883 chr8 89135728 89135728 TCGA-KK-A8IK DEL 15 2 * * chr9 10593509 10593519 chr1 186357800 186357811 TCGA-KK-A8IK BND 48 1 PTPRD TPR chr9 11255062 11255064 chr1 186418880 186418882 TCGA-KK-A8IK BND 48 7 * ODR4 chr9 113912102 113912102 chr9 116661146 116661146 TCGA-KK-A8IK DUP 13 9 ZNF618 ASTN2 chr9 24247499 24247499 chr9 24266108 24266108 TCGA-KK-A8IK DEL 24 27 * * chr9 25217533 25217533 chr13 107540968 107540968 TCGA-KK-A8IK BND 21 38 * FAM155A chr9 26073109 26073109 chr9 26158149 26158149 TCGA-KK-A8IK DEL 36 38 AL353753.1 * chr9 26130808 26130808 chr9 26229252 26229252 TCGA-KK-A8IK INS 46 42 * * chr9 26164452 26164452 chr9 26229320 26229320 TCGA-KK-A8IK DEL 41 23 * * chr9 26422188 26422188 chr11 90636406 90636406 TCGA-KK-A8IK BND 38 10 * DISC1FP1 chr9 27529244 27529244 chr9 29691477 29691477 TCGA-KK-A8IK DEL 20 11 MOB3B * chr9 28030772 28030772 chr7 33511251 33511251 TCGA-KK-A8IK BND 27 24 LINGO2 BBS9 chr9 28118298 28118298 chr7 32341805 32341805 TCGA-KK-A8IK BND 38 41 LINGO2 * chr9 29659777 29659777 chr17 9956271 9956271 TCGA-KK-A8IK BND 4 2 * GAS7 chr9 30678340 30678340 chr9 73408068 73408068 TCGA-KK-A8IK INV 43 45 * * chr9 3564100 3564100 chr9 3729689 3729689 TCGA-KK-A8IK DUP 20 25 RFX3-AS1 * chr9 62806331 62806331 chr9 62814083 62814084 TCGA-KK-A8IK INS 16 30 LINC01410 * chr9 69014460 69014460 chr9 69015714 69015714 TCGA-KK-A8IK INV 19 18 PRKACG * chr9 80275448 80275464 chr9 126618504 126618504 TCGA-KK-A8IK INV 47 18 * LMX1B chr9 80275448 80275464 chr17 19554148 19554148 TCGA-KK-A8IK BND 3 27 * SLC47A1 chr9 80667323 80667323 chr9 82181382 82181382 TCGA-KK-A8IK INV 11 4 * AL162726.3 chrX 36928983 36928983 chrX 36931860 36931860 TCGA-KK-A8IK DEL 32 24 * * chrX 64590466 64590466 chrX 64592360 64592360 TCGA-KK-A8IK DEL 43 23 * * chrX 66800183 66800183 chrX 66998706 66998706 TCGA-KK-A8IK DUP 21 38 * * chrX 66831691 66831691 chrX 67037464 67037464 TCGA-KK-A8IK DUP 20 11 * * chrX 95233985 95233985 chrX 95234215 95234215 TCGA-KK-A8IK DEL 3 21 * * chrY 11824616 11824616 chrY 13086678 13086678 TCGA-KK-A8IK INS 31 8 * SFPQP1 chrY 11905938 11905938 chrY 11906585 11906585 TCGA-KK-A8IK INS 8 11 * * chr10 115534502 115534502 chr10 115585575 115585575 TCGA-HC-8262 DUP 6 47 ATRNL1 ATRNL1 chr10 116555128 116555128 chr10 116589780 116589780 TCGA-HC-8262 DUP 21 26 PNLIP PNLIPRP1 chr10 131120322 131120322 chr10 131123010 131123010 TCGA-HC-8262 INV 45 10 TCERG1L TCERG1L chr10 131121019 131121019 chr11 11928426 11928437 TCGA-HC-8262 BND 4 25 TCERG1L USP47 chr10 131123460 131123460 chr21 43423504 43423504 TCGA-HC-8262 BND 6 32 TCERG1L SIK1 chr10 26020048 26020048 chr10 26311821 26311821 TCGA-HC-8262 DEL 39 2 MYO3A * chr10 47705093 47705093 chr13 21998031 21998031 TCGA-HC-8262 BND 37 30 SHLD2P3 * chr10 49104754 49104754 chr10 49147392 49147392 TCGA-HC-8262 DUP 29 34 VSTM4 FAM170B-AS1 chr10 50705065 50705065 chr10 57911899 57911899 TCGA-HC-8262 DUP 47 34 * * chr10 52064526 52064526 chr10 87931070 87931070 TCGA-HC-8262 DEL 43 25 PRKG1 PTEN chr10 55035879 55035879 chr10 55044505 55044505 TCGA-HC-8262 DEL 50 29 PCDH15 PCDH15 chr10 56322392 56322392 chr13 28737092 28737092 TCGA-HC-8262 BND 17 9 * * chr10 56500701 56500701 chr10 61265918 61265918 TCGA-HC-8262 DUP 22 13 * * chr10 56508583 56508583 chr10 56509670 56509670 TCGA-HC-8262 INV 49 30 * * chr10 60667589 60667589 chr10 67273831 67273831 TCGA-HC-8262 DEL 31 24 ANK3 CTNNA3 chr10 65350036 65350036 chr13 28623282 28623282 TCGA-HC-8262 BND 16 25 * * chr10 68950939 68950939 chr22 29048711 29048711 TCGA-HC-8262 BND 19 3 * ZNRF3 chr10 74461758 74461758 chr10 74463724 74463724 TCGA-HC-8262 INV 40 18 ADK ADK chr10 74843818 74843818 chr10 74903182 74903182 TCGA-HC-8262 DUP 6 24 KAT6B KAT6B chr10 74987296 74987296 chr10 75058996 75058996 TCGA-HC-8262 INV 5 48 KAT6B DUSP29 chr10 78269973 78269973 chr10 78270500 78270500 TCGA-HC-8262 INV 46 44 AC012560.1 AC012560.1 chr10 78363411 78363411 chr10 78404687 78404687 TCGA-HC-8262 DUP 12 47 AC012560.1 AC012560.1 chr10 79119857 79119857 chr10 79119948 79119948 TCGA-HC-8262 INV 34 42 ZMIZ1 ZMIZ1 chr10 80739001 80739001 chr10 80790188 80790188 TCGA-HC-8262 DUP 32 39 * * chr10 84414126 84414126 chr10 84450713 84450713 TCGA-HC-8262 DUP 3 15 CCSER2 CCSER2 chr10 84808372 84808372 chr13 39588712 39588712 TCGA-HC-8262 BND 50 49 * LHFPL6 chr10 87870500 87870500 chr10 99239281 99239281 TCGA-HC-8262 INV 6 45 PTEN * chr10 99239754 99239754 chr10 99279979 99279979 TCGA-HC-8262 DUP 31 40 * * chr11 114482363 114482363 chr11 114525955 114525955 TCGA-HC-8262 DUP 11 45 * NXPE1 chr11 11923177 11923177 chr13 22805615 22805626 TCGA-HC-8262 BND 10 5 USP47 * chr11 11923243 11923243 chr11 13153614 13153614 TCGA-HC-8262 DEL 42 23 USP47 * chr11 11928426 11928437 chr11 13153698 13153698 TCGA-HC-8262 INV 16 49 USP47 * chr11 120420349 120420349 chr11 120464964 120464964 TCGA-HC-8262 DUP 48 42 ARHGEF12 ARHGEF12 chr11 126653196 126653196 chr11 126653544 126653544 TCGA-HC-8262 INV 44 3 KIRREL3 KIRREL3 chr11 1861676 1861690 chr11 1894007 1894007 TCGA-HC-8262 DUP 6 20 LSP1 * chr11 4947056 4947056 chr11 4955603 4955603 TCGA-HC-8262 INS 48 20 MMP26 MMP26 chr11 5752811 5752811 chr11 5825572 5825572 TCGA-HC-8262 DUP 36 7 TRIM5 TRIM5 chr11 65064787 65064787 chr12 102803276 102803276 TCGA-HC-8262 BND 50 40 * * chr11 93136275 93136275 chr11 93143244 93143244 TCGA-HC-8262 INS 5 29 * * chr11 93420242 93420242 chr11 93428253 93428253 TCGA-HC-8262 INS 34 18 DEUP1 DEUP1 chr12 102477958 102477958 chr12 102523494 102523494 TCGA-HC-8262 DUP 19 44 IGF1 * chr12 102803321 102803321 chr22 41100922 41100922 TCGA-HC-8262 BND 28 50 * EP300 chr12 108164926 108164926 chr12 108202968 108202968 TCGA-HC-8262 DUP 47 7 WSCD2 WSCD2 chr12 11037154 11037154 chr12 11097914 11097914 TCGA-HC-8262 DUP 34 14 PRH1 PRH1 chr12 117412860 117412860 chr6 115737513 115737513 TCGA-HC-8262 BND 50 4 NOS1 * chr12 12710233 12710233 chr12 19288134 19288134 TCGA-HC-8262 DEL 17 11 * PLEKHA5 chr12 127770890 127770890 chr12 127802708 127802708 TCGA-HC-8262 DUP 43 44 * * chr12 14371381 14371381 chr12 29913275 29913275 TCGA-HC-8262 INV 39 23 ATF7IP * chr12 15185765 15185765 chr12 16055981 16055981 TCGA-HC-8262 INV 31 47 RERG * chr12 15188376 15188376 chr12 15212828 15212828 TCGA-HC-8262 INV 1 21 RERG RERG chr12 15210046 15210046 chr12 21293234 21293234 TCGA-HC-8262 INV 24 37 RERG SLCO1A2 chr12 15403879 15403879 chr12 15404234 15404234 TCGA-HC-8262 INV 35 17 PTPRO PTPRO chr12 16036990 16036990 chr12 22263033 22263033 TCGA-HC-8262 DUP 32 50 DERA ST8SIA1 chr12 16040964 16040964 chr12 16058264 16058264 TCGA-HC-8262 DEL 1 47 * * chr12 16088146 16088146 chr12 16088486 16088486 TCGA-HC-8262 INV 29 50 * * chr12 16578613 16578635 chr12 17798857 17798857 TCGA-HC-8262 DUP 2 5 MGST1 * chr12 16578613 16578635 chr12 19301182 19301182 TCGA-HC-8262 DUP 35 27 MGST1 PLEKHA5 chr12 16891670 16891670 chr12 16891937 16891937 TCGA-HC-8262 INV 26 28 * * chr12 17632515 17632515 chr12 17632717 17632717 TCGA-HC-8262 INV 32 35 * * chr12 17733023 17733023 chr12 19685719 19685719 TCGA-HC-8262 INV 10 16 * AEBP2 chr12 19240917 19240917 chr12 19688935 19688935 TCGA-HC-8262 INV 45 27 PLEKHA5 AEBP2 chr12 19770917 19770917 chr12 19770957 19770957 TCGA-HC-8262 INV 20 24 * * chr12 20124238 20124257 chr12 20124238 20124257 TCGA-HC-8262 INV 21 10 LINC02468 LINC02468 chr12 20245687 20245687 chr12 20245870 20245870 TCGA-HC-8262 INV 2 21 * * chr12 20718492 20718492 chr12 20718681 20718681 TCGA-HC-8262 INV 8 7 SLCO1C1 SLCO1C1 chr12 20955145 20955145 chr12 20955501 20955501 TCGA-HC-8262 INV 42 40 SLCO1B3-SLCO1B7 SLCO1B3-SLCO1B7 chr12 20991621 20991621 chr12 20991779 20991779 TCGA-HC-8262 INV 47 29 SLCO1B3-SLCO1B7 SLCO1B3-SLCO1B7 chr12 21111536 21111536 chr12 21111582 21111582 TCGA-HC-8262 INV 8 20 AC022335.1 AC022335.1 chr12 21453113 21453113 chr12 21453398 21453398 TCGA-HC-8262 INV 41 13 PYROXD1 PYROXD1 chr12 21933900 21933900 chr12 21934086 21934086 TCGA-HC-8262 INV 18 32 ABCC9 ABCC9 chr12 22053849 22053849 chr12 22054259 22054259 TCGA-HC-8262 INV 24 7 CMAS CMAS chr12 22198183 22198183 chr12 22841906 22841906 TCGA-HC-8262 DUP 12 17 ST8SIA1 AC084816.1 chr12 22216258 22216258 chr12 22216477 22216477 TCGA-HC-8262 INV 10 35 ST8SIA1 ST8SIA1 chr12 22805734 22805734 chr12 22805761 22805761 TCGA-HC-8262 INV 4 45 AC084816.1 AC084816.1 chr12 23068282 23068282 chr12 23068312 23068312 TCGA-HC-8262 INV 30 24 AC084816.1 AC084816.1 chr12 23293714 23293714 chr12 23294099 23294099 TCGA-HC-8262 INV 24 36 * * chr12 23813918 23813918 chr12 23814152 23814152 TCGA-HC-8262 INV 14 37 SOX5 SOX5 chr12 24044815 24044815 chr12 24094129 24094129 TCGA-HC-8262 DUP 29 18 SOX5 SOX5 chr12 24476940 24476940 chr12 24477404 24477404 TCGA-HC-8262 INV 12 34 SOX5 SOX5 chr12 24630302 24630302 chr12 24630411 24630411 TCGA-HC-8262 INV 46 24 * * chr12 26631885 26631885 chr12 26632109 26632109 TCGA-HC-8262 INV 8 28 ITPR2 ITPR2 chr12 27338020 27338020 chr12 27338154 27338154 TCGA-HC-8262 INV 38 36 ARNTL2 ARNTL2 chr12 29360004 29360004 chr12 29360158 29360158 TCGA-HC-8262 INV 16 34 ERGIC2 ERGIC2 chr12 30397959 30397959 chr12 30397997 30397997 TCGA-HC-8262 INV 10 21 * * chr12 33594869 33594869 chr12 34106231 34106231 TCGA-HC-8262 DEL 39 35 * * chr12 38378532 38378532 chr12 38421867 38421867 TCGA-HC-8262 DUP 8 17 * * chr12 44041167 44041167 chr12 44087536 44087536 TCGA-HC-8262 DUP 31 12 TMEM117 TMEM117 chr12 46304728 46304728 chr12 79535535 79535535 TCGA-HC-8262 DEL 35 43 * * chr12 52849251 52849251 chr12 52897016 52897016 TCGA-HC-8262 DUP 1 29 KRT78 * chr12 77297775 77297775 chr12 77346523 77346523 TCGA-HC-8262 DUP 37 29 * NAV3 chr12 87913024 87913024 chr12 87969796 87969796 TCGA-HC-8262 DUP 36 50 * * chr13 114071961 114071961 chr13 114102268 114102268 TCGA-HC-8262 DUP 50 37 RASA3 RASA3 chr13 21525867 21525867 chr13 22805615 22805626 TCGA-HC-8262 INV 47 27 MICU2 * chr13 22932957 22932957 chr13 24355452 24355452 TCGA-HC-8262 INV 5 48 * * chr13 26363739 26363739 chr13 34344469 34344469 TCGA-HC-8262 INV 47 7 CDK8 * chr13 33931648 33931648 chr2 241665433 241665433 TCGA-HC-8262 BND 6 30 RFC3 ATG4B chr13 34306952 34306952 chr13 34342154 34342154 TCGA-HC-8262 DUP 8 29 * * chr13 35041214 35041214 chr13 35073461 35073461 TCGA-HC-8262 DUP 7 27 NBEA NBEA chr13 38385495 38385495 chr13 38385621 38385621 TCGA-HC-8262 INV 49 31 * * chr13 44077948 44077948 chr13 45013968 45013968 TCGA-HC-8262 DUP 8 6 * GPALPP1 chr13 44077948 44077948 chr13 62410858 62410858 TCGA-HC-8262 INV 8 23 * * chr13 44140426 44140426 chr13 44140530 44140530 TCGA-HC-8262 INV 41 44 SMIM2-AS1 SMIM2-AS1 chr13 44173314 44173314 chr13 44205766 44205766 TCGA-HC-8262 DUP 10 46 SMIM2-AS1 SMIM2-AS1 chr13 44321470 44321470 chr13 44321525 44321525 TCGA-HC-8262 INV 24 11 * * chr13 44637457 44637457 chr13 44637926 44637926 TCGA-HC-8262 INV 41 30 * * chr13 44670798 44670798 chr13 44710431 44710431 TCGA-HC-8262 DUP 7 49 LINC00407 AL356515.1 chr13 44856524 44856524 chr13 55860473 55860473 TCGA-HC-8262 DUP 39 24 * * chr13 45014204 45014204 chr13 62431395 62431395 TCGA-HC-8262 INV 26 15 GPALPP1 * chr13 54924572 54924572 chr13 54927150 54927150 TCGA-HC-8262 DEL 38 29 * * chr13 55797125 55797133 chrX 67670230 67670230 TCGA-HC-8262 BND 14 49 * AR chr13 68483729 68483729 chr13 68516319 68516319 TCGA-HC-8262 DUP 42 34 * * chr13 92538360 92538360 chr13 92580092 92580092 TCGA-HC-8262 DUP 42 49 GPC5 GPC5 chr14 105564088 105564088 chr14 105684257 105684277 TCGA-HC-8262 DUP 47 35 * * chr14 40140411 40140411 chr14 40148818 40148818 TCGA-HC-8262 INS 25 36 * * chr14 85301417 85301417 chr14 85304754 85304754 TCGA-HC-8262 DEL 36 2 * * chr15 48828225 48828225 chr15 48867571 48867571 TCGA-HC-8262 DUP 11 50 SHC4 SHC4 chr15 70071879 70071879 chr15 70102685 70102685 TCGA-HC-8262 DUP 43 46 TLE3 * chr16 16463283 16463283 chr16 18248654 18248654 TCGA-HC-8262 DUP 39 24 * * chr16 2171475 2171475 chr16 2208871 2208871 TCGA-HC-8262 DUP 43 36 TRAF7 MLST8 chr16 32317511 32317511 chr20 53862693 53862693 TCGA-HC-8262 BND 28 31 * * chr16 62498982 62498982 chr16 62550640 62550640 TCGA-HC-8262 DEL 15 1 * * chr16 72582585 72582585 chr16 72697078 72697078 TCGA-HC-8262 DUP 8 16 LINC01572 AC004943.2 chr16 86419194 86419200 chr21 31784913 31784938 TCGA-HC-8262 BND 26 23 * * chr17 30319004 30319004 chr17 30350853 30350853 TCGA-HC-8262 DUP 15 29 TMIGD1 * chr17 30596803 30596811 chr17 35108308 35108308 TCGA-HC-8262 INV 12 22 AC005562.1 AC004223.3 chr17 59170117 59170117 chr17 59306416 59306416 TCGA-HC-8262 DEL 39 37 PRR11 * chr17 67858091 67858091 chr17 68237932 68237932 TCGA-HC-8262 DUP 40 9 BPTF * chr17 7473720 7473720 chr17 8099747 8099747 TCGA-HC-8262 DEL 15 27 ZBTB4 ALOXE3 chr17 7653298 7653298 chr17 8047243 8047243 TCGA-HC-8262 DEL 10 17 ATP1B2 ALOX15B chr17 77858533 77858533 chr19 33872829 33872829 TCGA-HC-8262 BND 9 4 * * chr17 81532333 81532333 chr20 63443360 63443360 TCGA-HC-8262 BND 24 25 FSCN2 KCNQ2 chr18 24421348 24421348 chr22 28669931 28669932 TCGA-HC-8262 BND 9 39 * TTC28 chr18 41783288 41783288 chr18 41823990 41823990 TCGA-HC-8262 DUP 28 5 * * chr19 19952463 19952463 chr19 19996141 19996141 TCGA-HC-8262 DUP 29 38 ZNF93 * chr19 3042052 3042052 chr19 52399318 52399318 TCGA-HC-8262 INV 6 23 TLE2 ZNF528 chr19 3715446 3715446 chr19 52398640 52398640 TCGA-HC-8262 DUP 48 6 TJP3 ZNF528-AS1 chr19 45646815 45646815 chr3 147775207 147775207 TCGA-HC-8262 BND 41 36 EML2 * chr19 47724528 47724528 chr19 47763383 47763383 TCGA-HC-8262 DUP 46 14 AC010519.1 NOP53-AS1 chr19 52399130 52399130 chr22 41100262 41100262 TCGA-HC-8262 BND 34 12 ZNF528-AS1 EP300 chr19 52537946 52537946 chr19 52577863 52577863 TCGA-HC-8262 DUP 49 21 ZNF808 ZNF701 chr1 100436713 100436713 chr1 178252350 178252350 TCGA-HC-8262 DEL 19 36 CDC14A RASAL2 chr1 100485391 100485391 chr1 179695957 179695957 TCGA-HC-8262 DUP 4 25 CDC14A * chr1 100488565 100488565 chr20 46717424 46717424 TCGA-HC-8262 BND 43 29 CDC14A SLC2A10 chr1 161640155 161640155 chr1 241520067 241520067 TCGA-HC-8262 INV 12 23 * FH chr1 161652771 161652771 chr1 179697106 179697106 TCGA-HC-8262 INV 23 25 * * chr1 169233781 169233781 chr1 169302743 169302743 TCGA-HC-8262 DUP 12 27 NME7 NME7 chr1 172050111 172050111 chr20 57331843 57331843 TCGA-HC-8262 BND 23 41 DNM3 SPO11 chr1 177931721 177931721 chr1 177942512 177942512 TCGA-HC-8262 INV 48 41 SEC16B SEC16B chr1 177931771 177931771 chr1 241519986 241519986 TCGA-HC-8262 INV 35 19 SEC16B FH chr1 178243183 178243183 chr20 46725996 46725996 TCGA-HC-8262 BND 27 27 RASAL2 SLC2A10 chr1 187004116 187004116 chr1 187007447 187007447 TCGA-HC-8262 DEL 37 41 * * chr1 187920909 187920909 chr1 191924449 191924449 TCGA-HC-8262 INS 26 19 * LINC02770 chr1 190363963 190363963 chr1 190404068 190404068 TCGA-HC-8262 DUP 1 4 BRINP3 BRINP3 chr1 201347260 201347260 chr4 44456516 44456516 TCGA-HC-8262 BND 3 7 * * chr1 205676788 205676788 chr7 13940168 13940168 TCGA-HC-8262 BND 33 41 SLC45A3 ETV1 chr1 20625977 20625977 chr16 22818919 22818919 TCGA-HC-8262 BND 27 3 * HS3ST2 chr1 217606453 217606453 chr1 217653209 217653209 TCGA-HC-8262 DUP 24 21 GPATCH2 SPATA17 chr1 229676790 229676790 chr1 229685511 229685511 TCGA-HC-8262 INS 44 38 * * chr1 233149972 233149972 chr1 233198741 233198741 TCGA-HC-8262 DUP 50 2 PCNX2 PCNX2 chr1 26031034 26031034 chr12 102807930 102807930 TCGA-HC-8262 BND 22 49 EXTL1 * chr1 31049092 31049092 chr12 105509290 105509290 TCGA-HC-8262 BND 15 7 PUM1 * chr1 39817592 39817592 chr1 47076482 47076482 TCGA-HC-8262 DEL 35 1 LINC02811 CYP4Z1 chr1 43961718 43961718 chr7 145495984 145495984 TCGA-HC-8262 BND 47 37 IPO13 * chr1 44560130 44560130 chr1 46451279 46451279 TCGA-HC-8262 DUP 35 19 RNF220 FAAHP1 chr1 44561032 44561032 chr1 58316595 58316595 TCGA-HC-8262 INV 36 4 RNF220 DAB1 chr1 45495533 45495533 chr1 51451598 51451598 TCGA-HC-8262 DEL 32 40 CCDC163 EPS15 chr1 46450677 46450677 chr1 58316386 58316386 TCGA-HC-8262 INV 30 46 FAAHP1 DAB1 chr1 52319496 52319496 chr1 59326809 59326809 TCGA-HC-8262 INV 26 50 ZFYVE9 FGGY chr1 57191622 57191622 chr11 57976390 57976390 TCGA-HC-8262 BND 17 49 DAB1 * chr1 59245798 59245798 chr1 59413763 59413763 TCGA-HC-8262 DUP 34 22 HSD52 FGGY chr1 65416612 65416612 chr8 61488457 61488457 TCGA-HC-8262 BND 10 40 * CLVS1 chr1 72289971 72289971 chr1 72298391 72298391 TCGA-HC-8262 INS 43 37 * * chr1 72741477 72741477 chr1 72779232 72779232 TCGA-HC-8262 DUP 23 36 * AL583808.1 chr1 74397941 74397941 chr1 74401927 74401927 TCGA-HC-8262 DEL 6 46 TNNI3K TNNI3K chr1 80938927 80938927 chr1 80945771 80945771 TCGA-HC-8262 INS 36 42 * * chr1 81614512 81614512 chr1 81650149 81650149 TCGA-HC-8262 DUP 13 18 ADGRL2 ADGRL2 chr1 84051721 84051721 chr1 84058966 84058966 TCGA-HC-8262 INS 30 35 AC104454.2 AC104454.2 chr1 84587028 84587028 chr1 84627961 84627961 TCGA-HC-8262 DUP 48 40 * * chr1 94247658 94247658 chr1 94282392 94282392 TCGA-HC-8262 DUP 28 4 ARHGAP29 ARHGAP29-AS1 chr1 99804467 99804467 chr1 100495117 100495117 TCGA-HC-8262 DEL 21 36 * CDC14A chr1 99806270 99806270 chr1 172479028 172479028 TCGA-HC-8262 DEL 43 5 * * chr1 99806294 99806294 chr20 46717046 46717046 TCGA-HC-8262 BND 2 8 * SLC2A10 chr1 99950018 99950018 chr1 172081862 172081862 TCGA-HC-8262 INV 27 49 * DNM3 chr20 1552381 1552381 chr20 1617183 1617183 TCGA-HC-8262 DUP 46 1 AL049634.1 SIRPB1 chr20 36432390 36432390 chr20 36466091 36466091 TCGA-HC-8262 DUP 40 47 DLGAP4 DLGAP4 chr20 47803370 47803370 chr20 47896022 47896022 TCGA-HC-8262 DUP 40 6 * * chr20 51066243 51066243 chr20 51090285 51090285 TCGA-HC-8262 DEL 40 34 * * chr20 56345273 56345273 chr20 57368397 57368397 TCGA-HC-8262 DEL 22 35 * RAE1 chr20 57993808 57993808 chr20 57993949 57993949 TCGA-HC-8262 INV 41 44 * * chr21 17486090 17486090 chr21 17533414 17533414 TCGA-HC-8262 DUP 37 47 * CXADR chr21 38449570 38449570 chr21 41500040 41500040 TCGA-HC-8262 DEL 39 6 ERG TMPRSS2 chr21 38542693 38542693 chr21 41497030 41497030 TCGA-HC-8262 DEL 49 14 ERG TMPRSS2 chr21 38706349 38706349 chr21 41328887 41328887 TCGA-HC-8262 DEL 29 16 * FAM3B chr21 44590588 44590588 chr21 44637073 44637073 TCGA-HC-8262 DUP 39 42 TSPEAR TSPEAR chr22 40919083 40919083 chr22 40962759 40962759 TCGA-HC-8262 DUP 13 19 XPNPEP3 RBX1 chr2 11129578 11129578 chr2 233978769 233978769 TCGA-HC-8262 INV 17 48 AC062028.1 TRPM8 chr2 11840283 11840283 chr2 20248427 20248427 TCGA-HC-8262 INV 8 27 * * chr2 12387853 12387853 chr2 12423033 12423033 TCGA-HC-8262 DUP 41 37 MIR3681HG MIR3681HG chr2 12417346 12417346 chr4 174008497 174008497 TCGA-HC-8262 BND 30 1 MIR3681HG * chr2 12417556 12417556 chr4 169615834 169615834 TCGA-HC-8262 BND 25 14 MIR3681HG CLCN3 chr2 125685627 125685627 chr2 125694254 125694273 TCGA-HC-8262 INS 29 18 * * chr2 12848036 12848036 chr4 80112717 80112717 TCGA-HC-8262 BND 24 15 * ANTXR2 chr2 148856830 148856830 chr2 148904079 148904079 TCGA-HC-8262 DUP 3 4 * KIF5C chr2 153976013 153976013 chr2 154014863 154014863 TCGA-HC-8262 DUP 31 47 GALNT13 GALNT13 chr2 155656796 155656796 chr2 155704890 155704890 TCGA-HC-8262 DUP 9 20 * * chr2 177087198 177087198 chr4 85018115 85018115 TCGA-HC-8262 BND 43 14 AC074286.1 * chr2 177163080 177163080 chr4 79748898 79748898 TCGA-HC-8262 BND 31 27 AC074286.1 * chr2 182464075 182464075 chr7 121900432 121900432 TCGA-HC-8262 BND 24 7 PDE1A PTPRZ1 chr2 194357888 194357888 chr2 194391036 194391036 TCGA-HC-8262 DUP 22 49 LINC01821 LINC01821 chr2 197400595 197400595 chr2 197444630 197444630 TCGA-HC-8262 DUP 9 42 SF3B1 * chr2 20248799 20248799 chr4 85011518 85011518 TCGA-HC-8262 BND 39 44 PUM2 * chr2 20278028 20278028 chr5 180834314 180834314 TCGA-HC-8262 BND 41 1 PUM2 LINC00847 chr2 20316157 20316157 chr4 87668007 87668007 TCGA-HC-8262 BND 5 18 PUM2 AC093895.1 chr2 20352899 20352899 chr2 25535449 25535449 TCGA-HC-8262 DUP 17 22 PUM2 DTNB chr2 20437031 20437031 chr4 89084770 89084770 TCGA-HC-8262 BND 14 36 * FAM13A chr2 20449111 20449111 chr16 74035056 74035056 TCGA-HC-8262 BND 26 47 RHOB AC138627.1 chr2 20449559 20449559 chr4 87680188 87680188 TCGA-HC-8262 BND 36 1 AC023137.1 AC093895.1 chr2 206995978 206995978 chr2 207004322 207004322 TCGA-HC-8262 INS 12 28 * * chr2 207539035 207539035 chr2 207582485 207582485 TCGA-HC-8262 DUP 33 28 CREB1 CREB1 chr2 209180994 209180994 chr2 209217258 209217258 TCGA-HC-8262 INV 7 20 MEAF6P1 * chr2 216657218 216657218 chr2 216687650 216687650 TCGA-HC-8262 DUP 36 26 IGFBP2 IGFBP5 chr2 231005043 231005043 chrX 2383423 2383423 TCGA-HC-8262 BND 3 40 SPATA3 DHRSX chr2 231986901 231986901 chr2 232021549 232021549 TCGA-HC-8262 DUP 47 27 DIS3L2 DIS3L2 chr2 24090804 24090804 chr4 89108848 89108848 TCGA-HC-8262 BND 26 43 FAM228B FAM13A chr2 24102120 24102120 chr16 74008562 74008562 TCGA-HC-8262 BND 44 25 FAM228B AC138627.1 chr2 241403194 241403194 chr2 241943169 241943169 TCGA-HC-8262 DEL 5 5 FARP2 LINC01237 chr2 241990547 241990562 chr9 134685443 134685443 TCGA-HC-8262 BND 42 4 LINC01237 COL5A1 chr2 25402470 25402470 chr4 80186217 80186217 TCGA-HC-8262 BND 43 4 DTNB PRDM8 chr2 30215995 30215995 chr2 30238080 30238080 TCGA-HC-8262 DEL 19 46 * LBH chr2 30223014 30223014 chr2 177133003 177133003 TCGA-HC-8262 INV 41 29 * AC074286.1 chr2 30243326 30243326 chr16 74045084 74045084 TCGA-HC-8262 BND 9 8 LBH AC138627.1 chr2 43515215 43515215 chrX 66699975 66699993 TCGA-HC-8262 BND 16 34 THADA * chr2 65605720 65605720 chr2 65647098 65647098 TCGA-HC-8262 DUP 40 23 AC007389.1 AC007389.1 chr2 85191043 85191043 chr11 19859184 19859184 TCGA-HC-8262 BND 18 36 TCF7L1 NAV2 chr2 95537195 95537195 chr2 95573128 95573128 TCGA-HC-8262 DUP 24 5 AC009237.8 * chr3 109587993 109587993 chr3 109613071 109613071 TCGA-HC-8262 DEL 2 47 * * chr3 111411441 111411441 chr3 111455769 111455769 TCGA-HC-8262 DUP 45 44 CD96 CD96 chr3 113024461 113024461 chr3 113033032 113033032 TCGA-HC-8262 INS 45 10 AC078785.1 AC078785.1 chr3 115760512 115760512 chr3 115976839 115976839 TCGA-HC-8262 DEL 10 35 * LSAMP chr3 124328531 124328531 chr12 11545794 11545794 TCGA-HC-8262 BND 15 36 KALRN AC007450.1 chr3 132253326 132253326 chr17 71174152 71174152 TCGA-HC-8262 BND 23 27 CPNE4 CASC17 chr3 132324198 132324198 chr17 70990230 70990230 TCGA-HC-8262 BND 45 5 ACP3 * chr3 134983939 134983939 chr3 134988798 134988798 TCGA-HC-8262 DEL 31 29 EPHB1 EPHB1 chr3 143233928 143233928 chr3 143267411 143267411 TCGA-HC-8262 DUP 15 13 * SLC9A9 chr3 15126946 15126946 chr11 71654987 71654987 TCGA-HC-8262 BND 15 40 * * chr3 153844423 153844423 chr3 153888938 153888938 TCGA-HC-8262 DUP 33 4 LINC02006 LINC02006 chr3 155238663 155238663 chr3 155274661 155274661 TCGA-HC-8262 DUP 34 46 * * chr3 156999048 156999048 chr3 157036695 157036695 TCGA-HC-8262 DUP 26 8 LEKR1 LEKR1 chr3 163825121 163825121 chr3 163828822 163828822 TCGA-HC-8262 DEL 38 39 * * chr3 16508875 16508875 chr3 78600374 78600374 TCGA-HC-8262 INS 20 9 RFTN1 ROBO1 chr3 172931869 172931869 chr3 172978376 172978376 TCGA-HC-8262 DUP 9 15 SPATA16 SPATA16 chr3 176413391 176413391 chr3 176461693 176461693 TCGA-HC-8262 DUP 42 33 * * chr3 18522912 18522912 chr3 19977971 19977971 TCGA-HC-8262 DEL 10 25 SATB1-AS1 RAB5A chr3 44547659 44547659 chr3 44600302 44600302 TCGA-HC-8262 DUP 24 5 * ZKSCAN7-AS1 chr3 47167237 47167237 chr3 76362007 76362007 TCGA-HC-8262 DUP 2 28 KIF9-AS1 ROBO2 chr3 47193681 47193681 chr3 76368993 76368993 TCGA-HC-8262 INV 42 30 KIF9-AS1 ROBO2 chr3 61979338 61979338 chr22 41736656 41736656 TCGA-HC-8262 BND 26 13 PTPRG MEI1 chr3 68690418 68690418 chr3 68698829 68698829 TCGA-HC-8262 INS 26 50 * * chr3 70980937 70980937 chr3 80585078 80585078 TCGA-HC-8262 INV 12 26 FOXP1 * chr3 71891728 71891728 chr3 76522940 76522940 TCGA-HC-8262 INV 28 37 * ROBO2 chr3 72750658 72750658 chr3 72795978 72795978 TCGA-HC-8262 DUP 19 11 SHQ1 SHQ1 chr3 76209577 76209577 chr3 77842414 77842414 TCGA-HC-8262 DUP 36 42 ROBO2 * chr3 76346560 76346560 chr3 76347053 76347053 TCGA-HC-8262 INV 3 43 ROBO2 ROBO2 chr3 76775186 76775186 chr3 76997073 76997073 TCGA-HC-8262 DUP 5 11 ROBO2 ROBO2 chr3 76906829 76906829 chr3 76907101 76907101 TCGA-HC-8262 INV 21 16 ROBO2 ROBO2 chr3 76972985 76972985 chr3 76997446 76997446 TCGA-HC-8262 DEL 29 36 ROBO2 ROBO2 chr3 76991522 76991522 chr3 76993746 76993746 TCGA-HC-8262 INV 49 17 ROBO2 ROBO2 chr3 77141628 77141628 chr3 77141713 77141713 TCGA-HC-8262 INV 19 8 ROBO2 ROBO2 chr3 81564161 81564161 chr3 81564233 81564233 TCGA-HC-8262 INV 5 48 GBE1 GBE1 chr3 82545057 82545057 chr3 82545089 82545089 TCGA-HC-8262 INV 18 40 * * chr3 83637519 83637519 chr3 83649713 83649713 TCGA-HC-8262 DEL 31 35 * * chr3 84833755 84833755 chr3 84833906 84833906 TCGA-HC-8262 INV 22 9 LINC00971 LINC00971 chr3 85322893 85322893 chr3 85325917 85325917 TCGA-HC-8262 INV 4 2 CADM2 CADM2 chr3 85899668 85899668 chr3 85899914 85899914 TCGA-HC-8262 INV 34 38 CADM2 CADM2 chr3 86121111 86121111 chr3 86121146 86121146 TCGA-HC-8262 INV 20 17 * * chr3 86305751 86305751 chr3 86306022 86306022 TCGA-HC-8262 INV 49 6 * * chr3 86511846 86511846 chr3 86512072 86512072 TCGA-HC-8262 INV 27 45 * * chr3 88176090 88176090 chr3 88176223 88176223 TCGA-HC-8262 INV 28 42 * * chr3 89225470 89225470 chr3 89225972 89225972 TCGA-HC-8262 INV 26 20 EPHA3 EPHA3 chr3 89460144 89460144 chr3 89467052 89467052 TCGA-HC-8262 INS 1 16 EPHA3 EPHA3 chr3 90126319 90126319 chr3 90171080 90171080 TCGA-HC-8262 DUP 27 31 * * chr4 102401688 102401688 chr4 102439505 102439505 TCGA-HC-8262 DUP 20 5 SLC39A8 AC098487.1 chr4 10390807 10390807 chr4 10400379 10400379 TCGA-HC-8262 INS 48 27 * * chr4 104864179 104864179 chr7 132716720 132716720 TCGA-HC-8262 BND 26 1 AC004053.1 FLJ40288 chr4 105091214 105091214 chr12 21223671 21223671 TCGA-HC-8262 BND 7 46 AC096577.1 SLCO1B1 chr4 106235020 106235020 chr12 79535601 79535601 TCGA-HC-8262 BND 21 41 TBCK * chr4 110458712 110458712 chr4 110504434 110504434 TCGA-HC-8262 DUP 3 7 ENPEP ENPEP chr4 113171415 113171415 chr4 167301817 167301817 TCGA-HC-8262 DEL 2 33 ANK2 * chr4 121016050 121016050 chr16 71719236 71719236 TCGA-HC-8262 BND 18 2 * PHLPP2 chr4 134247087 134247087 chrX 81421775 81421775 TCGA-HC-8262 BND 32 10 * AL445213.1 chr4 138017982 138017982 chr4 138061768 138061768 TCGA-HC-8262 DUP 46 2 * LINC00616 chr4 139563888 139563888 chr4 160909355 160909355 TCGA-HC-8262 INV 43 15 SETD7 * chr4 139772134 139772134 chr4 139772558 139772558 TCGA-HC-8262 INV 21 27 MAML3 MAML3 chr4 139823306 139823306 chr4 139823652 139823652 TCGA-HC-8262 INV 29 11 MAML3 MAML3 chr4 140395595 140395595 chr4 140395662 140395662 TCGA-HC-8262 INV 34 21 CLGN CLGN chr4 140464898 140464898 chr4 140464966 140464966 TCGA-HC-8262 INV 39 31 MGAT4D MGAT4D chr4 143179033 143179033 chr4 143210355 143210355 TCGA-HC-8262 DUP 17 22 AC104596.1 USP38 chr4 14422540 14422540 chr4 14472823 14472823 TCGA-HC-8262 DUP 9 39 * LINC00504 chr4 147573337 147573337 chr4 147580444 147580444 TCGA-HC-8262 INS 24 30 LINC02507 LINC02507 chr4 148096296 148096296 chr13 44849635 44849635 TCGA-HC-8262 BND 40 12 NR3C2 * chr4 148208157 148208157 chr4 170973905 170973905 TCGA-HC-8262 DEL 14 36 NR3C2 * chr4 148229128 148229128 chr4 148229371 148229371 TCGA-HC-8262 INV 12 42 NR3C2 NR3C2 chr4 148289636 148289636 chr4 148289683 148289683 TCGA-HC-8262 INV 34 1 NR3C2 NR3C2 chr4 148300768 148300768 chr4 148357134 148357134 TCGA-HC-8262 DUP 36 24 NR3C2 NR3C2 chr4 148366480 148366480 chrX 70587187 70587187 TCGA-HC-8262 BND 9 31 NR3C2 TEX11 chr4 15149727 15149727 chr4 15515434 15515434 TCGA-HC-8262 DEL 1 35 C1QTNF7-AS1 CC2D2A chr4 153367306 153367306 chr4 153405910 153405910 TCGA-HC-8262 DUP 32 44 MND1 MND1 chr4 161111942 161111942 chrX 71179740 71179740 TCGA-HC-8262 BND 2 26 * * chr4 166796424 166796424 chr4 166863263 166863263 TCGA-HC-8262 DEL 21 29 SPOCK3 SPOCK3 chr4 168651588 168651588 chr4 169615928 169615928 TCGA-HC-8262 INV 5 13 PALLD CLCN3 chr4 169259595 169259595 chr4 171895008 171895008 TCGA-HC-8262 INV 6 33 SH3RF1 GALNTL6 chr4 169399244 169399244 chr4 169434878 169434878 TCGA-HC-8262 DUP 27 18 NEK1 NEK1 chr4 171192321 171192321 chr4 171194943 171194943 TCGA-HC-8262 DEL 21 49 * * chr4 171922320 171922320 chr13 33336949 33336949 TCGA-HC-8262 BND 36 28 GALNTL6 STARD13 chr4 171922737 171922737 chr13 73132271 73132271 TCGA-HC-8262 BND 2 30 GALNTL6 * chr4 172354181 172354181 chr13 55797125 55797133 TCGA-HC-8262 BND 46 44 GALNTL6 * chr4 172354242 172354242 chrX 67656980 67656980 TCGA-HC-8262 BND 2 26 GALNTL6 AR chr4 174018982 174018982 chr5 181126009 181126009 TCGA-HC-8262 BND 9 28 * OR2V1 chr4 174024637 174024637 chr5 139569719 139569719 TCGA-HC-8262 BND 15 39 * UBE2D2 chr4 175901349 175901349 chr5 180833891 180833891 TCGA-HC-8262 BND 49 23 GPM6A LINC00847 chr4 180580882 180580882 chr4 180627669 180627669 TCGA-HC-8262 DUP 5 28 * * chr4 184309366 184309366 chr6 165128033 165128033 TCGA-HC-8262 BND 3 41 * * chr4 189270450 189270450 chr4 189279311 189279311 TCGA-HC-8262 INS 6 25 * * chr4 23171789 23171789 chr4 23218441 23218441 TCGA-HC-8262 DUP 6 44 * * chr4 30668768 30668768 chr4 30713047 30713047 TCGA-HC-8262 DUP 43 40 * * chr4 34554191 34554191 chr4 56093828 56093828 TCGA-HC-8262 DEL 18 15 * CRACD chr4 36981815 36981815 chr8 49481137 49481137 TCGA-HC-8262 BND 12 40 * * chr4 40734740 40734740 chr4 106226437 106226437 TCGA-HC-8262 INV 11 44 * TBCK chr4 40887542 40887542 chr4 40921480 40921480 TCGA-HC-8262 DUP 29 5 APBB2 APBB2 chr4 57989394 57989394 chr4 57990641 57990641 TCGA-HC-8262 INV 45 23 * * chr4 58442548 58442548 chr4 73426902 73426902 TCGA-HC-8262 DEL 28 37 * * chr4 59078215 59078215 chr4 59084922 59084922 TCGA-HC-8262 INS 49 39 * * chr4 69063264 69063264 chr4 70128342 70128342 TCGA-HC-8262 DUP 17 16 UGT2B7 * chr4 70107106 70107106 chr4 73570515 73570515 TCGA-HC-8262 INV 10 2 * * chr4 79779077 79779077 chr4 120722019 120722019 TCGA-HC-8262 DEL 19 14 * PRDM5 chr4 80187062 80187062 chr4 87637538 87637538 TCGA-HC-8262 INV 10 41 PRDM8 AC093895.1 chr4 83286563 83286563 chr16 71718783 71718783 TCGA-HC-8262 BND 10 19 * PHLPP2 chr4 83342804 83342804 chr16 73875772 73875772 TCGA-HC-8262 BND 4 29 * ZFHX3 chr4 83608244 83608244 chr4 83611970 83611970 TCGA-HC-8262 INV 36 25 * * chr4 87669906 87669906 chr4 89122004 89122004 TCGA-HC-8262 DUP 13 6 AC093895.1 * chr4 87730365 87730365 chr4 89135725 89135725 TCGA-HC-8262 INV 34 2 AC093895.1 * chr4 87730523 87730523 chr4 120721558 120721558 TCGA-HC-8262 DUP 22 27 AC093895.1 PRDM5 chr4 89102295 89102295 chr4 89142086 89142086 TCGA-HC-8262 INV 10 46 FAM13A * chr4 89137762 89137762 chr4 120722043 120722043 TCGA-HC-8262 INV 48 1 * PRDM5 chr4 90734429 90734429 chr4 90766024 90766024 TCGA-HC-8262 DUP 30 44 CCSER1 CCSER1 chr4 94794617 94794617 chr4 94837349 94837349 TCGA-HC-8262 DUP 28 21 BMPR1B BMPR1B chr5 131993798 131993798 chr5 132033317 132033317 TCGA-HC-8262 DUP 38 27 AC034228.3 * chr5 1388536 1388536 chr5 1419713 1419713 TCGA-HC-8262 DUP 43 19 * SLC6A3 chr5 139570491 139570491 chr5 139606238 139606238 TCGA-HC-8262 DUP 42 32 UBE2D2 UBE2D2 chr5 139573434 139573434 chr5 181126178 181126178 TCGA-HC-8262 INV 14 43 UBE2D2 OR2V1 chr5 139611373 139611373 chr5 139650431 139650431 TCGA-HC-8262 DUP 19 34 UBE2D2 CXXC5 chr5 139615471 139615471 chr13 33335904 33335904 TCGA-HC-8262 BND 47 48 UBE2D2 STARD13 chr5 139615560 139615560 chr5 181126115 181126115 TCGA-HC-8262 DUP 44 10 UBE2D2 OR2V1 chr5 61015980 61015980 chr5 61140936 61140936 TCGA-HC-8262 DEL 21 34 NDUFAF2 NDUFAF2 chr5 81510146 81510146 chr5 92141369 92141369 TCGA-HC-8262 DEL 17 22 SSBP2 AC114316.1 chr5 84430581 84430581 chr5 88834328 88834328 TCGA-HC-8262 INS 34 43 EDIL3-DT MEF2C chr5 89044738 89044738 chr5 104911762 104911762 TCGA-HC-8262 INS 24 42 MEF2C-AS1 AC099520.1 chr6 100095235 100095235 chr6 100126542 100126542 TCGA-HC-8262 DUP 6 36 AL080285.2 * chr6 153750450 153750450 chr6 153829217 153829217 TCGA-HC-8262 DEL 10 42 * * chr6 153963349 153963349 chrX 67452287 67452287 TCGA-HC-8262 BND 39 2 * * chr6 163110943 163110943 chr6 163184083 163184083 TCGA-HC-8262 DEL 8 50 PACRG PACRG chr6 32652357 32652357 chr6 32751561 32751561 TCGA-HC-8262 DUP 6 11 * * chr6 42436361 42436361 chr6 42478414 42478414 TCGA-HC-8262 DUP 5 4 TRERF1 * chr6 62518466 62518466 chr6 63097873 63097873 TCGA-HC-8262 INS 3 28 * * chr6 71793838 71793838 chr6 126671605 126671605 TCGA-HC-8262 DEL 3 4 * * chr6 72277404 72277404 chr6 72326827 72326827 TCGA-HC-8262 DUP 26 37 RIMS1 RIMS1 chr6 77717404 77717404 chr6 77726278 77726278 TCGA-HC-8262 INS 32 16 MEI4 MEI4 chr6 83737536 83737536 chr6 83784416 83784416 TCGA-HC-8262 DUP 18 43 * * chr6 91262984 91262984 chr6 91294312 91294312 TCGA-HC-8262 DUP 10 44 * * chr7 104022571 104022571 chr7 104329369 104329369 TCGA-HC-8262 INV 21 15 * LHFPL3 chr7 104195382 104195382 chr7 104197784 104197784 TCGA-HC-8262 INV 38 14 ORC5 ORC5 chr7 104586856 104586856 chr7 106367348 106367348 TCGA-HC-8262 DEL 34 49 LHFPL3 * chr7 105539747 105539747 chr12 16578613 16578635 TCGA-HC-8262 BND 1 4 RINT1 MGST1 chr7 105539747 105539747 chr12 17798288 17798288 TCGA-HC-8262 BND 31 38 RINT1 * chr7 105550917 105550917 chr7 106368151 106368151 TCGA-HC-8262 DUP 42 26 RINT1 * chr7 105563082 105563082 chr12 19301607 19301607 TCGA-HC-8262 BND 29 47 RINT1 PLEKHA5 chr7 105817887 105817887 chr7 106863162 106863162 TCGA-HC-8262 DUP 36 28 ATXN7L1 * chr7 105829381 105829381 chr7 105829409 105829409 TCGA-HC-8262 INV 29 13 ATXN7L1 ATXN7L1 chr7 105833910 105833910 chr12 16484972 16484972 TCGA-HC-8262 BND 49 25 ATXN7L1 MGST1 chr7 105844942 105844942 chr21 9000683 9000683 TCGA-HC-8262 BND 41 37 ATXN7L1 CR392039.3 chr7 105844973 105844973 chr7 105846148 105846148 TCGA-HC-8262 INV 4 22 ATXN7L1 ATXN7L1 chr7 106066942 106066942 chr7 106104250 106104250 TCGA-HC-8262 DUP 2 3 * SYPL1 chr7 106092819 106092819 chr7 106092894 106092894 TCGA-HC-8262 INV 36 3 SYPL1 SYPL1 chr7 106092982 106092982 chr7 106093051 106093051 TCGA-HC-8262 INV 26 10 SYPL1 SYPL1 chr7 106114955 106114955 chr7 106115007 106115007 TCGA-HC-8262 INV 4 36 * * chr7 106164759 106164759 chr7 106518546 106518546 TCGA-HC-8262 DEL 50 47 * AC004917.1 chr7 106174833 106174833 chr7 106367265 106367265 TCGA-HC-8262 DUP 31 20 * * chr7 106314608 106314608 chr7 106316381 106316381 TCGA-HC-8262 INV 14 33 LARP1BP2 * chr7 106523759 106523759 chr7 106523830 106523830 TCGA-HC-8262 INV 47 33 AC004917.1 AC004917.1 chr7 106617967 106617967 chr7 106870764 106870764 TCGA-HC-8262 DEL 18 18 AC004917.1 PIK3CG chr7 106682543 106682543 chr7 106690348 106690348 TCGA-HC-8262 INV 44 33 AC004917.1 AC004917.1 chr7 106788564 106788564 chr7 106788725 106788725 TCGA-HC-8262 INV 5 18 LINC02577 LINC02577 chr7 107026913 107026913 chr7 107041865 107041865 TCGA-HC-8262 INV 15 44 * * chr7 109831052 109831052 chr7 109837860 109837860 TCGA-HC-8262 DEL 13 27 * * chr7 112242370 112242370 chr7 112279251 112279251 TCGA-HC-8262 DUP 6 34 ZNF277 ZNF277 chr7 137601656 137601656 chr12 60082097 60082097 TCGA-HC-8262 BND 36 42 DGKI * chr7 1577718 1577718 chr19 48903405 48903405 TCGA-HC-8262 BND 44 43 PSMG3-AS1 NUCB1 chr7 158778803 158778803 chr7 158799097 158799097 TCGA-HC-8262 DEL 17 40 ESYT2 ESYT2 chr7 158799040 158799040 chr17 30596803 30596811 TCGA-HC-8262 BND 13 42 ESYT2 AC005562.1 chr7 22119283 22119283 chr7 22161239 22161239 TCGA-HC-8262 DUP 38 20 RAPGEF5 RAPGEF5 chr7 38348752 38348752 chr7 38357692 38357692 TCGA-HC-8262 INS 17 7 TRG-AS1 TRG-AS1 chr7 48861417 48861417 chr7 48910688 48910688 TCGA-HC-8262 INV 11 35 * * chr7 52323512 52323512 chr11 87645958 87645958 TCGA-HC-8262 BND 40 36 * * chr7 55075589 55075589 chr7 55117108 55117108 TCGA-HC-8262 DUP 30 21 EGFR EGFR chr7 55937177 55937177 chr7 55969514 55969514 TCGA-HC-8262 DUP 9 14 ZNF713 NIPSNAP2 chr7 69838930 69838930 chr7 69882735 69882735 TCGA-HC-8262 DUP 28 17 AUTS2 AUTS2 chr7 72106695 72106695 chr9 28189905 28189905 TCGA-HC-8262 BND 45 13 CALN1 LINGO2 chr7 83670896 83670896 chr7 83692645 83692645 TCGA-HC-8262 INV 26 41 * * chr7 90308393 90308393 chr12 10683722 10683729 TCGA-HC-8262 BND 28 20 CFAP69 * chr7 96175514 96175514 chr12 10683722 10683729 TCGA-HC-8262 BND 42 28 SLC25A13 * chr7 97104343 97104343 chr12 11545976 11545976 TCGA-HC-8262 BND 29 8 * AC007450.1 chr7 98158936 98158936 chr12 14233720 14233720 TCGA-HC-8262 BND 27 32 LMTK2 * chr7 99975326 99975326 chr12 19546847 19546847 TCGA-HC-8262 BND 18 19 AZGP1 AEBP2 chr8 113032010 113032010 chr8 113032227 113032227 TCGA-HC-8262 INV 26 16 CSMD3 CSMD3 chr8 115155956 115155956 chr8 115203165 115203165 TCGA-HC-8262 DUP 4 37 * * chr8 118036904 118036904 chr8 118037087 118037087 TCGA-HC-8262 INV 46 2 EXT1 EXT1 chr8 123771758 123771758 chr8 123771908 123771908 TCGA-HC-8262 INV 17 17 FAM91A1 FAM91A1 chr8 124741271 124741271 chr8 124741469 124741469 TCGA-HC-8262 INV 24 39 * * chr8 128074019 128074019 chr8 128074132 128074132 TCGA-HC-8262 INV 26 34 PVT1 PVT1 chr8 128452853 128452853 chr8 128460082 128460082 TCGA-HC-8262 INS 30 42 LINC00824 LINC00824 chr8 129682599 129682599 chr8 129688703 129688703 TCGA-HC-8262 DEL 22 47 CCDC26 AC103718.1 chr8 130308357 130308357 chr8 130308506 130308506 TCGA-HC-8262 INV 39 3 ASAP1 ASAP1 chr8 132038033 132038033 chr8 132038128 132038128 TCGA-HC-8262 INV 24 15 OC90 OC90 chr8 132360456 132360456 chr8 132360499 132360499 TCGA-HC-8262 INV 46 29 KCNQ3 KCNQ3 chr8 133841974 133841974 chr8 133842242 133842242 TCGA-HC-8262 INV 30 38 * * chr8 139129636 139129636 chr8 139129904 139129904 TCGA-HC-8262 INV 15 14 * * chr8 142228756 142228756 chr8 142230860 142230860 TCGA-HC-8262 INV 39 7 TSNARE1 TSNARE1 chr8 143977296 143977296 chr8 144015365 144015365 TCGA-HC-8262 DUP 30 47 PLEC SPATC1 chr8 21914475 21914475 chr8 29006029 29006029 TCGA-HC-8262 DEL 46 31 DOK2 HMBOX1 chr8 29010736 29010736 chr8 29051538 29051538 TCGA-HC-8262 DEL 4 34 HMBOX1 HMBOX1 chr8 3061157 3061157 chr8 112786802 112786802 TCGA-HC-8262 DEL 6 3 CSMD1 CSMD3 chr8 35700222 35700222 chr8 35746939 35746939 TCGA-HC-8262 DUP 39 18 UNC5D UNC5D chr8 43164457 43164457 chr8 43217041 43217041 TCGA-HC-8262 DUP 29 33 HGSNAT * chr8 48240242 48240242 chr8 48533589 48533589 TCGA-HC-8262 DUP 34 16 * * chr8 49595996 49595996 chr8 53051727 53051727 TCGA-HC-8262 DEL 4 16 * * chr8 49664626 49664626 chr8 53289147 53289147 TCGA-HC-8262 DEL 38 15 * * chr8 52923851 52923851 chr12 28741649 28741649 TCGA-HC-8262 BND 16 41 * * chr8 52924880 52924880 chr12 28717171 28717171 TCGA-HC-8262 BND 21 33 * * chr8 53729761 53729761 chr8 53771041 53771041 TCGA-HC-8262 DUP 21 20 ATP6V1H ATP6V1H chr8 55610928 55610928 chr8 86245763 86245763 TCGA-HC-8262 INS 15 41 * SLC7A13 chr8 63888668 63888668 chr8 63959180 63959180 TCGA-HC-8262 DEL 2 4 LINC01414 LINC01414 chr8 68564601 68564601 chr8 68565914 68565914 TCGA-HC-8262 DEL 49 8 C8orf34 C8orf34 chr8 69370503 69370503 chr8 69408845 69408845 TCGA-HC-8262 DUP 6 37 * * chr8 71186541 71186541 chr8 86526006 86526006 TCGA-HC-8262 INS 11 2 AC015687.1 CPNE3 chr8 72983321 72983321 chr8 73021078 73021078 TCGA-HC-8262 DUP 46 44 * TERF1 chr8 79417186 79417186 chr8 79417431 79417431 TCGA-HC-8262 INV 24 38 * * chr8 83157717 83157717 chr8 83195765 83195765 TCGA-HC-8262 DUP 20 2 * * chr8 84977346 84977346 chr8 85615283 85615283 TCGA-HC-8262 DEL 12 9 * * chr8 85373872 85373872 chr8 85461452 85461452 TCGA-HC-8262 DEL 45 47 CA1 CA3-AS1 chr8 90119864 90119864 chr8 90174741 90174741 TCGA-HC-8262 DUP 48 23 * * chr8 91971488 91971488 chr8 92007525 92007525 TCGA-HC-8262 DUP 49 5 RUNX1T1 RUNX1T1 chr9 133564191 133564191 chrX 25815085 25815085 TCGA-HC-8262 BND 3 19 ADAMTSL2 * chr9 17621953 17621953 chr9 17664160 17664160 TCGA-HC-8262 DUP 35 41 SH3GL2 SH3GL2 chr9 22496307 22496307 chr9 22504371 22504371 TCGA-HC-8262 INS 5 14 * * chr9 61533896 61533896 chr9 61993824 61993824 TCGA-HC-8262 INV 8 33 * * chr9 62806331 62806331 chr9 62814083 62814084 TCGA-HC-8262 INS 26 23 LINC01410 * chr9 84589613 84589613 chr9 84589668 84589668 TCGA-HC-8262 INV 43 7 AL157886.1 AL157886.1 chr9 91733063 91733063 chr9 91775390 91775390 TCGA-HC-8262 DUP 31 11 ROR2 ROR2 chr9 9521157 9521157 chr9 9712796 9712796 TCGA-HC-8262 DEL 37 25 PTPRD PTPRD chrX 147374987 147374987 chrX 147387353 147387353 TCGA-HC-8262 DEL 47 9 * * chrX 21158400 21158400 chrX 21176064 21176064 TCGA-HC-8262 INV 16 14 BX088723.1 AL807742.1 chrX 66500339 66500339 chrX 68330467 68330467 TCGA-HC-8262 DUP 12 42 * OPHN1 chrX 66528062 66528062 chrX 68830035 68830035 TCGA-HC-8262 DUP 39 31 * EFNB1 chrX 66640374 66640374 chrX 67860220 67860220 TCGA-HC-8262 DUP 35 41 EDA2R * chrX 66709017 66709017 chrX 66709083 66709083 TCGA-HC-8262 INV 30 39 * * chrX 66737033 66737033 chrX 66737059 66737059 TCGA-HC-8262 INV 27 37 * * chrX 66777046 66777066 chrX 66777046 66777066 TCGA-HC-8262 INV 40 38 * * chrX 66781303 66781303 chrX 66781325 66781325 TCGA-HC-8262 INV 40 17 * * chrX 66817482 66817482 chrX 66817522 66817522 TCGA-HC-8262 INV 28 17 * * chrX 67228194 67228208 chrX 67228194 67228208 TCGA-HC-8262 INV 2 4 * * chrX 67339434 67339434 chrX 67339583 67339583 TCGA-HC-8262 INV 25 27 * * chrX 67341999 67341999 chrX 67342086 67342086 TCGA-HC-8262 INV 39 15 * * chrX 67443387 67443387 chrX 67443496 67443496 TCGA-HC-8262 INV 26 3 * * chrX 67505709 67505709 chrX 67505811 67505811 TCGA-HC-8262 INV 32 2 * * chrX 67644081 67644081 chrX 67644694 67644694 TCGA-HC-8262 INV 38 48 AR AR chrX 67689127 67689127 chrX 67689171 67689171 TCGA-HC-8262 INV 34 8 AR AR chrX 67719926 67719926 chrX 67719997 67719997 TCGA-HC-8262 INV 30 17 AR AR chrX 67848892 67848892 chrX 67848914 67848914 TCGA-HC-8262 INV 43 3 * * chrX 67889694 67889694 chrX 67890227 67890227 TCGA-HC-8262 INV 47 41 * * chrX 67911555 67911555 chrX 67911673 67911673 TCGA-HC-8262 INV 12 22 * * chrX 68046332 68046332 chrX 68046641 68046641 TCGA-HC-8262 INV 9 26 OPHN1 OPHN1 chrX 68111720 68111720 chrX 68111778 68111778 TCGA-HC-8262 INV 5 34 OPHN1 OPHN1 chrX 68179277 68179277 chrX 68179363 68179363 TCGA-HC-8262 INV 31 9 OPHN1 OPHN1 chrX 68522601 68522601 chrX 68522839 68522839 TCGA-HC-8262 INV 46 9 YIPF6 YIPF6 chrX 68729189 68729189 chrX 68729271 68729271 TCGA-HC-8262 INV 10 46 * * chrX 68769400 68769400 chrX 68769540 68769540 TCGA-HC-8262 INV 14 14 * * chrX 68827544 68827544 chrX 68827736 68827736 TCGA-HC-8262 INV 23 34 EFNB1 EFNB1 chrX 73546447 73546447 chrX 74285567 74285567 TCGA-HC-8262 DUP 4 38 MAP2K4P1 FTX chrX 73830446 73830446 chrX 73830535 73830535 TCGA-HC-8262 INV 43 31 XIST XIST chrX 74065897 74065897 chrX 74066108 74066108 TCGA-HC-8262 INV 5 48 JPX JPX chrX 74207075 74207075 chrX 74207314 74207314 TCGA-HC-8262 INV 37 23 FTX FTX chrX 74243057 74243057 chrX 74243089 74243089 TCGA-HC-8262 INV 28 49 FTX FTX chrX 80860321 80860321 chrX 82082143 82082143 TCGA-HC-8262 DEL 34 37 * * chr10 46058207 46058207 chr10 46128054 46128054 TCGA-TK-A8OK DEL 16 18 * AGAP7P chr12 60528842 60528842 chr12 60659447 60659447 TCGA-TK-A8OK DEL 3 49 * * chr13 41465379 41465379 chr13 84068268 84068268 TCGA-TK-A8OK DEL 49 22 RGCC AL445604.1 chr13 41478815 41478815 chr13 58995062 58995062 TCGA-TK-A8OK DEL 50 19 * * chr13 53189680 53189680 chr13 81342076 81342076 TCGA-TK-A8OK INS 5 43 * * chr13 53250918 53250918 chr13 59671376 59671376 TCGA-TK-A8OK DEL 46 2 * DIAPH3 chr13 54228231 54228231 chr13 92792883 92792883 TCGA-TK-A8OK INS 50 42 * GPC5 chr13 54302980 54302980 chr13 83849201 83849201 TCGA-TK-A8OK INS 44 50 * * chr13 54605114 54605114 chr13 84048345 84048345 TCGA-TK-A8OK INS 41 3 * * chr13 55231707 55231707 chr13 92090505 92090505 TCGA-TK-A8OK INS 17 50 * GPC5 chr13 55632156 55632156 chr13 87551699 87551699 TCGA-TK-A8OK INS 8 43 * MIR4500HG chr13 55654107 55654107 chr13 102142705 102142705 TCGA-TK-A8OK DEL 12 12 * FGF14 chr13 55694399 55694399 chr13 91330813 91330813 TCGA-TK-A8OK INS 10 9 * * chr13 56236057 56236057 chr13 90021594 90021594 TCGA-TK-A8OK DEL 27 16 * * chr13 56937941 56937941 chr13 64319890 64319890 TCGA-TK-A8OK DEL 45 33 * * chr13 57254206 57254206 chr13 66788054 66788059 TCGA-TK-A8OK INS 49 16 * PCDH9 chr13 58437958 58437958 chr13 94506420 94506420 TCGA-TK-A8OK DEL 32 45 * * chr13 59480728 59480728 chr13 92295106 92295106 TCGA-TK-A8OK DEL 12 13 * GPC5 chr13 61437234 61437234 chr13 65967966 65967966 TCGA-TK-A8OK INS 27 2 * * chr13 63189784 63189784 chr13 86102165 86102165 TCGA-TK-A8OK DEL 40 49 LINC00376 AL354994.1 chr13 63546641 63546641 chr13 69729319 69729319 TCGA-TK-A8OK DEL 15 27 * KLHL1 chr13 64642355 64642355 chr13 69340458 69340458 TCGA-TK-A8OK DEL 35 46 * * chr13 65646557 65646557 chr13 86127228 86127228 TCGA-TK-A8OK DEL 34 30 * AL354994.1 chr13 66136742 66136742 chr13 66443268 66443268 TCGA-TK-A8OK DEL 43 19 * PCDH9 chr13 79117288 79117288 chr13 79123045 79123045 TCGA-TK-A8OK DEL 2 34 * * chr13 79672279 79672279 chr13 79700722 79700722 TCGA-TK-A8OK DEL 21 6 * * chr13 80009831 80009831 chr13 80020236 80020236 TCGA-TK-A8OK DEL 24 31 AL158064.1 AL158064.1 chr13 80626570 80626570 chr13 84214947 84214947 TCGA-TK-A8OK INS 18 49 * * chr13 80644984 80644984 chr13 86094417 86094417 TCGA-TK-A8OK INS 22 41 * AL354994.1 chr13 86105688 86105688 chr13 92583994 92583994 TCGA-TK-A8OK DEL 41 5 AL354994.1 GPC5 chr13 86959281 86959281 chr13 86988975 86988975 TCGA-TK-A8OK DEL 43 16 * * chr13 87583149 87583149 chr13 87912302 87912302 TCGA-TK-A8OK INS 2 42 MIR4500HG * chr13 88643653 88643653 chr13 90985610 90985610 TCGA-TK-A8OK DEL 7 36 * * chr14 37651654 37651654 chr14 37715834 37715834 TCGA-TK-A8OK DEL 42 7 TTC6 TTC6 chr14 42940831 42940831 chr14 42942056 42942056 TCGA-TK-A8OK DEL 33 34 * * chr17 16452053 16452053 chr17 16483268 16483268 TCGA-TK-A8OK DEL 11 28 SNHG29 LRRC75A chr18 24284517 24284517 chr18 26151676 26151676 TCGA-TK-A8OK DEL 19 2 OSBPL1A PSMA8 chr18 26728204 26728204 chr18 29849218 29849218 TCGA-TK-A8OK DEL 8 31 AQP4-AS1 * chr18 75211235 75211235 chr18 75212852 75212852 TCGA-TK-A8OK DEL 7 1 TSHZ1 TSHZ1 chr18 76504177 76504177 chr18 76519753 76519753 TCGA-TK-A8OK DEL 33 34 * * chr18 78199560 78199560 chr18 78199711 78199711 TCGA-TK-A8OK DEL 26 16 * * chr20 15182854 15182854 chr20 15231521 15231521 TCGA-TK-A8OK DEL 20 20 MACROD2 MACROD2 chr21 10754367 10754367 chr13 91090574 91090574 TCGA-TK-A8OK BND 3 44 * LINC00380 chr22 28670390 28670390 chr13 64875484 64875484 TCGA-TK-A8OK BND 35 43 TTC28 * chr2 141609836 141609836 chr2 152891683 152891683 TCGA-TK-A8OK DEL 37 41 LRP1B * chr2 142311564 142311564 chr2 143062111 143062111 TCGA-TK-A8OK INS 42 7 * * chr2 143208954 143208954 chr2 143209518 143209518 TCGA-TK-A8OK INS 40 50 ARHGAP15 ARHGAP15 chr2 143398992 143398992 chr2 145509663 145509663 TCGA-TK-A8OK DEL 49 20 ARHGAP15 * chr2 163547774 163547774 chr2 163622396 163622396 TCGA-TK-A8OK DEL 35 31 * FIGN chr2 163642034 163642034 chr2 163655239 163655239 TCGA-TK-A8OK DEL 14 24 FIGN FIGN chr2 163952161 163952161 chr2 163969691 163969691 TCGA-TK-A8OK DEL 18 15 AC016766.1 AC016766.1 chr2 25723067 25723067 chr2 86643666 86643666 TCGA-TK-A8OK INS 39 30 * RNF103-CHMP3 chr2 25730461 25730461 chr2 79397700 79397700 TCGA-TK-A8OK DEL 41 26 * CTNNA2 chr2 57397260 57397260 chr2 80194959 80194959 TCGA-TK-A8OK INS 30 5 * CTNNA2 chr2 85133063 85133063 chr2 85139363 85139363 TCGA-TK-A8OK DEL 39 27 TCF7L1 TCF7L1 chr3 100431361 100431361 chr3 102028458 102028458 TCGA-TK-A8OK DEL 35 27 LNP1 * chr3 15527497 15527497 chr3 80585136 80585136 TCGA-TK-A8OK DEL 28 5 * * chr3 158898976 158898976 chr3 169781221 169781221 TCGA-TK-A8OK DEL 5 30 * MYNN chr3 16095566 16095566 chr3 16251414 16251414 TCGA-TK-A8OK DEL 4 27 * * chr3 16106847 16106847 chr3 81114885 81114885 TCGA-TK-A8OK DEL 19 49 * * chr3 165278818 165278818 chr3 166342254 166342254 TCGA-TK-A8OK INS 24 8 LINC01322 * chr3 165646726 165646726 chr3 166017096 166017096 TCGA-TK-A8OK INS 12 23 LINC01322 * chr3 165792701 165792701 chr3 166195397 166195397 TCGA-TK-A8OK DEL 5 14 BCHE * chr3 181609203 181609203 chr3 181755745 181755745 TCGA-TK-A8OK INS 44 24 SOX2-OT SOX2-OT chr3 1934957 1934957 chr3 4428323 4428323 TCGA-TK-A8OK INS 35 20 * SUMF1 chr3 55754784 55754784 chr6 76897444 76897444 TCGA-TK-A8OK BND 50 47 ERC2 * chr3 780497 780497 chr3 2370781 2370781 TCGA-TK-A8OK DEL 28 20 LINC01266 CNTN4 chr3 786950 786950 chr3 4431348 4431348 TCGA-TK-A8OK DEL 41 37 LINC01266 SUMF1 chr3 81109540 81109540 chr3 81113233 81113233 TCGA-TK-A8OK DEL 19 13 * * chr3 85488549 85488549 chr3 85731052 85731052 TCGA-TK-A8OK DEL 45 8 CADM2 CADM2 chr3 96328430 96328430 chr3 96329166 96329166 TCGA-TK-A8OK DEL 25 11 * * chr3 98002796 98002796 chr3 98002953 98002953 TCGA-TK-A8OK DEL 18 10 GABRR3 GABRR3 chr3 99624761 99624761 chr3 100925341 100925341 TCGA-TK-A8OK DEL 27 4 * ABI3BP chr3 99752267 99752267 chr3 100899037 100899037 TCGA-TK-A8OK INS 46 32 COL8A1 ABI3BP chr4 111133530 111133530 chr4 132073096 132073096 TCGA-TK-A8OK DEL 25 41 * AC093916.1 chr4 158454750 158454750 chr4 158462200 158462200 TCGA-TK-A8OK DEL 2 8 RXFP1 RXFP1 chr4 161174660 161174660 chr4 177791470 177791470 TCGA-TK-A8OK INS 35 31 * LINC01098 chr4 161194619 161194619 chr4 161199591 161199591 TCGA-TK-A8OK DEL 21 47 * * chr4 161512799 161512799 chr4 161550470 161550470 TCGA-TK-A8OK DEL 25 45 FSTL5 FSTL5 chr4 166567781 166567781 chr4 179009997 179009997 TCGA-TK-A8OK DEL 40 23 * * chr4 166879136 166879136 chr4 179634008 179634008 TCGA-TK-A8OK INS 22 37 SPOCK3 * chr4 176989325 176989325 chr4 177010291 177010291 TCGA-TK-A8OK DEL 28 16 * * chr4 177084992 177084992 chr4 177120677 177120677 TCGA-TK-A8OK DEL 20 12 * * chr4 177656717 177656717 chr4 177657170 177657170 TCGA-TK-A8OK DEL 38 27 AC078881.1 AC078881.1 chr4 57119771 57119771 chr4 59475857 59475857 TCGA-TK-A8OK DEL 49 4 IGFBP7-AS1 * chr4 57122926 57122926 chr4 59570027 59570027 TCGA-TK-A8OK INS 25 14 IGFBP7-AS1 AC096588.1 chr4 58255947 58255947 chr4 66487767 66487767 TCGA-TK-A8OK DEL 1 23 * * chr4 59461924 59461924 chr4 66143523 66143523 TCGA-TK-A8OK DEL 45 6 * AC116049.1 chr4 66889019 66889019 chr4 66889895 66889895 TCGA-TK-A8OK DEL 39 21 * * chr4 91459637 91459637 chr4 91729222 91729222 TCGA-TK-A8OK INS 26 3 CCSER1 * chr5 102079021 102079021 chr5 102097663 102097663 TCGA-TK-A8OK DEL 6 49 * * chr5 103549658 103549658 chr5 152597625 152597625 TCGA-TK-A8OK INS 16 25 NUDT12 * chr5 130517149 130517149 chr5 130520585 130520585 TCGA-TK-A8OK DEL 41 38 * * chr5 152153110 152153110 chr5 152156169 152156169 TCGA-TK-A8OK DEL 48 39 LINC01933 LINC01933 chr5 152259017 152259017 chr5 152348620 152348620 TCGA-TK-A8OK INS 7 31 LINC01933 * chr5 153612191 153612191 chr5 153679174 153679174 TCGA-TK-A8OK INS 34 24 GRIA1 GRIA1 chr5 160081337 160081337 chr5 160083244 160083244 TCGA-TK-A8OK DEL 26 23 PWWP2A PWWP2A chr5 165224329 165224329 chr5 165262354 165262354 TCGA-TK-A8OK DEL 42 6 LINC01938 * chr5 166911920 166911920 chr5 166948473 166948473 TCGA-TK-A8OK DEL 30 6 LINC01947 * chr5 18970726 18970726 chr5 105217547 105217547 TCGA-TK-A8OK DEL 19 14 AC106744.1 AC099520.1 chr5 19014290 19014290 chr5 19731605 19731605 TCGA-TK-A8OK INS 5 43 AC106744.1 CDH18 chr5 19159138 19159138 chr5 19175244 19175244 TCGA-TK-A8OK DEL 5 1 * * chr5 19706022 19706022 chr5 19711228 19711228 TCGA-TK-A8OK DEL 48 48 CDH18 CDH18 chr5 21458731 21458731 chr5 26824701 26824701 TCGA-TK-A8OK INS 3 8 GUSBP1 * chr5 21459390 21459390 chr5 25881967 25881967 TCGA-TK-A8OK DEL 30 45 GUSBP1 * chr5 24598656 24598656 chr5 25669364 25669364 TCGA-TK-A8OK INS 14 43 CDH10 * chr5 26185562 26185562 chr5 105214654 105214654 TCGA-TK-A8OK INS 47 42 * AC099520.1 chr5 26196818 26196818 chr5 103787002 103787002 TCGA-TK-A8OK DEL 20 27 * * chr5 26307047 26307047 chr5 103512935 103512935 TCGA-TK-A8OK INS 30 11 * PDZPH1P chr5 26822506 26822506 chr5 26824834 26824834 TCGA-TK-A8OK DEL 38 1 * * chr5 26828047 26828047 chr5 103798308 103798308 TCGA-TK-A8OK DEL 16 42 * * chr5 30259600 30259600 chr5 30262354 30262354 TCGA-TK-A8OK DEL 31 6 * * chr5 5393899 5393899 chr5 5394190 5394190 TCGA-TK-A8OK DEL 23 22 * * chr5 7253390 7253390 chr5 7413554 7413554 TCGA-TK-A8OK DEL 9 36 * ADCY2 chr6 17261179 17261179 chr6 17261349 17261349 TCGA-TK-A8OK DEL 13 22 * * chr6 41559153 41559153 chr6 41983148 41983148 TCGA-TK-A8OK DEL 26 37 FOXP4 CCND3 chr6 76672552 76672552 chr6 76710099 76710099 TCGA-TK-A8OK DEL 42 42 * * chr6 81890444 81890444 chr6 123263712 123263712 TCGA-TK-A8OK DEL 45 36 LINC02542 TRDN chr7 33467212 33467212 chr7 33467442 33467442 TCGA-TK-A8OK INS 3 8 BBS9 BBS9 chr8 103813984 103813984 chr8 107072402 107072402 TCGA-TK-A8OK DEL 42 2 RIMS2 * chr8 105813281 105813281 chr8 106185892 106185892 TCGA-TK-A8OK INS 5 13 ZFPM2-AS1 * chr8 121489033 121489033 chr8 122373816 122373816 TCGA-TK-A8OK DEL 26 6 * * chr8 16161479 16161479 chr8 34719921 34719922 TCGA-TK-A8OK DEL 5 17 MSR1 * chr8 35106296 35106296 chr8 35106519 35106519 TCGA-TK-A8OK DEL 12 46 * * chr8 56210598 56210598 chr8 56901866 56901866 TCGA-TK-A8OK DEL 37 43 PLAG1 * chr8 56231671 56231671 chr8 75055798 75055798 TCGA-TK-A8OK INS 44 15 * * chr8 58459756 58459756 chr8 58459978 58459978 TCGA-TK-A8OK INS 38 33 * * chr8 83563026 83563026 chr8 83974003 83974003 TCGA-TK-A8OK DEL 3 23 * AC015522.1 chr8 88220988 88220990 chr8 88429487 88429487 TCGA-TK-A8OK DEL 30 30 MMP16 AC090578.1 chr8 90074181 90074181 chr8 106430509 106430509 TCGA-TK-A8OK INS 47 30 CALB1 OXR1 chrX 127379738 127379738 chrX 127379871 127379871 TCGA-TK-A8OK DEL 28 45 * * chrX 3691432 3691432 chrX 3691486 3691486 TCGA-TK-A8OK DEL 26 28 PRKX PRKX chr10 108078141 108078141 chr10 108106595 108106595 TCGA-J9-A52D DEL 8 14 LINC01435 LINC01435 chr10 108400263 108400263 chr10 108412177 108412177 TCGA-J9-A52D DEL 2 21 * * chr10 115763449 115763449 chr10 116058735 116058735 TCGA-J9-A52D DUP 35 40 ATRNL1 GFRA1 chr10 117080977 117080977 chr10 117111475 117111475 TCGA-J9-A52D DUP 23 40 SHTN1 SHTN1 chr10 122590479 122590479 chr10 123014158 123014159 TCGA-J9-A52D DUP 11 19 DMBT1 ACADSB chr10 124809564 124809564 chr10 125088313 125088313 TCGA-J9-A52D DUP 47 50 ABRAXAS2 CTBP2 chr10 13815294 13815294 chr10 14079970 14079970 TCGA-J9-A52D DUP 42 38 FRMD4A FRMD4A chr10 21900163 21900163 chr10 24332947 24332947 TCGA-J9-A52D DUP 38 16 DNAJC1 KIAA1217 chr10 30846437 30846437 chr10 30881527 30881527 TCGA-J9-A52D DEL 14 9 ZNF438 ZNF438 chr10 5095258 5095258 chr10 68842114 68842114 TCGA-J9-A52D INV 49 2 AKR1C3 STOX1 chr10 59656732 59656732 chr10 63119856 63119856 TCGA-J9-A52D DUP 45 39 SLC16A9 * chr10 61154425 61154425 chr10 64864813 64864813 TCGA-J9-A52D DUP 47 41 * * chr10 61242437 61242437 chr10 61680704 61680704 TCGA-J9-A52D DEL 13 42 * CABCOCO1 chr10 61958337 61958337 chr10 61992561 61992561 TCGA-J9-A52D DUP 30 37 ARID5B ARID5B chr10 66191647 66191647 chr10 87927788 87927788 TCGA-J9-A52D DUP 8 33 CTNNA3 PTEN chr10 7110003 7110004 chr10 7646544 7646544 TCGA-J9-A52D DUP 18 4 * ITIH5 chr10 7120906 7120906 chr10 7120936 7120936 TCGA-J9-A52D INV 7 40 * * chr10 75025393 75025394 chr10 75854288 75854288 TCGA-J9-A52D DUP 38 2 KAT6B LRMDA chr10 8422835 8422836 chr10 69585109 69585110 TCGA-J9-A52D DEL 9 43 AC025946.1 * chr10 8422835 8422836 chr10 69689233 69689234 TCGA-J9-A52D INV 1 10 AC025946.1 LINC02651 chr10 8524319 8524319 chr12 89226746 89226746 TCGA-J9-A52D BND 26 31 * * chr10 87850815 87850831 chr10 90898723 90898723 TCGA-J9-A52D DEL 3 40 * RPP30 chr10 87960433 87960433 chr10 124426425 124426425 TCGA-J9-A52D INV 2 42 PTEN * chr10 88915398 88915401 chr10 89141373 89141375 TCGA-J9-A52D DUP 6 20 STAMBPL1 * chr10 91480431 91480431 chr10 92051026 92051026 TCGA-J9-A52D DUP 3 20 HECTD2 CPEB3 chr11 100729298 100729298 chr11 100739879 100739879 TCGA-J9-A52D DUP 28 31 ARHGAP42 ARHGAP42 chr11 104660445 104660445 chr11 104703376 104703376 TCGA-J9-A52D DEL 49 32 * * chr11 105265777 105265777 chr11 107291240 107291240 TCGA-J9-A52D INS 39 45 CARD18 * chr11 109609994 109609994 chr11 109932104 109932104 TCGA-J9-A52D DUP 9 13 * RDX chr11 113846538 113846538 chr11 114107819 114107820 TCGA-J9-A52D DUP 39 40 USP28 ZBTB16 chr11 128571532 128571532 chr11 129003798 129003798 TCGA-J9-A52D DUP 44 41 ETS1 ARHGAP32 chr11 130025782 130025782 chr11 130864395 130864396 TCGA-J9-A52D DUP 31 17 * LINC02551 chr11 133250533 133250533 chr11 133277262 133277262 TCGA-J9-A52D DEL 41 34 OPCML OPCML chr11 133513402 133513402 chr11 133516526 133516526 TCGA-J9-A52D DEL 42 31 OPCML OPCML chr11 16424325 16424325 chr12 80521982 80521982 TCGA-J9-A52D BND 8 43 SOX6 PTPRQ chr11 1914833 1914833 chr11 1939710 1939710 TCGA-J9-A52D INV 10 26 * * chr11 19649229 19649230 chr11 22526579 22526579 TCGA-J9-A52D DUP 39 6 NAV2 * chr11 20489356 20489357 chr12 76579687 76579687 TCGA-J9-A52D BND 19 28 PRMT3 AC107032.2 chr11 20648784 20648784 chr11 23682990 23682990 TCGA-J9-A52D DUP 42 6 SLC6A5 * chr11 29364221 29364221 chr11 39815184 39815184 TCGA-J9-A52D DEL 34 11 LINC02755 * chr11 30707048 30707048 chr11 30711655 30711655 TCGA-J9-A52D DEL 41 26 * * chr11 31040170 31040170 chr11 37753086 37753086 TCGA-J9-A52D INS 6 14 DCDC1 * chr11 38022312 38022312 chr11 38052031 38052031 TCGA-J9-A52D DEL 30 33 * * chr11 42957281 42957281 chr11 49606754 49606754 TCGA-J9-A52D DEL 25 37 * AC136759.1 chr11 43149864 43149864 chr11 43438083 43438083 TCGA-J9-A52D DUP 46 17 HNRNPKP3 TTC17 chr11 62784023 62784023 chr11 62866371 62866371 TCGA-J9-A52D DEL 15 1 TAF6L SLC3A2 chr11 6321961 6321961 chr11 6322235 6322235 TCGA-J9-A52D DEL 3 27 CAVIN3 AC068733.3 chr11 66769537 66769537 chr11 70108468 70108468 TCGA-J9-A52D DUP 39 19 C11orf80 ANO1 chr11 66943813 66943814 chr11 67847729 67847729 TCGA-J9-A52D DUP 12 10 PC ENPP7P7 chr11 67201203 67201203 chr11 70258233 70258233 TCGA-J9-A52D DUP 41 34 KDM2A * chr11 78241390 78241390 chr11 82156255 82156256 TCGA-J9-A52D DUP 6 43 GAB2 MIR4300HG chr11 83436956 83436956 chr1 194337574 194337574 TCGA-J9-A52D BND 23 22 * * chr11 89511227 89511227 chr11 89656531 89656531 TCGA-J9-A52D DUP 44 34 * FOLH1B chr11 91366272 91366272 chr11 91817891 91817891 TCGA-J9-A52D DUP 13 24 * * chr11 93050943 93050943 chr11 96884227 96884227 TCGA-J9-A52D DUP 26 43 * * chr11 93177552 93177552 chr11 94099072 94099072 TCGA-J9-A52D DUP 29 45 SLC36A4 HEPHL1 chr11 97778063 97778063 chr11 97910702 97910702 TCGA-J9-A52D DUP 29 31 * LINC02713 chr11 99068637 99068637 chr11 99103704 99103704 TCGA-J9-A52D DEL 12 22 CNTN5 CNTN5 chr12 100430607 100430607 chr12 100431044 100431044 TCGA-J9-A52D INV 46 33 * * chr12 108997295 108997295 chr12 109477461 109477461 TCGA-J9-A52D DUP 23 7 SVOP KCTD10 chr12 11036551 11036551 chr12 11097852 11097852 TCGA-J9-A52D DUP 38 43 PRH1 PRH1 chr12 111787490 111787490 chr12 112040049 112040049 TCGA-J9-A52D DUP 8 10 ALDH2 NAA25 chr12 112957891 112957892 chr12 113710962 113710962 TCGA-J9-A52D DUP 48 33 OAS3 LINC01234 chr12 113968111 113968111 chr12 114115942 114115942 TCGA-J9-A52D DUP 44 1 * * chr12 116204456 116204456 chr12 119617854 119617855 TCGA-J9-A52D DUP 19 9 MED13L TMEM233 chr12 117680593 117680593 chr12 118177458 118177458 TCGA-J9-A52D DUP 34 48 KSR2 TAOK3 chr12 123168916 123168916 chr12 123327504 123327504 TCGA-J9-A52D DUP 18 32 MPHOSPH9 SBNO1 chr12 123484489 123484489 chr12 123754290 123754291 TCGA-J9-A52D DUP 48 2 RILPL1 ATP6V0A2 chr12 128565805 128565805 chr12 128832948 128832948 TCGA-J9-A52D DUP 6 33 TMEM132C * chr12 132348931 132348931 chr12 132650976 132650976 TCGA-J9-A52D DEL 21 46 * POLE chr12 132349578 132349578 chr12 132464246 132464274 TCGA-J9-A52D DUP 49 42 * * chr12 166757 166757 chr12 4104403 4104403 TCGA-J9-A52D DUP 35 48 IQSEC3 * chr12 17229471 17229479 chr21 29003766 29003766 TCGA-J9-A52D BND 33 1 * * chr12 17875477 17875477 chr21 32832172 32832172 TCGA-J9-A52D BND 28 37 * C21orf62-AS1 chr12 2063035 2063035 chr12 4196566 4196566 TCGA-J9-A52D DUP 17 15 CACNA1C * chr12 38959458 38959458 chr12 40586198 40586198 TCGA-J9-A52D DUP 7 4 * * chr12 3935327 3935327 chr12 3935689 3935689 TCGA-J9-A52D INV 41 37 * * chr12 4816540 4816540 chr12 7754953 7754954 TCGA-J9-A52D DUP 4 8 GALNT8 * chr12 50984057 50984058 chr12 53309481 53309481 TCGA-J9-A52D DUP 27 4 SLC11A2 AAAS chr12 51112897 51112898 chr12 54045139 54045139 TCGA-J9-A52D DUP 39 32 TFCP2 HOXC4 chr12 54133211 54133211 chr12 57001436 57001436 TCGA-J9-A52D DUP 14 42 SMUG1 ZBTB39 chr12 64424143 64424150 chr12 65110622 65110622 TCGA-J9-A52D DUP 9 20 XPOT WIF1 chr12 65078490 65078490 chr12 68025350 68025350 TCGA-J9-A52D INV 12 17 WIF1 IFNG-AS1 chr12 65604582 65604582 chr12 68051386 68051386 TCGA-J9-A52D DUP 1 23 AC025419.1 IFNG-AS1 chr12 65627061 65627061 chr12 65938482 65938482 TCGA-J9-A52D DUP 50 11 AC025419.1 HMGA2 chr12 68762118 68762119 chr12 72605612 72605612 TCGA-J9-A52D DUP 29 15 SLC35E3 TRHDE chr12 69899154 69899154 chr12 72751902 72751903 TCGA-J9-A52D DUP 28 45 MYRFL * chr12 80116853 80116853 chr3 82638152 82638152 TCGA-J9-A52D BND 7 17 OTOGL * chr12 91299598 91299598 chr12 91520042 91520042 TCGA-J9-A52D DUP 11 16 * * chr12 94508430 94508430 chr12 95172979 95172979 TCGA-J9-A52D DUP 38 38 * FGD6 chr12 953889 953889 chr1 24844649 24844649 TCGA-J9-A52D BND 35 21 RAD52 * chr12 96395267 96395267 chr12 100668619 100668628 TCGA-J9-A52D DUP 45 11 CDK17 * chr12 97165262 97165262 chr16 54664989 54664989 TCGA-J9-A52D BND 2 11 AC007656.2 * chr12 99682122 99682122 chr12 102895638 102895638 TCGA-J9-A52D DUP 2 44 ANKS1B PAH chr13 104735231 104735232 chr13 107329570 107329574 TCGA-J9-A52D DUP 9 15 * FAM155A chr13 108346093 108346093 chr13 108736693 108736694 TCGA-J9-A52D DUP 14 40 AL138694.1 MYO16 chr13 37877130 37877130 chr13 38100289 38100289 TCGA-J9-A52D DUP 36 28 * LINC00571 chr13 39394468 39394469 chr13 50335276 50335276 TCGA-J9-A52D DEL 11 4 LHFPL6 DLEU1 chr13 50791357 50791357 chr13 52021879 52021880 TCGA-J9-A52D DUP 15 25 DLEU7 ALG11 chr13 51817164 51817164 chr13 51955100 51955100 TCGA-J9-A52D DUP 47 50 AL162377.3 ATP7B chr13 52013670 52013670 chr13 52316322 52316322 TCGA-J9-A52D DUP 39 10 ALG11 TPTE2P2 chr13 53250124 53250124 chr13 53254009 53254009 TCGA-J9-A52D DEL 23 15 * * chr13 53713103 53713106 chr13 53930601 53930601 TCGA-J9-A52D DUP 49 4 * * chr13 54685049 54685049 chr13 54941570 54941570 TCGA-J9-A52D DUP 17 4 * AL390964.1 chr13 56098920 56098920 chr13 56100363 56100363 TCGA-J9-A52D DEL 49 22 * * chr13 66684569 66684569 chr13 67057332 67057332 TCGA-J9-A52D DUP 40 16 PCDH9 PCDH9 chr13 71883313 71883314 chr13 72369137 72369138 TCGA-J9-A52D DUP 15 3 * * chr13 71883313 71883314 chr13 81762409 81762409 TCGA-J9-A52D DUP 49 43 * * chr13 72369137 72369138 chr13 81762257 81762257 TCGA-J9-A52D DEL 17 37 * * chr13 81016816 81016817 chr13 81232213 81232213 TCGA-J9-A52D DUP 7 1 * * chr13 91634231 91634231 chr13 95563377 95563377 TCGA-J9-A52D DUP 46 1 GPC5 CLDN10 chr13 92076357 92076357 chr13 93037206 93037207 TCGA-J9-A52D DUP 21 45 GPC5 * chr14 105568898 105568911 chr14 105687187 105687187 TCGA-J9-A52D INV 18 27 * * chr14 22965584 22965584 chr14 25485143 25485143 TCGA-J9-A52D DUP 8 50 AL132780.3 * chr14 27292746 27292746 chr14 27443829 27443829 TCGA-J9-A52D DUP 32 20 AL390334.1 AL390334.1 chr14 42602263 42602263 chr14 42930375 42930375 TCGA-J9-A52D DUP 15 37 AL442163.1 * chr14 44169465 44169465 chr14 44408559 44408559 TCGA-J9-A52D DUP 21 40 LINC02307 * chr14 63511132 63511132 chr14 64211198 64211198 TCGA-J9-A52D DUP 17 35 PPP2R5E SYNE2 chr14 65593370 65593370 chr14 66182491 66182491 TCGA-J9-A52D DUP 10 44 FUT8 * chr14 65593370 65593370 chr15 58787684 58787684 TCGA-J9-A52D BND 22 1 FUT8 MINDY2 chr14 66181946 66181946 chrX 119891643 119891643 TCGA-J9-A52D BND 30 4 * * chr14 70918247 70918247 chr14 71302195 71302195 TCGA-J9-A52D DUP 48 48 PCNX1 AC005476.2 chr14 86767255 86767255 chr1 96216231 96216231 TCGA-J9-A52D BND 7 18 * * chr15 23381338 23381338 chr15 23668365 23668365 TCGA-J9-A52D DUP 28 9 * * chr15 24419528 24419528 chr15 30048264 30048264 TCGA-J9-A52D DUP 43 39 * * chr15 33991586 33991586 chr15 34440044 34440045 TCGA-J9-A52D DUP 36 3 AVEN * chr15 37933967 37933967 chr15 40396802 40396803 TCGA-J9-A52D DUP 9 44 TMCO5A * chr15 52062885 52062886 chr15 54615106 54615106 TCGA-J9-A52D DUP 32 50 MAPK6 UNC13C chr15 56386821 56386821 chrX 118424367 118424367 TCGA-J9-A52D BND 32 7 TEX9 WDR44 chr15 57680877 57680877 chr15 60532430 60532431 TCGA-J9-A52D DUP 48 15 GCOM1 RORA chr15 78540428 78540428 chr15 78961718 78961719 TCGA-J9-A52D DUP 27 33 PSMA4 RASGRF1 chr15 80745734 80745734 chr21 34347963 34347963 TCGA-J9-A52D BND 19 15 ABHD17C AP000317.2 chr15 86563411 86563411 chr15 86794086 86794086 TCGA-J9-A52D DUP 39 9 AGBL1 AGBL1 chr15 91156396 91156396 chr15 93240917 93240917 TCGA-J9-A52D DUP 20 27 SV2B * chr15 91291907 91291907 chr15 93213442 93213442 TCGA-J9-A52D DEL 48 35 SV2B * chr15 92258866 92258866 chr15 94031900 94031900 TCGA-J9-A52D DUP 29 2 AC116903.2 LINC01579 chr15 97475252 97475253 chr15 101295866 101295866 TCGA-J9-A52D DUP 35 1 LINC02254 SNRPA1 chr16 1677818 1677818 chr16 4873463 4873463 TCGA-J9-A52D DUP 47 49 CRAMP1 UBN1 chr16 1894655 1894655 chr16 2280503 2280503 TCGA-J9-A52D DUP 35 49 * ABCA3 chr16 20312019 20312019 chr18 43202295 43202295 TCGA-J9-A52D BND 13 47 GP2 * chr16 2302435 2302435 chr16 3278636 3278636 TCGA-J9-A52D DUP 35 16 ABCA3 ZNF263 chr16 23906881 23906881 chr18 46660870 46660870 TCGA-J9-A52D BND 22 36 PRKCB * chr16 2413375 2413375 chr16 2413531 2413531 TCGA-J9-A52D INV 8 40 ABCA17P ABCA17P chr16 59672745 59672745 chr16 59676076 59676076 TCGA-J9-A52D DEL 45 26 * * chr16 61106039 61106039 chr16 61240180 61240180 TCGA-J9-A52D DUP 43 22 * * chr16 72942122 72942122 chr16 80883475 80883475 TCGA-J9-A52D DUP 4 11 ZFHX3 ARLNC1 chr16 73206164 73206164 chr16 80404582 80404582 TCGA-J9-A52D DEL 12 25 ZFHX3 AC105411.1 chr16 73206724 73206724 chr16 80882583 80882584 TCGA-J9-A52D DEL 23 36 ZFHX3 ARLNC1 chr16 7914987 7914987 chr16 8178439 8178440 TCGA-J9-A52D DUP 24 20 * * chr16 80404472 80404472 chr16 80883174 80883174 TCGA-J9-A52D INV 6 14 AC105411.1 ARLNC1 chr16 86419633 86419633 chr16 89068889 89068889 TCGA-J9-A52D DEL 17 4 * * chr16 8963811 8963811 chr16 10734037 10734038 TCGA-J9-A52D DUP 31 14 USP7 * chr17 2462650 2462650 chr17 2831960 2831961 TCGA-J9-A52D DUP 23 50 METTL16 RAP1GAP2 chr17 31981037 31981037 chr17 33005717 33005717 TCGA-J9-A52D DUP 42 23 SUZ12 * chr17 35207202 35207202 chr17 35913253 35913253 TCGA-J9-A52D DUP 14 18 * LRRC37A9P chr17 35379677 35379677 chr17 35913203 35913203 TCGA-J9-A52D DUP 36 21 * LRRC37A9P chr17 37904729 37904729 chr17 40765569 40765569 TCGA-J9-A52D DUP 38 11 * * chr17 4786999 4786999 chr17 5606980 5606980 TCGA-J9-A52D DUP 26 45 VMO1 NLRP1 chr17 48268842 48268842 chr17 49652451 49652452 TCGA-J9-A52D DUP 43 20 SKAP1 SPOP chr17 48435407 48435407 chr17 52425225 52425225 TCGA-J9-A52D DUP 25 5 * LINC01982 chr17 58261435 58261435 chr17 60721024 60721025 TCGA-J9-A52D DUP 41 16 LPO BCAS3 chr17 72441195 72441195 chr17 75516843 75516843 TCGA-J9-A52D DUP 3 22 LINC00511 CASKIN2 chr17 74170479 74170479 chr17 77947381 77947382 TCGA-J9-A52D DUP 12 16 * * chr17 7672340 7672340 chr7 100426095 100426095 TCGA-J9-A52D BND 12 32 TP53 ZCWPW1 chr17 76876077 76876077 chr17 76906454 76906454 TCGA-J9-A52D DUP 18 2 MGAT5B MGAT5B chr17 79832218 79832218 chr17 80220815 80220815 TCGA-J9-A52D DUP 4 22 * SGSH chr18 11540501 11540501 chr18 11706783 11706783 TCGA-J9-A52D DUP 7 23 * GNAL chr18 21732675 21732675 chr18 24954167 24954167 TCGA-J9-A52D DUP 36 37 MIB1 LINC01894 chr18 33591117 33591117 chr18 33823139 33823139 TCGA-J9-A52D DUP 7 14 ASXL3 * chr18 62316430 62316431 chr18 65226032 65226045 TCGA-J9-A52D DUP 10 50 * * chr18 63276483 63276483 chr18 63327158 63327158 TCGA-J9-A52D DEL 41 32 BCL2 * chr18 63327796 63327796 chr18 65345059 65345061 TCGA-J9-A52D DEL 35 50 KDSR * chr18 64621046 64621046 chr18 70772213 70772213 TCGA-J9-A52D DEL 50 7 * * chr18 64800080 64800080 chr18 65521288 65521288 TCGA-J9-A52D DUP 32 2 * * chr18 72267229 72267229 chr18 78159573 78159573 TCGA-J9-A52D DEL 5 15 * * chr18 72765137 72765137 chr18 73074402 73074403 TCGA-J9-A52D DUP 38 41 NETO1 * chr19 16921210 16921210 chr19 17015007 17015007 TCGA-J9-A52D DUP 34 11 CPAMD8 CPAMD8 chr19 16938203 16938203 chr19 17260862 17260862 TCGA-J9-A52D DUP 22 47 CPAMD8 USHBP1 chr19 2177684 2177684 chr19 2698896 2698896 TCGA-J9-A52D DUP 10 12 DOT1L GNG7 chr19 29033214 29033214 chr19 29201948 29201948 TCGA-J9-A52D DUP 20 4 * * chr19 36320117 36320118 chr19 36347826 36347826 TCGA-J9-A52D DEL 5 1 LINC00665 ZFP14 chr19 3635159 3635163 chr19 5138155 5138157 TCGA-J9-A52D DUP 3 32 PIP5K1C KDM4B chr19 44246366 44246366 chr19 45063630 45063631 TCGA-J9-A52D DUP 17 6 ZNF235 CLASRP chr19 52001410 52001411 chr19 52415588 52415588 TCGA-J9-A52D DUP 49 42 ZNF615 ZNF528 chr19 52088071 52088071 chr19 52202321 52202321 TCGA-J9-A52D INV 41 19 ZNF432 PPP2R1A chr19 52196254 52196254 chr19 52200488 52200488 TCGA-J9-A52D INV 4 23 PPP2R1A PPP2R1A chr19 52202272 52202272 chr19 52206566 52206569 TCGA-J9-A52D INV 8 38 PPP2R1A PPP2R1A chr19 52204308 52204308 chr19 52285221 52285221 TCGA-J9-A52D INV 15 24 PPP2R1A ZNF766 chr19 53376648 53376648 chr19 53800043 53800044 TCGA-J9-A52D DUP 8 14 ZNF525 NLRP12 chr19 5401712 5401712 chr19 5404680 5404680 TCGA-J9-A52D INV 28 47 * * chr19 56112140 56112140 chr19 57046455 57046455 TCGA-J9-A52D DUP 16 21 ZNF787 * chr19 56575470 56575471 chr19 57375732 57375732 TCGA-J9-A52D DUP 50 10 ZNF470 ZNF547 chr19 9192811 9192812 chr19 10164569 10164569 TCGA-J9-A52D DUP 1 38 * DNMT1 chr1 107286497 107286497 chr1 110997067 110997067 TCGA-J9-A52D DUP 46 5 NTNG1 * chr1 119137586 119137586 chr1 144035250 144035250 TCGA-J9-A52D INV 2 37 WARS2 SRGAP2D chr1 150418713 150418714 chr1 150888379 150888379 TCGA-J9-A52D DUP 9 37 RPRD2 CTXND2 chr1 150741661 150741661 chr1 150960724 150960724 TCGA-J9-A52D DUP 42 31 CTSS SETDB1 chr1 154332340 154332340 chr1 155261467 155261467 TCGA-J9-A52D DUP 44 34 ATP8B2 SCAMP3 chr1 154990400 154990400 chr1 155742899 155742899 TCGA-J9-A52D DUP 6 50 FLAD1 * chr1 164154581 164154581 chr1 224110248 224110248 TCGA-J9-A52D DEL 3 14 * * chr1 164203057 164203057 chr1 164538574 164538574 TCGA-J9-A52D DUP 39 45 * * chr1 171623362 171623362 chr1 172106381 172106381 TCGA-J9-A52D DUP 28 9 MYOCOS DNM3 chr1 17495389 17495390 chr1 20306556 20306556 TCGA-J9-A52D DUP 44 41 * VWA5B1 chr1 182486872 182486873 chr1 186666054 186666054 TCGA-J9-A52D DUP 29 42 RGSL1 * chr1 184486107 184486107 chr1 191344610 191344610 TCGA-J9-A52D INS 46 44 C1orf21 * chr1 184499763 184499763 chr1 189791014 189791014 TCGA-J9-A52D DEL 2 44 C1orf21 LINC01701 chr1 184896484 184896484 chr1 185706597 185706597 TCGA-J9-A52D DUP 26 13 NIBAN1 * chr1 185074794 185074794 chr1 189214656 189214656 TCGA-J9-A52D INS 27 48 RNF2 * chr1 185098375 185098375 chr1 189039215 189039215 TCGA-J9-A52D DEL 6 25 RNF2 * chr1 186041062 186041062 chr1 193067878 193067878 TCGA-J9-A52D INS 28 31 HMCN1 RO60 chr1 186315467 186315467 chr1 189318794 189318794 TCGA-J9-A52D DEL 9 37 TPR * chr1 186824480 186824480 chr1 190789148 190789148 TCGA-J9-A52D INS 4 20 * LINC01720 chr1 187690449 187690449 chr1 189013876 189013876 TCGA-J9-A52D DEL 20 11 * LINC01035 chr1 188737091 188737091 chr1 189218281 189218281 TCGA-J9-A52D DEL 17 28 * * chr1 190897797 190897797 chr1 193303993 193303994 TCGA-J9-A52D DUP 5 1 AL138927.1 LINC01031 chr1 194763507 194763507 chr1 197855657 197855657 TCGA-J9-A52D DEL 28 17 * * chr1 213681997 213681997 chr1 217183326 217183326 TCGA-J9-A52D INS 9 32 * * chr1 216850588 216850588 chr1 220609233 220609233 TCGA-J9-A52D DUP 27 9 ESRRG MARK1 chr1 219546134 219546134 chr1 223137989 223137989 TCGA-J9-A52D DUP 4 39 * TLR5 chr1 227740934 227740934 chr1 230283934 230283934 TCGA-J9-A52D DUP 34 37 SNAP47 * chr1 234784311 234784311 chr1 237916285 237916285 TCGA-J9-A52D DUP 23 38 * AL359924.1 chr1 237011763 237011763 chr1 237077615 237077615 TCGA-J9-A52D DUP 25 4 * RYR2 chr1 238490308 238490308 chr1 238539783 238539783 TCGA-J9-A52D INV 9 49 KRT18P32 * chr1 238539547 238539548 chr1 238663139 238663140 TCGA-J9-A52D INV 31 34 * * chr1 239167094 239167094 chr1 241373122 241373123 TCGA-J9-A52D DUP 18 39 * * chr1 242205691 242205691 chr7 57656886 57656886 TCGA-J9-A52D BND 13 42 PLD5 * chr1 243375156 243375156 chr1 243379062 243379062 TCGA-J9-A52D DEL 9 39 SDCCAG8 SDCCAG8 chr1 24844649 24844649 chr12 953889 953889 TCGA-J9-A52D BND 35 24 * RAD52 chr1 31376613 31376613 chr1 31838075 31838076 TCGA-J9-A52D DUP 32 30 FABP3 * chr1 34099318 34099318 chr1 38513049 38513049 TCGA-J9-A52D DEL 49 12 CSMD2 * chr1 38513764 38513764 chr13 25811978 25811978 TCGA-J9-A52D BND 1 35 * ATP8A2 chr1 44274064 44274065 chr1 45390008 45390026 TCGA-J9-A52D DUP 1 5 ERI3 TESK2 chr1 44834154 44834154 chr1 44998041 44998041 TCGA-J9-A52D DUP 50 23 PTCH2 * chr1 46800398 46800398 chr1 48680572 48680572 TCGA-J9-A52D DUP 4 27 CYP4B1 AGBL4 chr1 50227600 50227600 chr1 53157627 53157628 TCGA-J9-A52D DUP 34 38 * * chr1 51800370 51800370 chr1 52074574 52074574 TCGA-J9-A52D DUP 26 41 NRDC BTF3L4 chr1 53997075 53997075 chr1 54089871 54089872 TCGA-J9-A52D DEL 34 16 * TCEANC2 chr1 58013611 58013611 chr1 60028764 60028765 TCGA-J9-A52D DUP 16 25 DAB1 C1orf87 chr1 73153293 73153293 chr1 73421279 73421279 TCGA-J9-A52D DUP 25 37 * * chr1 73524888 73524888 chrX 66587185 66587185 TCGA-J9-A52D BND 14 3 * * chr1 75995116 75995116 chr1 78515583 78515583 TCGA-J9-A52D DUP 27 3 AC092813.1 PTGFR chr1 8794089 8794089 chr1 9132753 9132753 TCGA-J9-A52D DUP 7 39 RERE * chr1 90333179 90333179 chr1 90334737 90334737 TCGA-J9-A52D DEL 7 49 * * chr1 96763277 96763277 chr1 97040196 97040196 TCGA-J9-A52D DUP 11 21 PTBP2 * chr1 97850706 97850706 chr19 52287203 52287203 TCGA-J9-A52D BND 27 32 DPYD ZNF766 chr1 98062061 98062081 chr19 52206566 52206569 TCGA-J9-A52D BND 42 33 * PPP2R1A chr20 15448400 15448400 chr20 15975855 15975855 TCGA-J9-A52D DEL 37 3 MACROD2 MACROD2 chr20 1571331 1571331 chr20 1609366 1609366 TCGA-J9-A52D DEL 43 43 SIRPB1 SIRPB1 chr20 23532503 23532503 chr16 63227862 63227862 TCGA-J9-A52D BND 41 1 CST13P * chr20 32548485 32548485 chr20 33959435 33959435 TCGA-J9-A52D DUP 48 39 NOL4L * chr20 38965120 38965120 chr20 39341193 39341194 TCGA-J9-A52D DUP 17 27 DHX35 * chr20 44896671 44896671 chr20 45324171 45324172 TCGA-J9-A52D DUP 36 50 YWHAB * chr20 47899337 47899337 chr20 48188001 48188001 TCGA-J9-A52D DUP 5 44 * * chr20 48688147 48688147 chr20 52031219 52031220 TCGA-J9-A52D DUP 28 25 PREX1 * chr20 53171397 53171400 chr20 54824873 54824873 TCGA-J9-A52D DUP 27 36 TSHZ2 * chr20 59723363 59723363 chr20 63377362 63377362 TCGA-J9-A52D DUP 30 24 PHACTR3 CHRNA4 chr21 14640585 14640586 chr21 16511600 16511600 TCGA-J9-A52D DUP 37 39 SAMSN1 MIR99AHG chr21 15891712 15891712 chr21 16136136 16136136 TCGA-J9-A52D DUP 8 22 * MIR99AHG chr21 27267168 27267168 chr21 27316937 27316937 TCGA-J9-A52D DUP 20 48 * * chr21 38426160 38426160 chr21 41500586 41500586 TCGA-J9-A52D DEL 45 32 ERG TMPRSS2 chr21 38512029 38512029 chr21 41505415 41505422 TCGA-J9-A52D DEL 6 2 ERG TMPRSS2 chr21 41497265 41497265 chr17 43556562 43556562 TCGA-J9-A52D BND 4 41 TMPRSS2 DHX8 chr21 9906266 9906266 chr21 10149151 10149151 TCGA-J9-A52D DUP 39 47 * * chr22 25325496 25325496 chr22 27657033 27657033 TCGA-J9-A52D DUP 50 31 * * chr22 32343341 32343341 chr22 32615929 32615930 TCGA-J9-A52D DUP 30 9 AL021937.3 SYN3 chr2 101940013 101940013 chr2 102189901 102189901 TCGA-J9-A52D DUP 35 49 * IL1RL2 chr2 103106598 103106598 chr2 103336287 103336287 TCGA-J9-A52D DUP 12 23 * * chr2 112304562 112304562 chr2 112921471 112921472 TCGA-J9-A52D DUP 46 16 ZC3H6 * chr2 114523256 114523256 chr2 114541927 114541927 TCGA-J9-A52D DEL 27 50 DPP10 DPP10 chr2 117419945 117419945 chr2 119427969 119427970 TCGA-J9-A52D DUP 10 43 * * chr2 123862682 123862682 chr2 124100775 124100775 TCGA-J9-A52D DUP 33 32 * CNTNAP5 chr2 13223947 13223947 chr2 13537783 13537783 TCGA-J9-A52D DUP 9 38 AC093912.1 AC073062.1 chr2 13224025 13224026 chr2 184398791 184398791 TCGA-J9-A52D DUP 35 40 AC093912.1 * chr2 13495736 13495736 chr2 14396675 14396675 TCGA-J9-A52D DUP 41 2 * LINC00276 chr2 13538300 13538301 chr2 184397717 184397717 TCGA-J9-A52D DEL 41 34 AC073062.1 * chr2 13671368 13671368 chr2 14167817 14167817 TCGA-J9-A52D DUP 30 34 * LINC00276 chr2 136909096 136909096 chr2 136925417 136925417 TCGA-J9-A52D DEL 21 2 THSD7B THSD7B chr2 13714627 13714627 chr2 14335080 14335080 TCGA-J9-A52D DUP 10 3 LINC00276 LINC00276 chr2 13741485 13741485 chr2 14544329 14544330 TCGA-J9-A52D DUP 8 9 LINC00276 * chr2 140296252 140296252 chr2 140515672 140515673 TCGA-J9-A52D DUP 44 15 LRP1B LRP1B chr2 150075464 150075464 chr2 155282737 155282737 TCGA-J9-A52D DEL 11 40 * * chr2 151240379 151240379 chr2 184123151 184123151 TCGA-J9-A52D INS 25 47 * * chr2 151399444 151399444 chr2 152998278 152998278 TCGA-J9-A52D DUP 40 15 * * chr2 153279531 153279531 chr2 153608517 153608517 TCGA-J9-A52D DUP 43 30 * * chr2 159731003 159731004 chr2 159997810 159997810 TCGA-J9-A52D DUP 48 33 MARCHF7 PLA2R1 chr2 16336139 16336139 chr2 72831684 72831685 TCGA-J9-A52D DUP 7 50 * * chr2 165723465 165723465 chr2 168567520 168567520 TCGA-J9-A52D DUP 21 43 * CERS6 chr2 18120517 18120517 chr2 19242619 19242619 TCGA-J9-A52D DUP 14 33 KCNS3 LINC01376 chr2 183619713 183619713 chr2 185758681 185758690 TCGA-J9-A52D DUP 11 12 * FSIP2 chr2 184086284 184086284 chr2 184282092 184282092 TCGA-J9-A52D DUP 10 7 * * chr2 188885022 188885022 chr18 54572622 54572622 TCGA-J9-A52D BND 28 29 * * chr2 191804922 191804922 chr18 52277942 52277942 TCGA-J9-A52D BND 14 3 AC098872.1 * chr2 199922025 199922025 chr2 201415343 201415343 TCGA-J9-A52D DUP 8 22 C2orf69 TRAK2 chr2 201337442 201337442 chr2 201378947 201378947 TCGA-J9-A52D DEL 28 19 FLACC1 TRAK2 chr2 20846634 20846634 chr2 68552812 68552812 TCGA-J9-A52D DEL 9 22 * APLF chr2 211719534 211719534 chr2 212053968 212053968 TCGA-J9-A52D DUP 12 27 ERBB4 ERBB4 chr2 227277335 227277335 chr2 227719225 227719226 TCGA-J9-A52D DUP 17 39 COL4A3 SLC19A3 chr2 231005597 231005597 chr20 63443265 63443265 TCGA-J9-A52D BND 6 42 SPATA3 KCNQ2 chr2 25771055 25771055 chr2 74100919 74100919 TCGA-J9-A52D DEL 44 45 ASXL2 TET3 chr2 2695808 2695808 chr2 3049860 3049860 TCGA-J9-A52D DUP 13 42 * LINC01250 chr2 30851843 30851843 chr2 31458612 31458612 TCGA-J9-A52D DUP 23 18 * * chr2 30993303 30993309 chr8 71934229 71934234 TCGA-J9-A52D BND 30 41 GALNT14 MSC-AS1 chr2 41302251 41302251 chr2 41305612 41305612 TCGA-J9-A52D DEL 36 45 * * chr2 4578934 4578934 chr2 4906146 4906146 TCGA-J9-A52D DUP 6 25 * * chr2 56199985 56199985 chr2 56422066 56422066 TCGA-J9-A52D DUP 43 10 AC007744.1 * chr2 56538338 56538338 chr2 56538941 56538941 TCGA-J9-A52D DEL 12 42 * * chr2 60323058 60323058 chr2 60333330 60333330 TCGA-J9-A52D DEL 22 36 * * chr2 62414333 62414333 chr2 62744048 62744049 TCGA-J9-A52D DUP 33 30 * EHBP1 chr2 63888423 63888424 chr2 68318161 68318162 TCGA-J9-A52D DUP 16 40 UGP2 CNRIP1 chr2 63888423 63888424 chr12 73330487 73330487 TCGA-J9-A52D BND 15 39 UGP2 * chr2 67255770 67255770 chr2 68012555 68012555 TCGA-J9-A52D DUP 24 43 LINC01828 * chr2 68318161 68318162 chr12 73330618 73330618 TCGA-J9-A52D BND 29 10 CNRIP1 * chr2 70110031 70110032 chr2 70447833 70447833 TCGA-J9-A52D DUP 36 19 * TGFA chr2 75688826 75688826 chr2 75880961 75880962 TCGA-J9-A52D DUP 49 36 MRPL19 * chr2 87305257 87305257 chr2 87587297 87587297 TCGA-J9-A52D DUP 4 39 * CYTOR chr2 88561259 88561259 chr8 127912206 127912213 TCGA-J9-A52D BND 30 13 EIF2AK3 PVT1 chr3 10011197 10011197 chr3 10349869 10349870 TCGA-J9-A52D DUP 15 17 EMC3 ATP2B2 chr3 101135446 101135446 chr3 101594801 101594801 TCGA-J9-A52D DUP 21 29 * * chr3 107329367 107329367 chr3 110819393 110819394 TCGA-J9-A52D DUP 32 26 CSP2 * chr3 121841567 121841567 chr3 123161926 123161941 TCGA-J9-A52D DUP 42 17 EAF2 PDIA5 chr3 122504150 122504150 chr3 122833373 122833373 TCGA-J9-A52D DUP 41 31 KPNA1 SLC49A4 chr3 137712824 137712824 chr3 138725578 138725579 TCGA-J9-A52D DUP 10 47 * PIK3CB chr3 139805353 139805353 chr3 140133937 140133937 TCGA-J9-A52D DUP 33 8 * CLSTN2 chr3 140828755 140828755 chr3 143119501 143119501 TCGA-J9-A52D DUP 47 20 * CHST2 chr3 149212609 149212609 chr3 149381768 149381769 TCGA-J9-A52D DUP 24 42 CP TM4SF1-AS1 chr3 150465789 150465789 chr3 150580664 150580665 TCGA-J9-A52D DUP 26 44 TSC22D2 SERP1 chr3 160382585 160382585 chr3 163130550 163130551 TCGA-J9-A52D DUP 9 17 IFT80 AC128685.1 chr3 164426582 164426582 chr3 164430580 164430580 TCGA-J9-A52D DEL 15 28 * * chr3 167716333 167716333 chr3 169580459 169580471 TCGA-J9-A52D DUP 48 4 PDCD10 MECOM chr3 167970106 167970106 chr3 168469073 168469073 TCGA-J9-A52D DUP 42 31 * EGFEM1P chr3 168950726 168950726 chr5 12201868 12201868 TCGA-J9-A52D BND 25 29 * * chr3 168950780 168950780 chr3 172206930 172206930 TCGA-J9-A52D DUP 26 25 * FNDC3B chr3 172207726 172207726 chr5 12202912 12202912 TCGA-J9-A52D BND 50 25 FNDC3B * chr3 179075235 179075235 chr3 179105311 179105311 TCGA-J9-A52D DUP 31 22 * AC076966.2 chr3 180304080 180304080 chr3 182591454 182591454 TCGA-J9-A52D DUP 16 16 * * chr3 18451258 18451259 chr3 18696640 18696640 TCGA-J9-A52D DUP 32 25 SATB1-AS1 SATB1-AS1 chr3 19127231 19127231 chr3 19129552 19129552 TCGA-J9-A52D DEL 49 11 * * chr3 192700225 192700225 chr3 192873862 192873862 TCGA-J9-A52D DUP 18 47 FGF12 MB21D2 chr3 2435840 2435859 chr3 2845998 2845998 TCGA-J9-A52D DUP 14 18 CNTN4 CNTN4 chr3 2435840 2435859 chr3 10703561 10703561 TCGA-J9-A52D DUP 17 5 CNTN4 ATP2B2 chr3 2723702 2723702 chr3 3514517 3514517 TCGA-J9-A52D INV 8 46 CNTN4 AC034195.1 chr3 2844153 2844153 chr3 7875129 7875129 TCGA-J9-A52D DEL 49 24 CNTN4 * chr3 2844268 2844268 chr3 10704974 10704974 TCGA-J9-A52D DUP 11 43 CNTN4 ATP2B2 chr3 31848059 31848059 chr3 34554930 34554930 TCGA-J9-A52D DUP 25 3 OSBPL10 LINC01811 chr3 3509236 3509236 chr3 3544499 3544499 TCGA-J9-A52D INV 45 17 AC034195.1 AC034195.1 chr3 42740149 42740149 chr3 45809959 45809959 TCGA-J9-A52D DUP 47 28 CCDC13 * chr3 5091999 5091999 chr3 5338259 5338259 TCGA-J9-A52D DUP 25 22 * * chr3 59420915 59420915 chr3 59768744 59768745 TCGA-J9-A52D INS 9 7 * FHIT chr3 68074872 68074872 chr3 71689710 71689710 TCGA-J9-A52D DUP 43 48 TAFA1 AC097634.4 chr3 7657685 7657685 chr3 8036635 8036635 TCGA-J9-A52D DUP 25 36 GRM7 LMCD1-AS1 chr3 77403444 77403444 chr3 77900595 77900596 TCGA-J9-A52D DUP 35 28 ROBO2 * chr3 77740998 77740998 chr3 79614032 79614032 TCGA-J9-A52D DEL 14 22 * ROBO1 chr3 97598100 97598100 chr3 98313053 98313053 TCGA-J9-A52D DUP 3 15 EPHA6 AC117473.1 chr3 97904153 97904164 chr3 98723141 98723141 TCGA-J9-A52D DUP 49 41 CRYBG3 ST3GAL6-AS1 chr4 105193206 105193207 chr4 105573973 105573973 TCGA-J9-A52D DUP 5 50 TET2 ARHGEF38 chr4 107133613 107133613 chr4 109141116 109141116 TCGA-J9-A52D DUP 34 47 DKK2 COL25A1 chr4 107227854 107227854 chr4 108640241 108640241 TCGA-J9-A52D DUP 50 15 DKK2 * chr4 119466644 119466644 chr4 123780091 123780091 TCGA-J9-A52D DUP 38 7 AC093752.1 LINC01091 chr4 120420915 120420915 chr4 120731686 120731686 TCGA-J9-A52D DUP 24 47 * PRDM5 chr4 126332670 126332670 chr4 129085941 129085941 TCGA-J9-A52D DUP 8 8 * SCLT1 chr4 127469225 127469232 chr9 104674652 104674659 TCGA-J9-A52D BND 38 7 AC093772.1 * chr4 145902228 145902228 chr4 146201695 146201695 TCGA-J9-A52D DUP 5 5 ZNF827 * chr4 147768307 147768307 chr4 148235975 148235975 TCGA-J9-A52D DUP 17 18 ARHGAP10 NR3C2 chr4 14888495 14888496 chr4 17870503 17870503 TCGA-J9-A52D DUP 30 17 LINC00504 LCORL chr4 149215366 149215366 chr4 149219932 149219932 TCGA-J9-A52D DEL 22 23 LINC02355 LINC02355 chr4 149270927 149270927 chr4 152439684 152439685 TCGA-J9-A52D DUP 15 30 LINC02355 FBXW7 chr4 150281999 150282000 chr4 150475234 150475234 TCGA-J9-A52D DUP 3 35 LRBA LRBA chr4 1590569 1590569 chr4 1990319 1990319 TCGA-J9-A52D DUP 7 25 * NELFA chr4 161342543 161342543 chr4 161342657 161342657 TCGA-J9-A52D DEL 43 14 * * chr4 1627424 1627424 chr4 1627759 1627759 TCGA-J9-A52D INV 28 40 FAM53A FAM53A chr4 1633340 1633340 chr4 1633747 1633747 TCGA-J9-A52D INV 4 20 FAM53A FAM53A chr4 170421966 170421966 chr4 170804478 170804478 TCGA-J9-A52D DUP 10 8 * * chr4 174884286 174884286 chr4 174891309 174891309 TCGA-J9-A52D DEL 45 36 ADAM29 ADAM29 chr4 17572723 17572723 chr4 17881112 17881113 TCGA-J9-A52D DUP 42 22 * LCORL chr4 175837000 175837000 chr4 179135220 179135220 TCGA-J9-A52D DUP 40 5 GPM6A * chr4 179373352 179373352 chr4 179699098 179699098 TCGA-J9-A52D DUP 22 28 * * chr4 180176792 180176800 chr4 180247260 180247260 TCGA-J9-A52D DUP 48 42 * * chr4 182829123 182829123 chr4 184855021 184855022 TCGA-J9-A52D DUP 10 7 * MIR3945HG chr4 18806936 18806936 chr4 19176023 19176024 TCGA-J9-A52D DUP 16 11 * LINC02438 chr4 20051121 20051121 chr19 5707926 5707926 TCGA-J9-A52D BND 2 46 * LONP1 chr4 23896578 23896578 chr4 24703779 24703780 TCGA-J9-A52D DUP 41 9 PPARGC1A * chr4 25721937 25721937 chr4 25906930 25906930 TCGA-J9-A52D DUP 27 18 MTCO3P44 SMIM20 chr4 28079865 28079865 chr4 28461965 28461965 TCGA-J9-A52D DUP 21 26 * AC097480.1 chr4 28525596 28525596 chr4 28911859 28911859 TCGA-J9-A52D DUP 8 27 AC097480.1 * chr4 33180572 33180572 chr4 33181080 33181080 TCGA-J9-A52D DEL 48 8 * * chr4 34536213 34536213 chr4 35203503 35203503 TCGA-J9-A52D DUP 36 4 * * chr4 34599445 34599445 chr4 34697779 34697779 TCGA-J9-A52D DUP 40 37 * * chr4 47179881 47179881 chr4 47520374 47520382 TCGA-J9-A52D DUP 18 22 GABRB1 ATP10D chr4 47187906 47187906 chr4 47503988 47503988 TCGA-J9-A52D DUP 30 42 GABRB1 ATP10D chr4 68933466 68933466 chr4 69162384 69162384 TCGA-J9-A52D DUP 3 42 UGT2A3 * chr4 70620084 70620084 chr4 72397497 72397497 TCGA-J9-A52D DUP 16 12 * ADAMTS3 chr4 71271175 71271175 chr4 76519030 76519032 TCGA-J9-A52D DUP 1 33 SLC4A4 SHROOM3 chr4 78206269 78206269 chr4 79123411 79123412 TCGA-J9-A52D DUP 11 7 FRAS1 LINC01088 chr4 78499482 78499482 chr4 79000620 79000620 TCGA-J9-A52D DUP 29 39 FRAS1 LINC01088 chr4 79949284 79949285 chr4 80144575 80144575 TCGA-J9-A52D DUP 32 41 ANTXR2 * chr4 892016 892016 chr4 1985222 1985222 TCGA-J9-A52D DUP 8 3 GAK NELFA chr4 91410548 91410548 chr4 91530631 91530631 TCGA-J9-A52D DEL 42 10 CCSER1 CCSER1 chr4 94590138 94590138 chr4 95086517 95086517 TCGA-J9-A52D DUP 11 27 PDLIM5 BMPR1B chr4 98799856 98799857 chr4 102306764 102306764 TCGA-J9-A52D DUP 46 8 * SLC39A8 chr5 101236555 101236555 chr5 101238781 101238781 TCGA-J9-A52D DEL 8 37 * * chr5 101369021 101369021 chr5 101413603 101413603 TCGA-J9-A52D DEL 47 2 * * chr5 103380171 103380171 chr5 103802884 103802884 TCGA-J9-A52D DUP 30 1 * * chr5 104245436 104245436 chr5 105320807 105320807 TCGA-J9-A52D DUP 11 4 * AC099520.1 chr5 105255584 105255599 chr5 108050003 108050003 TCGA-J9-A52D DUP 41 26 AC099520.1 FBXL17 chr5 105466282 105466283 chr5 105654281 105654281 TCGA-J9-A52D DUP 37 13 * * chr5 106619345 106619345 chr5 106619934 106619934 TCGA-J9-A52D DEL 26 26 * * chr5 107472988 107472988 chr5 107808833 107808833 TCGA-J9-A52D DUP 23 50 EFNA5 * chr5 109066267 109066267 chr5 109429310 109429310 TCGA-J9-A52D DUP 49 40 FER * chr5 110908524 110908524 chr5 115065716 115065717 TCGA-J9-A52D DUP 9 17 AC008782.1 * chr5 112756205 112756206 chr5 113097894 113097894 TCGA-J9-A52D DUP 32 48 APC MCC chr5 114182876 114182876 chr5 114424940 114424941 TCGA-J9-A52D DUP 27 5 KCNN2 KCNN2 chr5 119794653 119794653 chr5 123373477 123373478 TCGA-J9-A52D DUP 19 40 * CEP120 chr5 122499979 122499979 chr5 122873762 122873762 TCGA-J9-A52D DUP 28 25 * SNX24 chr5 128948511 128948511 chr10 87861267 87861267 TCGA-J9-A52D BND 35 40 SLC27A6 KLLN chr5 137178201 137178201 chr5 140797132 140797132 TCGA-J9-A52D DUP 35 50 SPOCK1 PCDHA1 chr5 152789093 152789093 chr5 152799034 152799034 TCGA-J9-A52D DEL 4 33 LINC01470 LINC01470 chr5 159765640 159765640 chr5 160548224 160548224 TCGA-J9-A52D DUP 32 1 AC008691.1 * chr5 162118414 162118414 chr5 162119416 162119416 TCGA-J9-A52D DEL 32 32 GABRG2 GABRG2 chr5 167742934 167742936 chr5 173533159 173533159 TCGA-J9-A52D DUP 41 14 TENM2 * chr5 176481129 176481129 chr5 178881875 178881875 TCGA-J9-A52D DUP 31 29 FAF2 ZNF354B chr5 176505373 176505373 chr5 180360327 180360327 TCGA-J9-A52D DUP 6 22 FAF2 * chr5 176964285 176964285 chr5 177008656 177008656 TCGA-J9-A52D DEL 41 25 UIMC1 UIMC1 chr5 179434006 179434006 chr5 179502578 179502578 TCGA-J9-A52D DUP 29 16 * * chr5 22316759 22316759 chr5 164029052 164029052 TCGA-J9-A52D DEL 30 18 CDH12 * chr5 28810221 28810221 chr5 28939234 28939234 TCGA-J9-A52D DUP 7 1 AC008825.1 * chr5 43076904 43076904 chr5 43371228 43371228 TCGA-J9-A52D DUP 43 39 ZNF131 * chr5 60578276 60578276 chr5 61255460 61255464 TCGA-J9-A52D DUP 14 29 * LINC02057 chr5 68635671 68635671 chr5 68646771 68646771 TCGA-J9-A52D DUP 35 36 * * chr5 7082415 7082415 chr5 7209747 7209747 TCGA-J9-A52D DEL 33 25 LINC02196 LINC02196 chr5 76036321 76036321 chr5 80599704 80599705 TCGA-J9-A52D DUP 49 33 * * chr5 76623181 76623181 chr5 77480032 77480032 TCGA-J9-A52D DUP 31 28 IQGAP2 WDR41 chr5 83967951 83967951 chr5 83986567 83986567 TCGA-J9-A52D DEL 30 20 EDIL3 EDIL3 chr5 85995436 85995436 chr5 151846617 151846617 TCGA-J9-A52D DEL 15 48 * GLRA1 chr5 91553044 91553044 chr5 153416670 153416670 TCGA-J9-A52D INS 6 41 * * chr5 97544096 97544096 chr5 126279460 126279460 TCGA-J9-A52D DEL 25 26 LINC01340 AC116362.1 chr5 98907628 98907628 chr5 98934105 98934105 TCGA-J9-A52D DEL 26 47 CHD1 LINC02062 chr6 102643700 102643701 chr6 102849505 102849505 TCGA-J9-A52D DUP 25 32 * * chr6 105893247 105893247 chr6 106705037 106705037 TCGA-J9-A52D DUP 13 22 AL591518.1 * chr6 107710291 107710291 chr6 107920495 107920495 TCGA-J9-A52D DUP 35 3 SCML4 SEC63 chr6 11586400 11586400 chr6 12162750 12162750 TCGA-J9-A52D DUP 23 20 * HIVEP1 chr6 120331723 120331723 chr6 120456274 120456274 TCGA-J9-A52D DUP 5 16 * * chr6 122138796 122138796 chr6 124673920 124673920 TCGA-J9-A52D DUP 12 20 * NKAIN2 chr6 133874549 133874549 chr6 134042027 134042028 TCGA-J9-A52D DUP 17 38 TARID SLC2A12 chr6 134063787 134063787 chr6 134330463 134330463 TCGA-J9-A52D DUP 29 43 * * chr6 135199635 135199635 chr6 138287146 138287146 TCGA-J9-A52D DUP 24 36 MYB ARFGEF3 chr6 148429547 148429547 chr6 151073753 151073753 TCGA-J9-A52D DUP 32 20 SASH1 MTHFD1L chr6 152118506 152118506 chr6 152533602 152533602 TCGA-J9-A52D DUP 31 3 ESR1 SYNE1 chr6 156330451 156330451 chr6 158870911 158870911 TCGA-J9-A52D DUP 16 8 * C6orf99 chr6 156612827 156612827 chr6 159239349 159239349 TCGA-J9-A52D DUP 2 26 * FNDC1 chr6 156766861 156766861 chr6 156767142 156767142 TCGA-J9-A52D INV 4 35 * * chr6 157984161 157984161 chr6 158124640 158124640 TCGA-J9-A52D DUP 41 30 SYNJ2 SERAC1 chr6 158054427 158054427 chr6 158055003 158055003 TCGA-J9-A52D INV 40 49 SYNJ2 SYNJ2 chr6 17256972 17256972 chr6 20336816 20336833 TCGA-J9-A52D DUP 36 24 * * chr6 23441946 23441946 chr6 23946558 23946559 TCGA-J9-A52D DUP 4 45 * * chr6 28803887 28803887 chr6 29043048 29043048 TCGA-J9-A52D DUP 10 29 * AL662791.2 chr6 32482938 32482982 chr6 32590581 32590598 TCGA-J9-A52D DUP 40 6 * HLA-DRB1 chr6 32483015 32483015 chr6 32531127 32531127 TCGA-J9-A52D DUP 19 43 * HLA-DRB5 chr6 37725468 37725468 chr6 39638335 39638335 TCGA-J9-A52D DUP 6 13 * KIF6 chr6 55333519 55333519 chr6 55601375 55601375 TCGA-J9-A52D DUP 8 24 GFRAL * chr6 69340297 69340298 chr6 71736336 71736336 TCGA-J9-A52D DUP 23 4 ADGRB3 * chr6 77707911 77707911 chr6 104191929 104191929 TCGA-J9-A52D INV 33 4 MEI4 * chr6 80266339 80266340 chr6 104647857 104647858 TCGA-J9-A52D INV 43 44 BCKDHB * chr6 82162330 82162330 chr6 103477855 103477855 TCGA-J9-A52D DEL 15 3 * * chr6 83196042 83196042 chr7 146447551 146447551 TCGA-J9-A52D BND 44 27 RWDD2A CNTNAP2 chr6 83542096 83542096 chr7 146445656 146445656 TCGA-J9-A52D BND 19 48 * CNTNAP2 chr6 88874500 88874500 chr6 89196947 89196947 TCGA-J9-A52D DUP 46 6 RNGTT GABRR1 chr6 96998586 96998586 chr6 97913108 97913108 TCGA-J9-A52D INS 46 23 KLHL32 AL589740.1 chr6 97806835 97806835 chr6 98144171 98144171 TCGA-J9-A52D INS 18 12 AL589740.1 AL589740.1 chr6 97999347 97999347 chr6 99588885 99588885 TCGA-J9-A52D INS 12 4 AL589740.1 TSTD3 chr7 101985181 101985181 chr11 45395830 45395831 TCGA-J9-A52D BND 2 34 CUX1 AC103855.3 chr7 101986066 101986066 chr11 45168117 45168117 TCGA-J9-A52D BND 41 33 CUX1 PRDM11 chr7 102930781 102930781 chr7 106105395 106105396 TCGA-J9-A52D DUP 27 11 FBXL13 SYPL1 chr7 103897549 103897549 chr11 45395830 45395831 TCGA-J9-A52D BND 33 25 RELN AC103855.3 chr7 105885641 105885642 chr7 118590978 118590978 TCGA-J9-A52D DEL 15 33 CDHR3 * chr7 114487709 114487709 chr7 114490484 114490484 TCGA-J9-A52D DEL 1 40 FOXP2 FOXP2 chr7 140962170 140962170 chr7 141084692 141084692 TCGA-J9-A52D DUP 43 33 * TMEM178B chr7 146451482 146451482 chr7 149523310 149523311 TCGA-J9-A52D DUP 25 19 CNTNAP2 * chr7 150004070 150004070 chr7 154093017 154093017 TCGA-J9-A52D DEL 14 22 AC092681.2 DPP6 chr7 151937008 151937008 chr7 153964027 153964027 TCGA-J9-A52D DUP 10 47 * DPP6 chr7 15457053 15457053 chr7 15458959 15458962 TCGA-J9-A52D INV 27 8 AGMO AGMO chr7 15458226 15458226 chr7 27205704 27205704 TCGA-J9-A52D INV 11 4 AGMO HOTTIP chr7 15458557 15458557 chr7 15730743 15730743 TCGA-J9-A52D DUP 13 15 AGMO * chr7 15458617 15458617 chr7 15493621 15493621 TCGA-J9-A52D DEL 45 30 AGMO AGMO chr7 15458959 15458962 chr7 15730803 15730803 TCGA-J9-A52D DEL 15 35 AGMO * chr7 25491248 25491248 chr7 25992205 25992205 TCGA-J9-A52D DUP 3 40 AC005100.2 * chr7 25946310 25946311 chr7 30002930 30002930 TCGA-J9-A52D DUP 47 26 * FKBP14-AS1 chr7 41673226 41673227 chr7 44870132 44870132 TCGA-J9-A52D DUP 37 23 INHBA * chr7 66376793 66376793 chr7 151315596 151315596 TCGA-J9-A52D DEL 23 45 TPST1 * chr7 68528747 68528747 chr7 68849446 68849446 TCGA-J9-A52D DUP 26 33 * * chr7 77397065 77397065 chr7 77614510 77614511 TCGA-J9-A52D DUP 19 44 GSAP PTPN12 chr7 81678781 81678781 chr7 83918177 83918177 TCGA-J9-A52D INS 19 47 AC008163.1 * chr7 81927793 81927793 chr7 151271052 151271052 TCGA-J9-A52D INS 5 38 * SMARCD3 chr7 85201322 85201322 chr7 85218611 85218611 TCGA-J9-A52D DEL 32 5 * * chr7 87458551 87458551 chr7 87753595 87753595 TCGA-J9-A52D DUP 36 33 ABCB4 RUNDC3B chr7 9199482 9199482 chr7 9210396 9210396 TCGA-J9-A52D DEL 6 16 * * chr7 92819141 92819141 chr7 93381916 93381917 TCGA-J9-A52D DUP 34 5 CDK6 * chr7 97755009 97755010 chr14 44171240 44171240 TCGA-J9-A52D BND 41 48 * LINC02307 chr7 97756906 97756906 chr7 97855240 97855257 TCGA-J9-A52D INV 36 26 * ASNS chr7 97853325 97853326 chr14 44172033 44172034 TCGA-J9-A52D BND 40 38 ASNS LINC02307 chr7 97855240 97855257 chr14 44172183 44172183 TCGA-J9-A52D BND 24 15 ASNS LINC02307 chr8 107735527 107735527 chr8 109896515 109896515 TCGA-J9-A52D DUP 47 30 * * chr8 108443364 108443364 chr3 47863937 47863937 TCGA-J9-A52D BND 21 50 EMC2 MAP4 chr8 109822698 109822698 chr8 110459575 110459576 TCGA-J9-A52D DUP 3 38 * * chr8 112376442 112376442 chr8 112376816 112376816 TCGA-J9-A52D DEL 15 44 CSMD3 CSMD3 chr8 124351705 124351705 chr8 128137962 128137962 TCGA-J9-A52D DUP 25 27 TMEM65 * chr8 125001203 125001203 chr8 126008850 126008851 TCGA-J9-A52D DUP 15 17 SQLE * chr8 127000205 127000205 chr8 127152875 127152875 TCGA-J9-A52D DUP 19 40 PCAT1 PCAT1 chr8 135202509 135202509 chr8 135467970 135467971 TCGA-J9-A52D DUP 24 40 * KHDRBS3 chr8 137377879 137377879 chr8 137627812 137627812 TCGA-J9-A52D DEL 42 32 * AC105213.1 chr8 139146605 139146605 chr8 140312902 140312903 TCGA-J9-A52D DUP 38 15 * TRAPPC9 chr8 22908506 22908506 chr8 25209095 25209096 TCGA-J9-A52D DUP 14 16 PEBP4 DOCK5 chr8 37613330 37613330 chr8 48212562 48212562 TCGA-J9-A52D INV 45 37 AC137579.2 * chr8 43950768 43950768 chr8 45957981 45957981 TCGA-J9-A52D DUP 17 42 * * chr8 46104516 46104516 chr8 47784803 47784803 TCGA-J9-A52D DUP 36 3 * PRKDC chr8 50857755 50857756 chr8 53487758 53487772 TCGA-J9-A52D DUP 8 11 * * chr8 62749717 62749717 chr8 63317488 63317489 TCGA-J9-A52D DUP 45 29 NKAIN3 * chr8 75142732 75142732 chr8 76098319 76098320 TCGA-J9-A52D DUP 48 45 * * chr8 78323879 78323879 chr8 80834348 80834348 TCGA-J9-A52D DUP 42 37 * ZNF704 chr8 85965296 85965296 chr8 87424577 87424577 TCGA-J9-A52D DUP 50 11 * CNBD1 chr8 9011350 9011350 chr8 12178524 12178524 TCGA-J9-A52D INV 36 5 ERI1 ALG1L11P chr9 102549161 102549161 chr9 103463042 103463042 TCGA-J9-A52D DUP 34 45 LINC00587 * chr9 103921088 103921088 chr9 104281459 104281459 TCGA-J9-A52D DUP 18 29 * TOPORSLP chr9 104674652 104674659 chr4 127469225 127469232 TCGA-J9-A52D BND 40 21 * AC093772.1 chr9 106264606 106264606 chr9 106440142 106440142 TCGA-J9-A52D DUP 13 37 LINC01505 LINC01505 chr9 106534532 106534533 chr9 108478447 108478447 TCGA-J9-A52D DUP 37 45 LINC01505 * chr9 108028650 108028650 chr9 111994620 111994620 TCGA-J9-A52D DUP 20 7 * * chr9 12505882 12505882 chr9 12846751 12846751 TCGA-J9-A52D DUP 27 44 * * chr9 130082975 130082978 chr9 130512321 130512321 TCGA-J9-A52D INV 35 11 GPR107 * chr9 13479858 13479858 chr9 13616501 13616502 TCGA-J9-A52D DUP 11 44 AL583785.1 * chr9 23874150 23874150 chr9 23898696 23898696 TCGA-J9-A52D DEL 15 5 * AL365204.2 chr9 338336 338336 chr19 19758241 19758241 TCGA-J9-A52D BND 4 32 DOCK8 LINC00663 chr9 35072041 35072041 chr9 37718512 37718512 TCGA-J9-A52D DUP 45 27 VCP AL138752.2 chr9 4259650 4259650 chr9 5243301 5243302 TCGA-J9-A52D DUP 31 15 GLIS3 * chr9 61533459 61533459 chr9 61992822 61992822 TCGA-J9-A52D INV 17 38 * * chr9 73629162 73629162 chr9 73639397 73639397 TCGA-J9-A52D DUP 44 45 * * chr9 74117563 74117563 chr9 74498538 74498538 TCGA-J9-A52D DUP 15 15 * RORB chr9 8328191 8328191 chr9 8440486 8440486 TCGA-J9-A52D INV 29 34 PTPRD PTPRD chr9 8433615 8433615 chr9 8441872 8441872 TCGA-J9-A52D INV 9 10 PTPRD PTPRD chr9 84763438 84763439 chr9 87951121 87951121 TCGA-J9-A52D DUP 1 3 NTRK2 * chr9 86854382 86854382 chr9 90705849 90705858 TCGA-J9-A52D DUP 45 21 * * chr9 87256269 87256269 chr9 87602554 87602554 TCGA-J9-A52D DUP 47 5 * DAPK1 chr9 87292362 87292363 chr18 28407299 28407300 TCGA-J9-A52D BND 18 42 * * chr9 87675238 87675238 chr9 88070842 88070842 TCGA-J9-A52D DUP 19 36 DAPK1 * chr9 87809599 87809599 chr9 88068511 88068519 TCGA-J9-A52D INV 13 25 AL772337.4 * chr9 88390679 88390679 chr18 25311043 25311043 TCGA-J9-A52D BND 9 46 SPIN1 ZNF521 chr9 97770973 97770973 chr9 98087759 98087759 TCGA-J9-A52D DUP 3 2 PTCSC2 TRIM14 chr9 9950237 9950237 chr9 10054909 10054909 TCGA-J9-A52D DUP 38 25 PTPRD PTPRD chrX 101187869 101187870 chrX 101603978 101603978 TCGA-J9-A52D DUP 9 39 * * chrX 111294719 111294719 chrX 114036555 114036555 TCGA-J9-A52D DUP 2 24 DCX XACT chrX 114777829 114777829 chrX 117219315 117219315 TCGA-J9-A52D DUP 47 14 HTR2C * chrX 119050263 119050263 chrX 121070638 121070638 TCGA-J9-A52D DUP 36 45 * * chrX 136235616 136235617 chrX 136778698 136778698 TCGA-J9-A52D DUP 29 14 MAP7D3 ARHGEF6 chrX 136571793 136571793 chrX 136746813 136746813 TCGA-J9-A52D INV 41 14 Y_RNA ARHGEF6 chrX 136613842 136613842 chrX 136903152 136903152 TCGA-J9-A52D INV 21 28 * * chrX 16086853 16086853 chrX 19271070 19271071 TCGA-J9-A52D DUP 38 11 * * chrX 25132161 25132161 chrX 25581070 25581070 TCGA-J9-A52D DUP 14 38 * * chrX 30904806 30904809 chrX 33487367 33487370 TCGA-J9-A52D DUP 2 5 TAB3 * chrX 32518976 32518977 chrX 34941454 34941457 TCGA-J9-A52D DUP 26 38 DMD FAM47B chrX 36473204 36473204 chrX 36474248 36474248 TCGA-J9-A52D DEL 1 32 * * chrX 46636905 46636905 chrX 46878935 46878935 TCGA-J9-A52D DUP 22 47 SLC9A7 RP2 chrX 47564881 47564881 chrX 47900981 47900981 TCGA-J9-A52D DUP 7 7 ARAF ZNF81 chrX 66895147 66895147 chrX 67344558 67344558 TCGA-J9-A52D DUP 44 25 * * chrX 7451963 7451963 chrX 30130842 30130842 TCGA-J9-A52D DUP 44 45 * * chrX 8611861 8611861 chrX 11769194 11769194 TCGA-J9-A52D DUP 33 30 ANOS1 MSL3 chrX 95702958 95702958 chrX 95703085 95703085 TCGA-J9-A52D DEL 38 5 * * chr16 11908462 11908462 chr16 11908788 11908788 TCGA-YL-A8SH DEL 3 26 GSPT1 GSPT1 chr9 10918178 10918178 chr9 10931072 10931072 TCGA-YL-A8SH DEL 22 10 * * chrX 6786632 6786632 chr22 28669931 28669932 TCGA-YL-A8SH BND 40 16 * TTC28 chr10 102349625 102349626 chr11 116744577 116744578 TCGA-G9-6369 BND 46 31 GBF1 * chr10 102670810 102670810 chr10 103073169 103073169 TCGA-G9-6369 DUP 6 21 * CNNM2 chr10 109171942 109171942 chr10 111238851 111238851 TCGA-G9-6369 DUP 29 18 * * chr10 109853320 109853320 chr10 110107169 110107169 TCGA-G9-6369 DUP 6 48 * ADD3 chr10 111049827 111049827 chr10 111342405 111342405 TCGA-G9-6369 DUP 36 48 * * chr10 113259305 113259305 chr10 113446538 113446538 TCGA-G9-6369 DUP 1 49 * * chr10 118056289 118056289 chr10 118388897 118388897 TCGA-G9-6369 DUP 7 8 CASC2 * chr10 16417011 16417011 chr10 16722745 16722745 TCGA-G9-6369 DUP 44 20 * RSU1 chr10 27100599 27100599 chr10 29643992 29643992 TCGA-G9-6369 DUP 33 41 ANKRD26 SVIL chr10 45351028 45351028 chr10 46068937 46068937 TCGA-G9-6369 INV 50 50 * * chr10 52109182 52109182 chr10 52314361 52314361 TCGA-G9-6369 DUP 3 8 PRKG1 DKK1 chr10 60263242 60263242 chr10 61713164 61713164 TCGA-G9-6369 DUP 9 32 ANK3 CABCOCO1 chr10 67120588 67120588 chr10 69302279 69302279 TCGA-G9-6369 DUP 39 4 CTNNA3 HK1 chr10 69084012 69084012 chr10 72598161 72598161 TCGA-G9-6369 DUP 37 50 * MICU1 chr10 71141770 71141770 chr10 71410923 71410923 TCGA-G9-6369 DUP 44 29 * CDH23 chr10 87860786 87860786 chr10 87872974 87872974 TCGA-G9-6369 DEL 44 45 KLLN PTEN chr10 89376743 89376745 chr12 47919155 47919157 TCGA-G9-6369 BND 2 38 LIPA VDR chr10 89699907 89699907 chr11 46719651 46719651 TCGA-G9-6369 BND 1 25 AL157400.3 F2 chr10 89700065 89700065 chr10 90661838 90661838 TCGA-G9-6369 DEL 7 23 AL157400.3 * chr10 94179528 94179528 chrX 79033078 79033078 TCGA-G9-6369 BND 14 23 PLCE1 * chr10 98855501 98855501 chr10 103396435 103396435 TCGA-G9-6369 DUP 16 44 HPSE2 ATP5MD chr11 101263181 101263181 chr11 132315452 132315452 TCGA-G9-6369 INV 23 50 * NTM chr11 103603658 103603658 chr11 105796277 105796277 TCGA-G9-6369 DUP 48 36 * GRIA4 chr11 103622332 103622334 chr19 2650816 2650816 TCGA-G9-6369 BND 24 5 * GNG7 chr11 103622332 103622334 chr11 105614592 105614592 TCGA-G9-6369 DEL 16 1 * GRIA4 chr11 103923893 103923893 chr11 134153950 134153950 TCGA-G9-6369 INV 36 10 PDGFD NCAPD3 chr11 103991062 103991062 chr11 104507345 104507345 TCGA-G9-6369 DUP 18 30 PDGFD LINC02552 chr11 104031235 104031235 chr11 104252669 104252669 TCGA-G9-6369 DUP 3 13 PDGFD * chr11 104154645 104154645 chr11 106400433 106400433 TCGA-G9-6369 DUP 49 25 PDGFD * chr11 104397236 104397236 chr11 104626995 104626995 TCGA-G9-6369 DUP 26 43 * * chr11 104412917 104412917 chr11 104412972 104412972 TCGA-G9-6369 INV 16 42 * * chr11 104743849 104743849 chr11 104743936 104743936 TCGA-G9-6369 INV 7 39 * * chr11 105300107 105300107 chr11 105466839 105466839 TCGA-G9-6369 DUP 34 29 CARD18 CARD18 chr11 107880732 107880732 chr11 108087417 108087417 TCGA-G9-6369 DUP 23 43 SLC35F2 CUL5 chr11 111161485 111161485 chr11 111893906 111893906 TCGA-G9-6369 DUP 22 13 LINC02550 * chr11 113686491 113686491 chr11 113990582 113990582 TCGA-G9-6369 DUP 19 9 * * chr11 116744577 116744578 chr10 102349625 102349626 TCGA-G9-6369 BND 48 24 * GBF1 chr11 118321500 118321500 chr11 123968388 123968388 TCGA-G9-6369 DUP 40 39 * * chr11 120093453 120093453 chr11 123874670 123874670 TCGA-G9-6369 DEL 38 7 * * chr11 120214880 120214880 chr11 120749417 120749417 TCGA-G9-6369 DUP 1 37 OAF GRIK4 chr11 134496091 134496091 chr11 134656226 134656226 TCGA-G9-6369 DUP 36 8 B3GAT1-DT * chr11 15465341 15465341 chr11 19342908 19342908 TCGA-G9-6369 DUP 28 39 * * chr11 16839903 16839903 chr11 17202912 17202912 TCGA-G9-6369 DUP 50 14 PLEKHA7 PIK3C2A chr11 18752080 18752080 chr11 18983380 18983380 TCGA-G9-6369 DUP 20 34 PTPN5 * chr11 30948758 30948758 chr11 31265147 31265147 TCGA-G9-6369 DUP 43 8 DCDC1 DCDC1 chr11 32309146 32309146 chr11 33544480 33544480 TCGA-G9-6369 DUP 49 36 THEM7P KIAA1549L chr11 37577812 37577812 chr11 40729790 40729790 TCGA-G9-6369 DUP 44 47 * LRRC4C chr11 40025076 40025076 chr11 40350774 40350774 TCGA-G9-6369 DUP 12 22 * LRRC4C chr11 47278776 47278776 chr11 49832844 49832844 TCGA-G9-6369 DEL 18 38 MADD * chr11 54879854 54879854 chr11 58579213 58579213 TCGA-G9-6369 INV 8 5 * LPXN chr11 62384187 62384187 chr11 63315211 63315211 TCGA-G9-6369 DUP 28 23 ASRGL1 SLC22A10 chr11 64630428 64630428 chr11 65649146 65649146 TCGA-G9-6369 DUP 16 15 NRXN2 SIPA1 chr11 65749521 65749521 chr11 66096122 66096122 TCGA-G9-6369 DUP 15 25 AP001266.2 PACS1 chr11 67657424 67657424 chr11 71898492 71898492 TCGA-G9-6369 DUP 22 22 * AP002495.1 chr11 68516402 68516402 chr11 69675552 69675552 TCGA-G9-6369 INV 42 28 PPP6R3 LTO1 chr11 68674767 68674767 chr11 69755445 69755445 TCGA-G9-6369 DUP 44 27 * * chr11 68912181 68912181 chr11 69266066 69266066 TCGA-G9-6369 DEL 11 34 IGHMBP2 * chr11 69075218 69075218 chr11 69075465 69075465 TCGA-G9-6369 INV 49 2 TPCN2 TPCN2 chr11 69183002 69183002 chr11 116523641 116523641 TCGA-G9-6369 INV 39 43 * * chr11 69312500 69312500 chrX 67082226 67082226 TCGA-G9-6369 BND 17 34 MYEOV * chr11 69368996 69368996 chrX 67670167 67670167 TCGA-G9-6369 BND 42 35 * AR chr11 69398496 69398496 chr11 69398681 69398681 TCGA-G9-6369 INV 42 24 * * chr11 69492799 69492799 chr11 69492833 69492833 TCGA-G9-6369 INV 22 31 LINC01488 LINC01488 chr11 69597869 69597869 chr11 69597942 69597942 TCGA-G9-6369 INV 32 34 * * chr11 69672823 69672823 chr11 69673136 69673136 TCGA-G9-6369 INV 21 43 LTO1 LTO1 chr11 69680976 69680976 chr11 70531883 70531883 TCGA-G9-6369 INV 41 33 * SHANK2 chr11 69854174 69854174 chr11 69854407 69854407 TCGA-G9-6369 INV 29 23 * * chr11 70458718 70458718 chr11 70459027 70459027 TCGA-G9-6369 INV 50 20 * * chr11 73329741 73329741 chr11 77273340 77273340 TCGA-G9-6369 DUP 2 34 ARHGEF17 GDPD4 chr11 78253462 78253462 chr11 78475121 78475121 TCGA-G9-6369 DUP 39 18 GAB2 NARS2 chr11 78647702 78647702 chr11 78859730 78859730 TCGA-G9-6369 DUP 44 40 * TENM4 chr11 86529185 86529185 chr11 86916118 86916118 TCGA-G9-6369 DUP 7 25 AP001831.1 PRSS23 chr11 88423572 88423572 chr11 88992947 88992947 TCGA-G9-6369 DUP 23 30 * GRM5 chr11 89523382 89523382 chr11 91007212 91007212 TCGA-G9-6369 DUP 30 49 * * chr11 89557965 89557965 chr11 89723851 89723851 TCGA-G9-6369 DUP 47 15 AP003400.1 AP003122.4 chr11 92541158 92541158 chr11 95233887 95233887 TCGA-G9-6369 DUP 50 3 FAT3 SESN3 chr11 96126458 96126458 chr11 96585690 96585690 TCGA-G9-6369 DUP 29 15 MAML2 * chr12 101627289 101627289 chr12 101774125 101774125 TCGA-G9-6369 DUP 43 30 MYBPC1 GNPTAB chr12 103887703 103887703 chr12 108912236 108912236 TCGA-G9-6369 DUP 13 45 TTC41P SVOP chr12 10396324 10396324 chr12 10604181 10604181 TCGA-G9-6369 DUP 27 39 KLRK1-AS1 * chr12 10434721 10434721 chr12 10857021 10857021 TCGA-G9-6369 INV 28 40 KLRC2 PRH1 chr12 10745218 10745218 chr12 11230689 11230689 TCGA-G9-6369 INV 13 37 * AC244131.2 chr12 107711026 107711026 chr12 108121561 108121561 TCGA-G9-6369 DUP 46 9 PWP1 * chr12 108154997 108154997 chr12 108381185 108381185 TCGA-G9-6369 DUP 1 6 WSCD2 * chr12 110210334 110210334 chr12 110607645 110607645 TCGA-G9-6369 DUP 41 8 IFT81 * chr12 11068619 11068622 chr12 11098150 11098166 TCGA-G9-6369 DEL 7 47 PRH1 PRH1 chr12 113654275 113654275 chr12 113944004 113944004 TCGA-G9-6369 DUP 33 6 * RBM19 chr12 116709661 116709661 chr12 120999745 120999745 TCGA-G9-6369 DUP 39 25 * HNF1A chr12 119457974 119457974 chr12 120640917 120640917 TCGA-G9-6369 DUP 32 6 CCDC60 CABP1 chr12 120809475 120809475 chr12 122604580 122604580 TCGA-G9-6369 DUP 45 7 SPPL3 KNTC1 chr12 123150890 123150890 chr12 123477474 123477474 TCGA-G9-6369 DUP 37 46 PITPNM2 RILPL1 chr12 126250076 126250076 chr12 126361739 126361739 TCGA-G9-6369 DUP 21 41 AC007368.1 AC007368.1 chr12 127709268 127709268 chr19 56543089 56543089 TCGA-G9-6369 BND 4 1 * ZFP28 chr12 17775178 17775178 chr12 17868250 17868250 TCGA-G9-6369 INV 6 26 * * chr12 23365893 23365893 chr12 23638587 23638587 TCGA-G9-6369 DUP 17 45 * SOX5 chr12 26509781 26509781 chr12 28665074 28665074 TCGA-G9-6369 DUP 20 35 ITPR2 * chr12 26549797 26549797 chr12 27314519 27314519 TCGA-G9-6369 DUP 35 17 ITPR2 STK38L chr12 26576564 26576564 chr12 28454260 28454260 TCGA-G9-6369 DEL 33 13 ITPR2 CCDC91 chr12 26868869 26868869 chr12 27062192 27062192 TCGA-G9-6369 DUP 38 21 * MED21 chr12 27017582 27017582 chr12 27017697 27017697 TCGA-G9-6369 INV 28 4 * * chr12 27510264 27510264 chr12 27628215 27628215 TCGA-G9-6369 DUP 47 9 * PPFIBP1 chr12 27890233 27890233 chr12 28042735 28042735 TCGA-G9-6369 DUP 8 25 * * chr12 28401005 28401005 chr12 28401327 28401327 TCGA-G9-6369 INV 24 20 CCDC91 CCDC91 chr12 28581297 28581297 chr12 28864809 28864809 TCGA-G9-6369 DUP 6 40 CCDC91 * chr12 28639098 28639098 chr12 28764614 28764614 TCGA-G9-6369 DEL 23 5 * * chr12 41709031 41709031 chr12 47695193 47695193 TCGA-G9-6369 DUP 27 48 * RPAP3 chr12 46450054 46450054 chr12 46680480 46680480 TCGA-G9-6369 DUP 22 8 AC008014.1 AC008014.1 chr12 47919155 47919157 chr10 89376743 89376745 TCGA-G9-6369 BND 9 49 VDR LIPA chr12 48584075 48584075 chr12 49341388 49341388 TCGA-G9-6369 DUP 36 34 * * chr12 54107733 54107733 chr12 54295088 54295088 TCGA-G9-6369 DUP 17 21 FLJ12825 AC078778.1 chr12 55957417 55957417 chr12 56402690 56402690 TCGA-G9-6369 DUP 22 37 PMEL * chr12 56352181 56352181 chr12 56575719 56575719 TCGA-G9-6369 DUP 26 41 STAT2 RBMS2 chr12 56518304 56518304 chr12 56725367 56725367 TCGA-G9-6369 DUP 23 5 * NACA chr12 5681907 5681907 chr12 5801898 5801898 TCGA-G9-6369 DUP 10 29 ANO2 ANO2 chr12 57624168 57624168 chr12 57764733 57764733 TCGA-G9-6369 DUP 6 5 SLC26A10 CYP27B1 chr12 62510604 62510604 chr12 62791982 62791982 TCGA-G9-6369 DEL 12 30 MON2 PPM1H chr12 63629159 63629159 chr12 66820997 66820997 TCGA-G9-6369 DUP 24 1 DPY19L2 GRIP1 chr12 66910764 66910764 chr12 67109057 67109057 TCGA-G9-6369 DUP 18 13 GRIP1 * chr12 68589344 68589344 chr12 68823096 68823096 TCGA-G9-6369 DUP 28 30 * MDM2 chr12 70074405 70074405 chr12 73053756 73053756 TCGA-G9-6369 DUP 21 12 PRANCR * chr12 80232810 80232810 chr12 80431686 80431686 TCGA-G9-6369 DUP 44 30 OTOGL PTPRQ chr12 85220208 85220208 chr12 85541705 85541705 TCGA-G9-6369 DUP 6 42 LRRIQ1 * chr12 87500501 87500501 chr12 90026250 90026250 TCGA-G9-6369 DUP 44 31 * * chr12 89930075 89930075 chr12 90101623 90101623 TCGA-G9-6369 DUP 50 6 AC009522.1 * chr12 96801309 96801309 chr12 101775443 101775443 TCGA-G9-6369 DUP 50 22 CFAP54 GNPTAB chr12 96821036 96821036 chr12 101626922 101626922 TCGA-G9-6369 DEL 20 8 CFAP54 MYBPC1 chr12 96971096 96971096 chr12 101447760 101447760 TCGA-G9-6369 DEL 34 33 * * chr13 108813186 108813186 chr13 111026465 111026465 TCGA-G9-6369 DUP 34 44 MYO16 * chr13 108929602 108929602 chr13 108929798 108929798 TCGA-G9-6369 INV 46 21 MYO16 MYO16 chr13 109286521 109286521 chr13 109286629 109286629 TCGA-G9-6369 INV 43 17 LINC00370 LINC00370 chr13 109626948 109626948 chr13 109626972 109626972 TCGA-G9-6369 INV 40 15 AL163541.1 AL163541.1 chr13 109646587 109646587 chr13 109646841 109646841 TCGA-G9-6369 INV 11 21 AL163541.1 AL163541.1 chr13 110253487 110253487 chr13 110253814 110253814 TCGA-G9-6369 INV 18 22 COL4A1 COL4A1 chr13 110295915 110295915 chr13 112066500 112066500 TCGA-G9-6369 DUP 26 9 COL4A1 SOX1 chr13 110382146 110382146 chr13 110382240 110382240 TCGA-G9-6369 INV 15 47 COL4A2 COL4A2 chr13 110384021 110384021 chr13 110384051 110384051 TCGA-G9-6369 INV 40 40 COL4A2 COL4A2 chr13 110807634 110807634 chr13 110807730 110807730 TCGA-G9-6369 INV 23 16 * * chr13 110883243 110883243 chr13 110883530 110883530 TCGA-G9-6369 INV 20 44 ANKRD10 ANKRD10 chr13 111022579 111022579 chr13 111022628 111022628 TCGA-G9-6369 INV 29 45 * * chr13 111451474 111451474 chr13 111451673 111451673 TCGA-G9-6369 INV 48 30 * * chr13 111984949 111984949 chr13 111985132 111985132 TCGA-G9-6369 INV 23 41 * * chr13 112554492 112554492 chr13 112709260 112709260 TCGA-G9-6369 DUP 45 24 TUBGCP3 ATP11A chr13 25293891 25293891 chr13 25484875 25484875 TCGA-G9-6369 DUP 47 12 * ATP8A2 chr13 34060711 34060711 chr13 34323173 34323173 TCGA-G9-6369 DUP 28 14 * * chr13 36912528 36912528 chr13 37328654 37328654 TCGA-G9-6369 DUP 11 39 SMAD9 * chr13 38120375 38120375 chr13 78141506 78141506 TCGA-G9-6369 DEL 30 37 LINC00571 OBI1-AS1 chr13 45641708 45641708 chr13 49254388 49254388 TCGA-G9-6369 DUP 5 6 * CDADC1 chr13 55212569 55212569 chr13 57638935 57638935 TCGA-G9-6369 DUP 7 14 * PCDH17 chr13 55898178 55898178 chr13 56105143 56105143 TCGA-G9-6369 DUP 26 22 * * chr13 65126933 65126933 chr13 65322232 65322232 TCGA-G9-6369 DUP 46 42 * * chr13 81898719 81898719 chr13 82497947 82497947 TCGA-G9-6369 DUP 35 5 * * chr13 83762604 83762604 chr13 84563108 84563108 TCGA-G9-6369 DUP 12 2 * LINC00333 chr13 83829175 83829175 chr13 84018140 84018140 TCGA-G9-6369 DUP 39 5 * * chr13 87588050 87588050 chr13 90479039 90479039 TCGA-G9-6369 DUP 15 4 MIR4500HG * chr13 87983893 87983893 chr13 88093523 88093523 TCGA-G9-6369 DUP 28 40 * * chr13 91608072 91608072 chr13 91752651 91752651 TCGA-G9-6369 DUP 44 26 GPC5 GPC5 chr13 94183211 94183211 chr13 94327623 94327623 TCGA-G9-6369 DUP 3 26 GPC6 GPC6 chr13 95367102 95367102 chr13 99279019 99279019 TCGA-G9-6369 DUP 1 23 * UBAC2 chr13 95512662 95512662 chr13 97406813 97406813 TCGA-G9-6369 DEL 43 45 CLDN10 * chr13 95778106 95778106 chr13 96621515 96621515 TCGA-G9-6369 DEL 15 32 DNAJC3 HS6ST3 chr14 101637644 101637644 chr14 101981377 101981377 TCGA-G9-6369 DUP 12 9 LINC02320 DYNC1H1 chr14 105565608 105565608 chr14 105685408 105685408 TCGA-G9-6369 DUP 34 14 * * chr14 105568937 105568981 chr14 105691017 105691017 TCGA-G9-6369 DUP 16 8 * * chr14 105569529 105569547 chr14 105690208 105690226 TCGA-G9-6369 DEL 22 28 * * chr14 105569655 105569663 chr14 105689120 105689120 TCGA-G9-6369 DEL 13 9 * * chr14 105570342 105570342 chr14 105683976 105683976 TCGA-G9-6369 INV 26 23 * * chr14 20803905 20803905 chr14 23549105 23549105 TCGA-G9-6369 DUP 16 9 RNASE1 ZFHX2 chr14 23460839 23460839 chr14 26916138 26916138 TCGA-G9-6369 DUP 41 34 * AL110292.1 chr14 24115091 24115091 chr14 24115239 24115239 TCGA-G9-6369 DEL 7 16 NRL NRL chr14 26546278 26546278 chr14 26623544 26623544 TCGA-G9-6369 DUP 50 14 NOVA1 LINC02588 chr14 30991173 30991173 chr14 31171083 31171083 TCGA-G9-6369 DUP 17 11 STRN3 HECTD1 chr14 32290752 32290752 chr14 32393176 32393176 TCGA-G9-6369 DUP 6 8 * AKAP6 chr14 35214231 35214231 chr14 38795246 38795246 TCGA-G9-6369 DUP 38 29 PRORP LINC00639 chr14 36424302 36424302 chr14 37397239 37397239 TCGA-G9-6369 DUP 18 19 AL132857.1 MIPOL1 chr14 37476281 37476281 chr14 37589046 37589046 TCGA-G9-6369 DUP 29 15 MIPOL1 * chr14 39078770 39078770 chr14 42387786 42387786 TCGA-G9-6369 DUP 43 41 SEC23A AL442163.1 chr14 40434815 40434815 chr14 40694386 40694386 TCGA-G9-6369 DUP 6 50 * * chr14 40525676 40525676 chr14 41393174 41393174 TCGA-G9-6369 DEL 21 39 * * chr14 41754756 41754756 chr14 41857194 41857194 TCGA-G9-6369 DUP 3 49 LRFN5 LRFN5 chr14 42659300 42659300 chr14 42795368 42795368 TCGA-G9-6369 DUP 22 34 AL442163.1 * chr14 48005356 48005356 chr14 48264153 48264153 TCGA-G9-6369 DUP 40 31 * * chr14 49135370 49135370 chr14 51553778 51553778 TCGA-G9-6369 DUP 50 36 * FRMD6 chr14 49336644 49336644 chr14 50461129 50461129 TCGA-G9-6369 DUP 28 40 * MAP4K5 chr14 55958230 55958230 chr14 56141083 56141083 TCGA-G9-6369 DUP 15 13 AL163952.1 PELI2 chr14 58852300 58852300 chr14 59192211 59192211 TCGA-G9-6369 DUP 21 13 LINC01500 DAAM1 chr14 62887826 62887826 chr14 63988618 63988618 TCGA-G9-6369 DUP 1 43 KCNH5 SYNE2 chr14 63402836 63402836 chr14 63699507 63699507 TCGA-G9-6369 DUP 1 17 PPP2R5E SGPP1 chr14 64201436 64201436 chr14 64436237 64436237 TCGA-G9-6369 DUP 30 27 SYNE2 MTHFD1 chr14 65448509 65448509 chr14 67685207 67685207 TCGA-G9-6369 DUP 39 22 FUT8 RDH11 chr14 66690096 66690096 chr14 66694488 66694488 TCGA-G9-6369 DEL 5 23 GPHN GPHN chr14 66697825 66697825 chr14 66869939 66869939 TCGA-G9-6369 DUP 4 14 GPHN GPHN chr14 71285796 71285796 chr14 75552314 75552314 TCGA-G9-6369 DUP 20 50 * * chr14 79542874 79542874 chr14 82205289 82205289 TCGA-G9-6369 DUP 1 37 NRXN3 * chr14 83195236 83195236 chr14 85540676 85540676 TCGA-G9-6369 DUP 49 39 * FLRT2 chr14 89292660 89292660 chr14 89491060 89491060 TCGA-G9-6369 DUP 25 12 FOXN3 FOXN3 chr15 100168763 100168763 chr15 100341123 100341123 TCGA-G9-6369 DUP 41 36 ADAMTS17 ADAMTS17 chr15 100325150 100325150 chr15 100681983 100681983 TCGA-G9-6369 DUP 29 1 ADAMTS17 * chr15 23989916 23989916 chr15 24267490 24267490 TCGA-G9-6369 DUP 35 38 PWRN4 * chr15 23989996 23989996 chr15 24101763 24101763 TCGA-G9-6369 DUP 27 39 PWRN4 * chr15 26494017 26494017 chr15 26625610 26625610 TCGA-G9-6369 DUP 32 44 * GABRB3 chr15 27588873 27588873 chr6 106206854 106206854 TCGA-G9-6369 BND 16 29 * ATG5 chr15 37760185 37760185 chr15 38258137 38258137 TCGA-G9-6369 DUP 22 34 * SPRED1 chr15 40434959 40434959 chr15 42484945 42484945 TCGA-G9-6369 DEL 16 30 IVD ZNF106 chr15 42272105 42272105 chr15 86591305 86591305 TCGA-G9-6369 DEL 17 8 TMEM87A AGBL1 chr15 42277582 42277582 chr6 64235872 64235872 TCGA-G9-6369 BND 40 17 GANC EYS chr15 50250300 50250300 chr15 51317822 51317822 TCGA-G9-6369 DUP 4 19 HDC CYP19A1 chr15 52137109 52137109 chr15 53905756 53905756 TCGA-G9-6369 DUP 13 28 GNB5 * chr15 52304904 52304904 chr15 54645744 54645744 TCGA-G9-6369 DUP 36 21 * * chr15 55178941 55178941 chr15 55831460 55831460 TCGA-G9-6369 DUP 24 23 * NEDD4 chr15 66022374 66022374 chr15 69454802 69454802 TCGA-G9-6369 DUP 37 23 MEGF11 RPLP1 chr15 98726386 98726386 chr15 98974450 98974450 TCGA-G9-6369 DUP 3 34 IGF1R PGPEP1L chr16 10442975 10442975 chr16 10762539 10762539 TCGA-G9-6369 DUP 45 30 ATF7IP2 NUBP1 chr16 23178450 23178450 chr16 23496367 23496367 TCGA-G9-6369 DUP 11 16 AC099482.2 GGA2 chr16 25587374 25587374 chr16 25707671 25707671 TCGA-G9-6369 DUP 25 48 * HS3ST4 chr16 26736466 26736466 chr16 26870652 26870652 TCGA-G9-6369 DUP 9 8 * * chr16 28204726 28204726 chr16 28833337 28833337 TCGA-G9-6369 DUP 50 44 XPO6 ATXN2L chr16 4517824 4517824 chr16 7076638 7076638 TCGA-G9-6369 DUP 34 22 CDIP1 RBFOX1 chr16 5276976 5276976 chr16 5516305 5516305 TCGA-G9-6369 DUP 45 9 RBFOX1 RBFOX1 chr16 5712639 5712639 chr16 5712861 5712861 TCGA-G9-6369 INV 34 4 RBFOX1 RBFOX1 chr16 6258568 6258568 chr16 7859577 7859577 TCGA-G9-6369 DUP 7 42 RBFOX1 * chr16 63970721 63970721 chr16 64217161 64217161 TCGA-G9-6369 DUP 48 23 * * chr16 70626601 70626602 chr16 72607903 72607903 TCGA-G9-6369 DUP 16 24 IL34 LINC01572 chr16 70626601 70626602 chr19 34747955 34747955 TCGA-G9-6369 BND 29 49 IL34 * chr16 76869470 76869470 chr16 77212771 77212771 TCGA-G9-6369 DUP 20 3 AC106729.1 SYCE1L chr16 7745914 7745914 chr16 7865871 7865871 TCGA-G9-6369 DUP 13 45 * * chr16 79616118 79616118 chr16 80016616 80016616 TCGA-G9-6369 DUP 30 35 * * chr16 86603554 86603554 chr16 86603796 86603796 TCGA-G9-6369 DEL 17 39 * * chr16 8931209 8931209 chr16 9261384 9261384 TCGA-G9-6369 DUP 13 35 USP7 * chr17 15842149 15842149 chr17 16161356 16161356 TCGA-G9-6369 DUP 4 20 SPECC1P1 NCOR1 chr17 16846230 16846230 chr17 18426792 18426792 TCGA-G9-6369 INV 26 3 KRT17P1 KRT17P2 chr17 1973287 1973287 chr17 47190578 47190578 TCGA-G9-6369 INV 49 36 RTN4RL1 CDC27 chr17 29773529 29773529 chr17 30016960 30016960 TCGA-G9-6369 DUP 39 38 SSH2 EFCAB5 chr17 39433050 39433050 chr17 39647747 39647747 TCGA-G9-6369 DUP 12 6 MED1 STARD3 chr17 42321828 42321828 chr17 42585746 42585746 TCGA-G9-6369 DUP 46 27 STAT3 RETREG3 chr17 45662131 45662131 chr17 49683627 49683627 TCGA-G9-6369 DUP 30 22 LINC02210-CRHR1 * chr17 53236484 53236484 chr17 53378927 53378927 TCGA-G9-6369 DUP 36 2 * AC034268.2 chr17 56382292 56382292 chr17 56923235 56923235 TCGA-G9-6369 DUP 40 28 ANKFN1 * chr17 56792396 56792401 chr17 66799437 66799437 TCGA-G9-6369 DUP 17 39 C17orf67 PRKCA chr17 57612746 57612746 chr17 57956638 57956638 TCGA-G9-6369 DUP 32 26 MSI2 CUEDC1 chr17 6364315 6364315 chr17 6595321 6595321 TCGA-G9-6369 DUP 12 48 * KIAA0753 chr17 7000413 7000413 chr17 7676961 7676961 TCGA-G9-6369 INV 36 15 ALOX12-AS1 TP53 chr17 76280923 76280923 chr17 80013465 80013465 TCGA-G9-6369 DUP 43 39 QRICH2 TBC1D16 chr17 7725109 7725109 chr17 10942141 10942141 TCGA-G9-6369 DUP 29 17 DNAH2 * chr17 78877826 78877826 chr17 79329405 79329405 TCGA-G9-6369 DUP 6 41 TIMP2 RBFOX3 chr17 8068929 8068929 chr17 8866355 8866355 TCGA-G9-6369 DUP 14 1 ALOXE3P1 PIK3R6 chr18 24499704 24499704 chr18 24766798 24766798 TCGA-G9-6369 DUP 40 49 * AC018697.1 chr18 25036201 25036201 chr18 25171307 25171307 TCGA-G9-6369 DUP 47 32 * ZNF521 chr18 30716464 30716464 chr18 30821916 30821916 TCGA-G9-6369 DUP 48 3 * * chr18 30815681 30815681 chr18 31293178 31293178 TCGA-G9-6369 DUP 17 50 * * chr18 35937146 35937146 chr18 36342434 36342434 TCGA-G9-6369 DUP 48 50 * FHOD3 chr18 37920615 37920615 chr18 42671995 42671995 TCGA-G9-6369 DUP 35 17 * LINC00907 chr18 44827897 44827897 chr18 49242579 49242579 TCGA-G9-6369 DUP 6 44 SETBP1 DYM chr18 49562239 49562239 chr18 50343983 50343983 TCGA-G9-6369 DUP 48 20 LIPG * chr18 57370180 57370180 chr18 58194473 58194473 TCGA-G9-6369 DUP 50 36 ST8SIA3 NEDD4L chr18 58276463 58276463 chr18 62796714 62796714 TCGA-G9-6369 DUP 2 42 NEDD4L PHLPP1 chr18 65432145 65432145 chr18 67508823 67508823 TCGA-G9-6369 DUP 14 34 LINC01916 DSEL chr18 68273387 68273387 chr18 70329117 70329117 TCGA-G9-6369 DUP 25 4 * SOCS6 chr18 74911889 74911889 chr18 74954181 74954181 TCGA-G9-6369 DEL 4 11 ZNF407 ZNF407 chr19 10387443 10387443 chr19 10718299 10718299 TCGA-G9-6369 DUP 48 39 * DNM2 chr19 16618780 16618780 chr19 19931006 19931006 TCGA-G9-6369 DUP 14 36 AC008764.1 ZNF93 chr19 17691813 17691813 chr19 21585823 21585823 TCGA-G9-6369 DUP 33 41 * AC123912.4 chr19 20653809 20653809 chr19 20699028 20699028 TCGA-G9-6369 DEL 38 39 AC010636.2 * chr19 23410034 23410034 chr19 23668161 23668161 TCGA-G9-6369 DUP 5 1 LINC01224 ZNF675 chr19 2651038 2651038 chr19 2842920 2842920 TCGA-G9-6369 DUP 24 15 GNG7 ZNF555 chr19 28888211 28888211 chr19 29092906 29092906 TCGA-G9-6369 DUP 12 2 * * chr19 34749061 34749061 chr19 38257431 38257431 TCGA-G9-6369 DUP 36 19 * SPINT2 chr19 4111994 4111994 chr19 6095136 6095136 TCGA-G9-6369 DUP 5 26 MAP2K2 RFX2 chr19 44318518 44318518 chr19 44436647 44436647 TCGA-G9-6369 DUP 22 48 * ZNF229 chr19 50856292 50856292 chr19 51299009 51299009 TCGA-G9-6369 DUP 48 24 KLK3 * chr19 50860305 50860305 chr19 50860676 50860676 TCGA-G9-6369 DEL 2 32 KLK3 KLK3 chr19 52111261 52111261 chr19 55065880 55065880 TCGA-G9-6369 DUP 16 35 AC011468.4 RDH13 chr19 53941032 53941032 chr19 54201275 54201275 TCGA-G9-6369 DUP 7 5 CACNG7 RPS9 chr19 55670424 55670424 chr19 55792248 55792248 TCGA-G9-6369 DUP 48 50 AC008735.2 NLRP11 chr19 55959706 55959706 chr12 127845710 127845710 TCGA-G9-6369 BND 27 8 NLRP8 * chr19 56543114 56543114 chr12 127845749 127845749 TCGA-G9-6369 BND 37 10 ZFP28 * chr1 104708742 104708742 chr1 105003717 105003717 TCGA-G9-6369 DUP 27 49 * AL591888.1 chr1 104853132 104853132 chr1 105170333 105170333 TCGA-G9-6369 DUP 45 2 * * chr1 115932166 115932166 chr1 118850521 118850521 TCGA-G9-6369 DUP 37 28 * * chr1 121743335 121743335 chr18 25971931 25971931 TCGA-G9-6369 BND 21 18 * * chr1 147620828 147620828 chr1 151279360 151279360 TCGA-G9-6369 INV 8 3 BCL9 * chr1 152005377 152005377 chr1 155946169 155946169 TCGA-G9-6369 DUP 14 44 AL450992.1 * chr1 153104490 153104490 chr1 155672745 155672745 TCGA-G9-6369 DUP 12 29 SPRR2E YY1AP1 chr1 154445765 154445765 chr1 154898570 154898570 TCGA-G9-6369 DUP 37 17 IL6R * chr1 154757999 154757999 chr1 154758259 154758259 TCGA-G9-6369 INV 1 39 KCNN3 KCNN3 chr1 166382838 166382838 chr1 166608177 166608177 TCGA-G9-6369 DUP 24 33 * FMO9P chr1 173856672 173856672 chr1 174212778 174212778 TCGA-G9-6369 DUP 14 6 DARS2 RABGAP1L chr1 192838872 192838872 chr1 198209726 198209726 TCGA-G9-6369 DUP 15 37 AL390957.1 NEK7 chr1 194298122 194298122 chr1 194571728 194571728 TCGA-G9-6369 DUP 50 26 * * chr1 200765520 200765520 chr1 205390012 205390012 TCGA-G9-6369 DUP 41 20 CAMSAP2 LEMD1 chr1 202674595 202674595 chr1 208365576 208365576 TCGA-G9-6369 DUP 29 5 SYT2 * chr1 205666186 205666186 chr7 13983465 13983465 TCGA-G9-6369 BND 12 13 SLC45A3 ETV1 chr1 211523512 211523512 chr1 212009647 212009647 TCGA-G9-6369 DUP 38 18 * INTS7 chr1 214404889 214404889 chr1 214684519 214684519 TCGA-G9-6369 DUP 39 8 PTPN14 * chr1 215892729 215892729 chr1 218097399 218097399 TCGA-G9-6369 DUP 6 24 USH2A * chr1 218456076 218456076 chr1 218849778 218849778 TCGA-G9-6369 DUP 9 36 * * chr1 229573342 229573342 chr1 234036339 234036339 TCGA-G9-6369 DUP 20 7 * SLC35F3 chr1 230671394 230671394 chr1 234392476 234392476 TCGA-G9-6369 DUP 31 6 COG2 TARBP1 chr1 238229573 238229573 chr1 238786539 238786539 TCGA-G9-6369 DUP 17 16 * * chr1 243306968 243306968 chr1 244615465 244615465 TCGA-G9-6369 DUP 42 39 SDCCAG8 CATSPERE chr1 24356747 24356747 chr1 25057575 25057575 TCGA-G9-6369 DUP 37 44 GRHL3 AL050344.1 chr1 243681904 243681904 chr1 245747618 245747618 TCGA-G9-6369 DUP 44 5 AKT3 * chr1 30900182 30900182 chr1 31093893 31093893 TCGA-G9-6369 DUP 25 40 SDC3 * chr1 3226440 3226440 chr1 3527844 3527844 TCGA-G9-6369 DUP 10 11 PRDM16 MEGF6 chr1 38739057 38739057 chr1 39232762 39232762 TCGA-G9-6369 DUP 41 14 * MACF1 chr1 41364221 41364221 chr1 43201949 43201949 TCGA-G9-6369 DUP 28 35 FOXO6 EBNA1BP2 chr1 42390951 42390951 chr1 42529869 42529869 TCGA-G9-6369 DUP 32 48 RIMKLA CCDC30 chr1 5367653 5367653 chr1 5840036 5840036 TCGA-G9-6369 DUP 22 44 * * chr1 5387188 5387188 chr7 150909719 150909719 TCGA-G9-6369 BND 33 33 * * chr1 56189953 56189953 chr1 60652662 60652662 TCGA-G9-6369 DUP 26 14 AC119674.1 * chr1 58049944 58049944 chr1 208365789 208365789 TCGA-G9-6369 INV 39 32 DAB1 * chr1 72299246 72299246 chr1 72370813 72370813 TCGA-G9-6369 INV 29 11 * * chr1 79649578 79649578 chr1 79937797 79937797 TCGA-G9-6369 DUP 22 27 * * chr1 95594411 95594411 chr1 95798260 95798260 TCGA-G9-6369 INV 48 24 LINC02607 * chr20 10844420 10844420 chr22 40854110 40854110 TCGA-G9-6369 BND 34 50 AL050403.2 ST13 chr20 10871582 10871582 chr20 10999528 10999528 TCGA-G9-6369 DUP 8 8 AL050403.2 * chr20 12919413 12919413 chr20 15492758 15492758 TCGA-G9-6369 DUP 42 34 LINC01722 MACROD2 chr20 13068482 13068482 chr20 14631269 14631269 TCGA-G9-6369 DUP 16 8 SPTLC3 MACROD2 chr20 16464498 16464498 chr20 18804645 18804645 TCGA-G9-6369 DUP 39 21 KIF16B * chr20 18237037 18237037 chr20 21729921 21729921 TCGA-G9-6369 DUP 21 9 * * chr20 20382131 20382131 chr20 24523148 24523148 TCGA-G9-6369 DUP 13 14 * SYNDIG1 chr20 20490310 20490310 chr20 20542743 20542743 TCGA-G9-6369 DEL 5 5 RALGAPA2 RALGAPA2 chr20 24741637 24741641 chr3 33703451 33703455 TCGA-G9-6369 BND 5 24 * CLASP2 chr20 30274391 30274391 chr20 30328813 30328813 TCGA-G9-6369 INV 34 31 * FAM242A chr20 304758 304758 chr20 400835 400835 TCGA-G9-6369 DUP 40 43 * * chr20 351245 351245 chr20 382583 382583 TCGA-G9-6369 DEL 9 23 NRSN2 TRIB3 chr20 41058654 41058654 chr20 41379008 41379008 TCGA-G9-6369 DUP 49 6 TOP1 * chr20 43510358 43510358 chr20 43767021 43767021 TCGA-G9-6369 DUP 8 49 L3MBTL1 * chr20 4610400 4610400 chr22 39945464 39945464 TCGA-G9-6369 BND 33 46 * GRAP2 chr20 48595828 48595828 chr20 49018132 49018132 TCGA-G9-6369 DUP 35 46 * ARFGEF2 chr20 5061968 5061968 chr20 5786335 5786335 TCGA-G9-6369 INV 9 34 AL121890.5 SHLD1 chr20 61657953 61657953 chr20 63854722 63854722 TCGA-G9-6369 DUP 37 11 CDH4 * chr21 16956413 16956413 chr21 17695588 17695588 TCGA-G9-6369 DUP 3 46 * * chr21 20742484 20742484 chr21 23449292 23449292 TCGA-G9-6369 DUP 46 21 * * chr21 20781716 20781716 chr21 21031165 21031165 TCGA-G9-6369 DUP 38 1 LINC00320 NCAM2 chr21 29550107 29550107 chr21 29793648 29793648 TCGA-G9-6369 DUP 3 23 BACH1 GRIK1 chr21 32703814 32703814 chr21 34557048 34557048 TCGA-G9-6369 DUP 39 12 SYNJ1 RCAN1 chr21 38486510 38486510 chr21 41500653 41500653 TCGA-G9-6369 DEL 6 32 ERG TMPRSS2 chr21 38492410 38492410 chr21 41500359 41500359 TCGA-G9-6369 DEL 43 10 ERG TMPRSS2 chr21 38595713 38595713 chr21 41500676 41500676 TCGA-G9-6369 DEL 42 49 ERG TMPRSS2 chr21 43508397 43508397 chr21 46222547 46222547 TCGA-G9-6369 DUP 32 44 * LSS chr22 18893039 18893039 chr22 19469719 19469719 TCGA-G9-6369 DUP 19 42 FAM230F UFD1 chr22 28884343 28884343 chr22 29218208 29218208 TCGA-G9-6369 DUP 28 39 ZNRF3 EMID1 chr22 34659926 34659926 chr22 35549333 35549333 TCGA-G9-6369 DUP 8 14 * RASD2 chr2 104824352 104824352 chr22 20162482 20162482 TCGA-G9-6369 BND 6 38 PANTR1 * chr2 104962804 104962804 chr2 105635292 105635292 TCGA-G9-6369 DUP 9 37 MRPS9-AS2 * chr2 106729411 106729411 chr2 106847186 106847186 TCGA-G9-6369 DUP 12 2 * ST6GAL2 chr2 107105375 107105375 chr2 107375790 107375790 TCGA-G9-6369 DUP 11 40 * AC096669.1 chr2 117622718 117622718 chr2 118015441 118015441 TCGA-G9-6369 DUP 45 1 * CCDC93 chr2 119849613 119849613 chr2 123907791 123907791 TCGA-G9-6369 DUP 31 41 PTPN4 * chr2 125492700 125492700 chr9 100106100 100106100 TCGA-G9-6369 BND 12 25 * INVS chr2 125891540 125891540 chr2 126123824 126123824 TCGA-G9-6369 DUP 44 10 * * chr2 127427159 127427159 chr9 97208063 97208063 TCGA-G9-6369 BND 24 3 PROC ANKRD18CP chr2 129368246 129368246 chr2 129531513 129531513 TCGA-G9-6369 DUP 35 10 * * chr2 131692664 131692664 chr2 131880787 131880787 TCGA-G9-6369 DUP 42 27 * * chr2 145502252 145502252 chr2 145547767 145547767 TCGA-G9-6369 DUP 30 15 * * chr2 153934698 153934698 chr2 156769237 156769237 TCGA-G9-6369 DUP 38 31 GALNT13 * chr2 154094293 154094293 chr2 157512086 157512086 TCGA-G9-6369 DUP 41 37 GALNT13 * chr2 154571306 154571306 chr2 154695012 154695012 TCGA-G9-6369 DEL 31 21 * * chr2 155934397 155934397 chr2 156175836 156175836 TCGA-G9-6369 DUP 37 27 * LINC01876 chr2 156004804 156004805 chr2 199112091 199112091 TCGA-G9-6369 DEL 11 40 * * chr2 156004804 156004805 chr2 157437905 157437906 TCGA-G9-6369 DEL 12 40 * CYTIP chr2 157437905 157437906 chr2 198929193 198929193 TCGA-G9-6369 INV 7 44 CYTIP AC020718.1 chr2 164520473 164520473 chr2 164899102 164899102 TCGA-G9-6369 DUP 28 8 GRB14 AC019197.1 chr2 171495710 171495710 chr2 210739719 210739719 TCGA-G9-6369 DUP 29 41 * * chr2 171925783 171925783 chr2 210480186 210480186 TCGA-G9-6369 DEL 4 47 SLC25A12 CPS1 chr2 175133053 175133053 chr2 175197848 175197848 TCGA-G9-6369 DUP 41 21 ATF2 * chr2 177710127 177710127 chr2 181678629 181678629 TCGA-G9-6369 DUP 18 8 PDE11A CERKL chr2 180730105 180730105 chr3 179192711 179192711 TCGA-G9-6369 BND 8 25 SCHLAP1 PIK3CA chr2 182130752 182130752 chr2 182478318 182478318 TCGA-G9-6369 DUP 32 2 PPP1R1C PDE1A chr2 18944968 18944968 chr2 20278730 20278730 TCGA-G9-6369 DUP 45 29 * PUM2 chr2 195215607 195215607 chr2 195504291 195504291 TCGA-G9-6369 DUP 11 39 * AC064834.1 chr2 196752655 196752655 chr2 196791484 196791484 TCGA-G9-6369 DUP 50 31 CCDC150 GTF3C3 chr2 199046068 199046068 chr2 199214509 199214509 TCGA-G9-6369 DUP 10 13 AC020718.1 * chr2 199844913 199844913 chr2 200022522 200022522 TCGA-G9-6369 DUP 25 27 FTCDNL1 * chr2 200405606 200405606 chr2 201314003 201314003 TCGA-G9-6369 DUP 17 10 SPATS2L FLACC1 chr2 202266238 202266238 chr2 205885831 205885831 TCGA-G9-6369 DUP 43 21 NOP58 * chr2 205988788 205988788 chr2 205988925 205988925 TCGA-G9-6369 DEL 2 21 AC007679.1 AC007679.1 chr2 212270603 212270603 chr2 212555729 212555729 TCGA-G9-6369 DUP 14 9 ERBB4 * chr2 223336920 223336920 chr2 223337275 223337275 TCGA-G9-6369 INS 33 27 * * chr2 225264846 225264846 chr2 225754196 225754196 TCGA-G9-6369 DUP 45 18 * * chr2 228236996 228236996 chr2 228587234 228587234 TCGA-G9-6369 DUP 11 9 * LINC01807 chr2 228241858 228241858 chr2 228471118 228471118 TCGA-G9-6369 DEL 33 49 * * chr2 229539990 229539990 chr2 230259405 230259405 TCGA-G9-6369 DUP 47 26 DNER SP140 chr2 230864744 230864744 chr2 234324782 234324782 TCGA-G9-6369 DUP 2 11 ITM2C * chr2 233032403 233032403 chr2 234058495 234058495 TCGA-G9-6369 DUP 5 17 NEU2 SPP2 chr2 236224689 236224689 chr2 236466489 236466489 TCGA-G9-6369 DUP 48 41 ASB18 IQCA1 chr2 237007082 237007082 chr2 237417308 237417308 TCGA-G9-6369 DUP 22 37 * * chr2 240218171 240218171 chr2 240281090 240281090 TCGA-G9-6369 DUP 41 46 * * chr2 241432706 241432706 chr2 241690965 241690965 TCGA-G9-6369 DUP 4 12 FARP2 ING5 chr2 241989700 241989700 chr22 49476831 49476831 TCGA-G9-6369 BND 19 26 LINC01237 C22orf34 chr2 26403897 26403897 chr2 27637306 27637306 TCGA-G9-6369 DUP 30 23 DRC1 GPN1 chr2 26608537 26608537 chr2 30470434 30470434 TCGA-G9-6369 DUP 18 11 CIB4 LCLAT1 chr2 26655104 26655118 chr5 174117935 174117935 TCGA-G9-6369 BND 2 27 * NSG2 chr2 26821615 26821615 chr2 27238542 27238542 TCGA-G9-6369 DUP 33 38 * CAD chr2 2728882 2728882 chr2 2851938 2851938 TCGA-G9-6369 DUP 2 36 * * chr2 28049299 28049299 chr2 29460362 29460362 TCGA-G9-6369 DEL 42 46 BABAM2 ALK chr2 34540967 34540967 chr2 34645257 34645257 TCGA-G9-6369 DUP 47 18 LINC01320 LINC01320 chr2 35273837 35273837 chr2 36469190 36469190 TCGA-G9-6369 DUP 21 17 * CRIM1 chr2 57091150 57091150 chr2 57814654 57814654 TCGA-G9-6369 DUP 21 29 * * chr2 61453446 61453446 chr2 66064698 66064698 TCGA-G9-6369 DUP 35 11 USP34 AC007389.1 chr2 62132176 62132176 chr2 65085570 65085570 TCGA-G9-6369 INV 45 4 COMMD1 CEP68 chr2 78467150 78467150 chr2 81580744 81580744 TCGA-G9-6369 DUP 30 37 * * chr2 80886965 80886965 chr2 80991516 80991516 TCGA-G9-6369 DUP 44 16 * * chr2 86058769 86058769 chr2 86834104 86834104 TCGA-G9-6369 DUP 32 35 POLR1A CD8B chr2 91710474 91710474 chr4 1910662 1910662 TCGA-G9-6369 BND 47 31 AC027612.2 NSD2 chr2 96870302 96870302 chr2 97205610 97205610 TCGA-G9-6369 DUP 44 19 SEMA4C ANKRD36 chr3 105713397 105713397 chr3 173220513 173220513 TCGA-G9-6369 INV 33 7 CBLB AC068759.1 chr3 128464511 128464511 chr3 130953495 130953495 TCGA-G9-6369 DUP 49 25 DNAJB8 ATP2C1 chr3 128499350 128499350 chr7 145498556 145498556 TCGA-G9-6369 BND 13 34 GATA2-AS1 * chr3 131096493 131096493 chr3 139377593 139377593 TCGA-G9-6369 INV 7 42 NEK11 COPB2 chr3 135683474 135683474 chr3 140849070 140849070 TCGA-G9-6369 DUP 29 26 * * chr3 139747624 139747624 chr3 142603119 142603119 TCGA-G9-6369 DUP 10 13 * PLS1 chr3 145972754 145972754 chr3 146223628 146223628 TCGA-G9-6369 DUP 15 5 * PLSCR4 chr3 14956088 14956091 chr3 17688063 17688063 TCGA-G9-6369 DUP 24 4 NR2C2 TBC1D5 chr3 14956088 14956091 chr3 17513035 17513035 TCGA-G9-6369 DEL 28 43 NR2C2 TBC1D5 chr3 151909937 151909937 chr3 152365692 152365692 TCGA-G9-6369 DUP 38 16 AADACL2-AS1 MBNL1 chr3 163177458 163177458 chr3 163200269 163200269 TCGA-G9-6369 DEL 4 1 AC128685.1 AC128685.1 chr3 16498718 16498718 chr3 17020685 17020685 TCGA-G9-6369 DUP 25 20 RFTN1 PLCL2 chr3 169677173 169677173 chr3 173181716 173181716 TCGA-G9-6369 DUP 23 21 * AC068759.1 chr3 16969032 16969032 chr3 17189120 17189120 TCGA-G9-6369 DUP 22 49 PLCL2 TBC1D5 chr3 171986246 171986246 chr3 172134504 172134504 TCGA-G9-6369 DUP 13 43 * FNDC3B chr3 175248566 175248566 chr3 194354931 194354931 TCGA-G9-6369 DUP 24 46 NAALADL2 * chr3 176037597 176037597 chr3 194100118 194100118 TCGA-G9-6369 DEL 47 3 * AC080129.1 chr3 176262912 176262912 chr3 176667218 176667218 TCGA-G9-6369 DUP 22 49 * * chr3 177201419 177201419 chr3 190678740 190678740 TCGA-G9-6369 DUP 39 47 TBL1XR1 * chr3 177770887 177770887 chr3 177770954 177770954 TCGA-G9-6369 INV 49 43 * * chr3 178981081 178981081 chr3 190194368 190194368 TCGA-G9-6369 DEL 19 25 * * chr3 184961816 184961816 chr3 185438020 185438020 TCGA-G9-6369 DUP 37 3 VPS8 MAP3K13 chr3 193147473 193147473 chr3 193157544 193157544 TCGA-G9-6369 DUP 50 30 AC092966.1 VEZF1P1 chr3 193519923 193519923 chr3 194426931 194426931 TCGA-G9-6369 DUP 46 6 ATP13A4 ATP13A3 chr3 193639150 193639150 chr3 194406491 194406491 TCGA-G9-6369 DEL 37 4 OPA1 ATP13A3 chr3 24967352 24967363 chr20 24933839 24933852 TCGA-G9-6369 BND 37 18 AC092422.1 * chr3 25384685 25384685 chr3 29209370 29209370 TCGA-G9-6369 DUP 33 35 RARB AC098650.1 chr3 2555940 2555940 chr3 2740204 2740204 TCGA-G9-6369 DUP 24 36 CNTN4 CNTN4 chr3 27504920 27504920 chr7 81550558 81550558 TCGA-G9-6369 BND 7 2 * AC008163.1 chr3 28774487 28774487 chr3 29024088 29024088 TCGA-G9-6369 DUP 44 11 AC098650.1 AC098650.1 chr3 33703451 33703455 chr20 24741637 24741641 TCGA-G9-6369 BND 48 28 CLASP2 * chr3 36643289 36643289 chr7 81875133 81875133 TCGA-G9-6369 BND 10 40 * * chr3 37466257 37466257 chr3 39896143 39896143 TCGA-G9-6369 DUP 36 22 ITGA9 MYRIP chr3 39317260 39317260 chr3 43194320 43194320 TCGA-G9-6369 DUP 26 48 * * chr3 45384422 45384422 chr3 49129020 49129020 TCGA-G9-6369 DUP 5 7 * LAMB2 chr3 47426701 47426701 chr3 47684653 47684653 TCGA-G9-6369 DUP 24 28 SCAP SMARCC1 chr3 51039107 51039107 chr3 52634852 52634852 TCGA-G9-6369 DUP 26 25 DOCK3 PBRM1 chr3 56371921 56371921 chr3 58358389 58358389 TCGA-G9-6369 DUP 15 6 ERC2 PXK chr3 57037083 57037083 chr3 57321538 57321538 TCGA-G9-6369 DUP 10 31 ARHGEF3 DNAH12 chr3 58826102 58826102 chr3 62723669 62723669 TCGA-G9-6369 DUP 7 31 CFAP20DC CADPS chr3 64070254 64070254 chr3 67110499 67110499 TCGA-G9-6369 DUP 31 16 PRICKLE2-AS1 * chr3 7362831 7362831 chr3 7974160 7974160 TCGA-G9-6369 DUP 49 41 GRM7 LMCD1-AS1 chr3 74785666 74785666 chr3 77010110 77010110 TCGA-G9-6369 DUP 24 35 * ROBO2 chr3 76213153 76213153 chr3 76356710 76356710 TCGA-G9-6369 DUP 29 19 ROBO2 ROBO2 chr3 76355695 76355695 chr3 76543941 76543941 TCGA-G9-6369 DUP 19 9 ROBO2 ROBO2 chr3 76967615 76967615 chr3 77281539 77281539 TCGA-G9-6369 DUP 12 38 ROBO2 ROBO2 chr3 78816958 78816958 chr3 79002357 79002357 TCGA-G9-6369 DUP 32 26 ROBO1 ROBO1 chr3 79572267 79572267 chr3 80587318 80587318 TCGA-G9-6369 DEL 13 50 ROBO1 * chr3 81809077 81809077 chr3 82033275 82033275 TCGA-G9-6369 DUP 2 26 * LINC02008 chr3 85002402 85002402 chr3 85082865 85082865 TCGA-G9-6369 DEL 9 42 CADM2 CADM2 chr3 85613776 85613776 chr3 88787742 88787742 TCGA-G9-6369 DUP 33 8 CADM2 * chr3 85954392 85954392 chr3 86088392 86088392 TCGA-G9-6369 DUP 46 30 CADM2 * chr3 86557711 86557711 chr3 89184619 89184619 TCGA-G9-6369 DUP 36 3 * EPHA3 chr3 95907534 95907534 chr3 96145910 96145910 TCGA-G9-6369 DUP 9 2 * * chr3 9636488 9636488 chr9 11643131 11643131 TCGA-G9-6369 BND 20 21 * AL353595.1 chr3 97713678 97713678 chr3 99476619 99476619 TCGA-G9-6369 DUP 29 40 EPHA6 * chr3 99836915 99836915 chr3 100251534 100251534 TCGA-G9-6369 DUP 31 50 CMSS1 * chr3 99902140 99902140 chr20 3712930 3712930 TCGA-G9-6369 BND 17 8 CMSS1 * chr4 119348391 119348391 chr4 119487176 119487176 TCGA-G9-6369 DUP 20 32 KLHL2P1 AC093752.1 chr4 123133611 123133611 chr4 125047733 125047733 TCGA-G9-6369 DUP 23 30 SPATA5 * chr4 12388692 12388692 chr4 16340755 16340755 TCGA-G9-6369 DUP 9 46 * * chr4 129152222 129152222 chr4 129319315 129319315 TCGA-G9-6369 DUP 50 17 * * chr4 135156551 135156551 chr4 136876063 136876063 TCGA-G9-6369 DUP 25 27 * LINC02511 chr4 137558631 137558631 chr4 138564275 138564275 TCGA-G9-6369 DUP 45 38 LINC02172 * chr4 139309045 139309045 chr4 139311356 139311356 TCGA-G9-6369 DEL 1 28 NAA15 NAA15 chr4 139926774 139926774 chr4 140259778 140259778 TCGA-G9-6369 DUP 19 2 MAML3 SCOC chr4 140857620 140857620 chr4 140857883 140857883 TCGA-G9-6369 INS 20 23 * * chr4 145079010 145079010 chr4 145611541 145611541 TCGA-G9-6369 DUP 27 16 AC098588.2 MMAA chr4 157068989 157068989 chr4 159923866 159923866 TCGA-G9-6369 DUP 32 26 * * chr4 159506883 159506883 chr4 161216623 161216623 TCGA-G9-6369 DUP 3 29 * * chr4 163375665 163375665 chr4 165581866 165581866 TCGA-G9-6369 DUP 6 23 * * chr4 164995355 164995355 chr4 167469198 167469198 TCGA-G9-6369 DUP 50 36 * * chr4 169071715 169071715 chr9 132103699 132103699 TCGA-G9-6369 BND 36 1 * * chr4 170774137 170774137 chr7 13566813 13566813 TCGA-G9-6369 BND 11 13 * AC011287.1 chr4 175636085 175636085 chr7 9763373 9763373 TCGA-G9-6369 BND 25 8 GPM6A AC060834.2 chr4 179449139 179449139 chr4 179534486 179534486 TCGA-G9-6369 DUP 24 42 AC020551.1 * chr4 181667535 181667535 chr4 184841071 184841071 TCGA-G9-6369 DUP 38 31 * * chr4 188854327 188854327 chr4 189075345 189075345 TCGA-G9-6369 DUP 24 17 * * chr4 20063163 20063163 chr4 20252569 20252569 TCGA-G9-6369 DUP 15 6 * SLIT2 chr4 21501056 21501056 chr4 21662714 21662714 TCGA-G9-6369 DUP 22 43 KCNIP4 KCNIP4 chr4 3574969 3574969 chr4 3590485 3590485 TCGA-G9-6369 DEL 8 23 * LINC00955 chr4 35888928 35888928 chr4 36030922 36030922 TCGA-G9-6369 DUP 15 14 * ARAP2 chr4 46134621 46134621 chr4 46265253 46265253 TCGA-G9-6369 DUP 12 2 * GABRA2 chr4 47666484 47666484 chr4 48035592 48035592 TCGA-G9-6369 DUP 5 40 CORIN NIPAL1 chr4 54136926 54136926 chr9 20848605 20848605 TCGA-G9-6369 BND 10 9 AC058822.1 FOCAD chr4 54844103 54844103 chr4 56735106 56735106 TCGA-G9-6369 DUP 29 48 AC097494.1 * chr4 56635976 56635976 chr4 56805224 56805224 TCGA-G9-6369 DUP 6 35 * RN7SL357P chr4 56885557 56885557 chr4 56897355 56897355 TCGA-G9-6369 INV 40 37 * * chr4 60102854 60102854 chr4 61990861 61990861 TCGA-G9-6369 DUP 15 47 * ADGRL3 chr4 62583227 62583227 chr4 62668098 62668098 TCGA-G9-6369 DUP 29 43 * * chr4 63983909 63983909 chr4 64075655 64075655 TCGA-G9-6369 DUP 39 45 * * chr4 71417793 71417793 chr4 75026087 75026087 TCGA-G9-6369 DUP 44 49 SLC4A4 PARM1 chr4 74815142 74815142 chr17 22067288 22067288 TCGA-G9-6369 BND 21 32 * NCOR1P2 chr4 74815773 74815773 chr17 22181586 22181586 TCGA-G9-6369 BND 26 14 * UBBP4 chr4 76572789 76572789 chr4 77893966 77893966 TCGA-G9-6369 DUP 24 18 SHROOM3 MRPL1 chr4 87111003 87111003 chr4 87111318 87111318 TCGA-G9-6369 DEL 20 49 AFF1 AFF1 chr4 89839479 89839479 chr4 165508882 165508882 TCGA-G9-6369 DEL 20 35 SNCA * chr4 90756372 90756372 chr20 49110170 49110170 TCGA-G9-6369 BND 6 17 CCSER1 * chr4 92644622 92644622 chr4 92796812 92796812 TCGA-G9-6369 DUP 34 34 GRID2 GRID2 chr4 93442370 93442370 chr4 93588710 93588710 TCGA-G9-6369 DUP 11 27 GRID2 GRID2 chr4 99808442 99808442 chr4 100376255 100376255 TCGA-G9-6369 DUP 28 6 * * chr5 102315561 102315561 chr5 102446788 102446788 TCGA-G9-6369 DUP 8 19 * SLCO6A1 chr5 111843000 111843000 chr7 112423778 112423778 TCGA-G9-6369 BND 18 2 NREP IFRD1 chr5 111992173 111992173 chr5 112501218 112501218 TCGA-G9-6369 DUP 32 37 NREP * chr5 121852159 121852159 chr5 122305744 122305744 TCGA-G9-6369 DUP 29 45 FTMT * chr5 126952563 126952563 chr5 131399815 131399815 TCGA-G9-6369 DUP 6 25 MARCHF3 * chr5 127724518 127724518 chr5 128328232 128328232 TCGA-G9-6369 DUP 13 27 CCDC192 FBN2 chr5 136234866 136234866 chr5 136398388 136398388 TCGA-G9-6369 DUP 2 4 TRPC7 AC063980.1 chr5 138203655 138203655 chr5 138345018 138345018 TCGA-G9-6369 DUP 26 40 CDC23 FAM53C chr5 145739083 145739083 chr5 146247033 146247033 TCGA-G9-6369 DUP 10 19 PRELID2 RBM27 chr5 14672554 14672554 chr5 15624467 15624467 TCGA-G9-6369 DUP 48 3 OTULIN FBXL7 chr5 148857096 148857096 chr5 152396316 152396316 TCGA-G9-6369 DUP 49 36 * NMUR2 chr5 151636192 151636192 chr5 151821245 151821245 TCGA-G9-6369 DUP 43 17 * * chr5 151638940 151638940 chr5 171210976 171210977 TCGA-G9-6369 INV 11 47 * RANBP17 chr5 151820444 151820444 chr5 172593974 172593974 TCGA-G9-6369 INV 18 22 * * chr5 1524357 1524357 chr5 1921372 1921372 TCGA-G9-6369 DUP 31 1 LPCAT1 * chr5 156446050 156446050 chr5 156823595 156823595 TCGA-G9-6369 DUP 16 49 SGCD * chr5 159271450 159271450 chr5 162081070 162081070 TCGA-G9-6369 DUP 23 16 UBLCP1 GABRG2 chr5 162872452 162872452 chr5 164345418 164345418 TCGA-G9-6369 DUP 5 41 AC113414.1 AC109466.1 chr5 163286689 163286689 chr5 166270218 166270218 TCGA-G9-6369 DUP 1 46 AC113414.1 * chr5 163411979 163411979 chr5 163565741 163565741 TCGA-G9-6369 DUP 10 27 AC113414.1 * chr5 163633122 163633122 chr5 163818851 163818851 TCGA-G9-6369 DUP 15 14 * * chr5 167693657 167693657 chr5 167859518 167859518 TCGA-G9-6369 DUP 38 9 TENM2 TENM2 chr5 169865497 169865497 chr5 172336525 172336525 TCGA-G9-6369 DUP 17 11 DOCK2 SH3PXD2B chr5 171210976 171210977 chr5 172605047 172605048 TCGA-G9-6369 DUP 23 23 RANBP17 * chr5 171487181 171487181 chr5 172914591 172914591 TCGA-G9-6369 DUP 40 34 * ERGIC1 chr5 172594194 172594194 chr5 172604098 172604098 TCGA-G9-6369 INV 50 30 * * chr5 176893782 176893782 chr5 177362625 177362625 TCGA-G9-6369 DUP 36 32 HK3 RGS14 chr5 23990662 23990662 chr5 24189275 24189275 TCGA-G9-6369 DUP 3 8 C5orf17 * chr5 25885807 25885807 chr5 29067391 29067391 TCGA-G9-6369 DUP 3 25 * * chr5 27292759 27292759 chr5 27459828 27459828 TCGA-G9-6369 DUP 29 19 * * chr5 30748047 30748047 chr5 30992155 30992155 TCGA-G9-6369 DUP 4 39 * * chr5 33982787 33982787 chr5 34120627 34120627 TCGA-G9-6369 DUP 38 21 SLC45A2 C1QTNF3-AMACR chr5 35188319 35188319 chr5 40034011 40034011 TCGA-G9-6369 DUP 33 39 PRLR LINC00603 chr5 37949016 37949016 chr5 38146924 38146924 TCGA-G9-6369 DUP 6 9 GDNF-AS1 * chr5 38012313 38012313 chr5 39204134 39204134 TCGA-G9-6369 DUP 27 16 * FYB1 chr5 38374841 38374841 chr5 38836113 38836113 TCGA-G9-6369 DUP 28 2 EGFLAM OSMR-AS1 chr5 38486216 38486216 chr5 38972530 38972530 TCGA-G9-6369 DUP 49 29 LIFR RICTOR chr5 40499680 40499680 chr5 41113818 41113818 TCGA-G9-6369 DUP 29 7 AC114977.1 * chr5 53954887 53954888 chr5 160672990 160672990 TCGA-G9-6369 DEL 48 33 ARL15 ATP10B chr5 53954887 53954888 chr5 95568178 95568179 TCGA-G9-6369 DEL 47 37 ARL15 ARSK chr5 53958138 53958138 chr5 95822136 95822136 TCGA-G9-6369 INV 42 24 ARL15 RHOBTB3 chr5 54093754 54093754 chr5 61589536 61589536 TCGA-G9-6369 DEL 34 3 ARL15 * chr5 54094441 54094441 chr5 60931900 60931900 TCGA-G9-6369 INV 30 7 ARL15 ERCC8 chr5 54129774 54129774 chr5 60837480 60837480 TCGA-G9-6369 INV 47 38 ARL15 ELOVL7 chr5 54129886 54129886 chr5 159525797 159525797 TCGA-G9-6369 INV 43 46 ARL15 AC008691.1 chr5 56433243 56433243 chr5 172605047 172605048 TCGA-G9-6369 DUP 45 13 * * chr5 56452902 56452902 chr5 59110855 59110855 TCGA-G9-6369 DUP 45 5 * PDE4D chr5 58017354 58017354 chr5 58027652 58027652 TCGA-G9-6369 DUP 41 20 * * chr5 605044 605044 chr5 3974810 3974810 TCGA-G9-6369 DUP 31 37 AC106772.1 * chr5 60797703 60797703 chr5 160617912 160617912 TCGA-G9-6369 INV 6 5 ELOVL7 ATP10B chr5 60854966 60854966 chr5 159524891 159524891 TCGA-G9-6369 DEL 44 48 * AC008691.1 chr5 60916226 60916226 chr5 61588980 61588980 TCGA-G9-6369 INV 16 42 ERCC8 * chr5 60996375 60996375 chr5 160662172 160662172 TCGA-G9-6369 DUP 28 13 NDUFAF2 ATP10B chr5 60997180 60997180 chr5 61307864 61307864 TCGA-G9-6369 DUP 41 4 NDUFAF2 * chr5 61045743 61045743 chr5 160673667 160673667 TCGA-G9-6369 DEL 17 18 NDUFAF2 ATP10B chr5 61047053 61047053 chr5 160550365 160550365 TCGA-G9-6369 INV 3 32 NDUFAF2 * chr5 61308006 61308006 chr5 160660437 160660437 TCGA-G9-6369 DEL 15 2 * ATP10B chr5 61312749 61312749 chr5 160542721 160542721 TCGA-G9-6369 DUP 29 10 * * chr5 61588001 61588001 chr5 95820979 95820979 TCGA-G9-6369 INV 31 14 * RHOBTB3 chr5 63693944 63693944 chr5 64073980 64073980 TCGA-G9-6369 DUP 23 43 * * chr5 65400409 65400409 chr5 65829433 65829433 TCGA-G9-6369 DUP 50 14 ADAMTS6 NLN chr5 77445024 77445024 chr5 77835105 77835105 TCGA-G9-6369 DUP 31 23 WDR41 TBCA chr5 83259711 83259711 chr5 87999234 87999234 TCGA-G9-6369 DUP 43 7 XRCC4 * chr5 85984344 85984344 chr5 86211886 86211886 TCGA-G9-6369 DUP 43 50 * * chr5 90661225 90661225 chr5 90866847 90866847 TCGA-G9-6369 DUP 46 28 ADGRV1 ADGRV1 chr5 95548170 95548170 chr5 159466569 159466569 TCGA-G9-6369 INV 14 13 TTC37 AC008691.1 chr5 95568178 95568179 chr5 160673641 160673641 TCGA-G9-6369 DUP 11 36 ARSK ATP10B chr6 109365187 109365187 chr6 112004219 112004219 TCGA-G9-6369 DUP 30 14 * * chr6 109545429 109545429 chr6 111103922 111103922 TCGA-G9-6369 DUP 20 41 AK9 SLC16A10 chr6 11395279 11395279 chr9 111696094 111696094 TCGA-G9-6369 BND 28 26 * SHOC1 chr6 124099135 124099135 chr6 125195922 125195922 TCGA-G9-6369 DUP 30 37 NKAIN2 TPD52L1 chr6 125465719 125465719 chr6 128928688 128928688 TCGA-G9-6369 DUP 34 6 * LAMA2 chr6 127252548 127252548 chr6 130978710 130978710 TCGA-G9-6369 DUP 39 37 * EPB41L2 chr6 129270747 129270747 chr6 132233727 132233727 TCGA-G9-6369 DUP 2 22 LAMA2 * chr6 129876058 129876058 chr6 132317980 132317980 TCGA-G9-6369 DUP 46 20 * MOXD1 chr6 131590420 131590420 chr6 131831858 131831858 TCGA-G9-6369 DUP 5 30 MED23 ENPP1 chr6 136478500 136478500 chr6 137175199 137175199 TCGA-G9-6369 DUP 6 31 MAP7 * chr6 137592683 137592683 chr6 138659048 138659048 TCGA-G9-6369 DUP 26 3 * NHSL1 chr6 138123119 138123119 chr6 138365019 138365019 TCGA-G9-6369 DUP 39 36 * * chr6 144029953 144029953 chr6 144545257 144545257 TCGA-G9-6369 DUP 16 3 PLAGL1 UTRN chr6 14619647 14619647 chr15 40614254 40614254 TCGA-G9-6369 BND 40 36 * KNL1 chr6 146255230 146255230 chr6 146255440 146255440 TCGA-G9-6369 DEL 42 26 GRM1 GRM1 chr6 146256272 146256272 chr6 146413740 146413740 TCGA-G9-6369 DEL 35 39 GRM1 GRM1 chr6 149346725 149346725 chr6 149641181 149641181 TCGA-G9-6369 DUP 26 47 TAB2 KATNA1 chr6 150890432 150890432 chr6 151493283 151493283 TCGA-G9-6369 DUP 3 49 MTHFD1L CCDC170 chr6 162041361 162041361 chr6 164671454 164671454 TCGA-G9-6369 DUP 39 41 PRKN * chr6 162120391 162120391 chr6 164496310 164496310 TCGA-G9-6369 DUP 33 32 PRKN * chr6 164257367 164257367 chr6 164435360 164435360 TCGA-G9-6369 DUP 37 47 * * chr6 167169873 167169873 chr6 167387108 167387108 TCGA-G9-6369 INV 1 26 TCP10L2 * chr6 1696559 1696559 chr6 4124740 4124740 TCGA-G9-6369 DUP 31 45 GMDS C6orf201 chr6 19741043 19741043 chr6 21586224 21586224 TCGA-G9-6369 DUP 47 48 LNC-LBCS AL512380.2 chr6 26205743 26205743 chr6 26236012 26236012 TCGA-G9-6369 DUP 42 39 H4C5 H1-3 chr6 26205743 26205743 chr6 27906426 27906427 TCGA-G9-6369 DUP 1 27 H4C5 * chr6 26229946 26229946 chr6 27906426 27906427 TCGA-G9-6369 DUP 15 46 * * chr6 29389645 29389645 chr6 120527400 120527400 TCGA-G9-6369 INV 37 21 OR5V1 RNU6-214P chr6 29582918 29582918 chr6 31339950 31339950 TCGA-G9-6369 DUP 16 22 GABBR1 HLA-B chr6 296057 296058 chr16 33529151 33529151 TCGA-G9-6369 BND 40 16 DUSP22 * chr6 30349980 30349980 chr6 30814298 30814298 TCGA-G9-6369 DUP 4 22 HLA-N LINC00243 chr6 32428271 32428271 chr6 32571140 32571140 TCGA-G9-6369 DUP 14 38 * * chr6 34052353 34052353 chr6 35566353 35566353 TCGA-G9-6369 DUP 11 43 GRM4 * chr6 52386421 52386421 chr6 57336853 57336853 TCGA-G9-6369 DUP 36 19 PAQR8 PRIM2 chr6 62661638 62661638 chr6 64802137 64802137 TCGA-G9-6369 DUP 3 16 * EYS chr6 64262806 64262806 chr6 65714162 65714162 TCGA-G9-6369 DEL 8 40 EYS * chr6 65041267 65041267 chr6 67641363 67641363 TCGA-G9-6369 DUP 40 42 EYS * chr6 72738490 72738490 chr6 72903202 72903202 TCGA-G9-6369 DUP 14 34 KCNQ5 KCNQ5 chr6 74516401 74516401 chr6 76348487 76348487 TCGA-G9-6369 DUP 7 22 AL357507.1 * chr6 74997264 74997264 chr6 75125312 75125312 TCGA-G9-6369 DUP 29 42 * COL12A1 chr6 80052282 80052282 chr6 80145867 80145867 TCGA-G9-6369 DUP 6 27 * BCKDHB chr6 82351932 82351932 chr6 87846052 87846052 TCGA-G9-6369 DEL 12 48 * * chr6 82396891 82396891 chr6 87776102 87776102 TCGA-G9-6369 DEL 21 1 * * chr6 82539875 82539875 chr6 85495737 85495737 TCGA-G9-6369 DUP 24 29 * NT5E chr6 83331608 83331608 chr6 83883098 83883098 TCGA-G9-6369 DUP 37 44 ME1 CYB5R4 chr6 84441746 84441746 chr6 87616563 87616563 TCGA-G9-6369 DEL 26 4 LINC01611 ORC3 chr6 85341619 85341619 chr6 87704782 87704782 TCGA-G9-6369 INS 6 8 * * chr6 85349350 85349350 chr15 40431791 40431791 TCGA-G9-6369 BND 18 31 * IVD chr6 85625209 85625209 chr6 86450437 86450437 TCGA-G9-6369 DUP 15 27 SYNCRIP * chr6 85716115 85716115 chr15 40434873 40434873 TCGA-G9-6369 BND 15 31 * IVD chr6 87841500 87841500 chr6 94903724 94903724 TCGA-G9-6369 INV 46 11 * * chr6 90106628 90106628 chr6 90303712 90303712 TCGA-G9-6369 DUP 11 14 BACH2 * chr6 96142101 96142101 chr6 98979363 98979363 TCGA-G9-6369 DUP 23 7 FUT9 * chr6 98758161 98758161 chr6 99022573 99022573 TCGA-G9-6369 DUP 3 1 * * chr7 10205161 10205161 chr7 11604809 11604809 TCGA-G9-6369 DUP 1 33 * THSD7A chr7 102384812 102384812 chr11 69182964 69182964 TCGA-G9-6369 BND 10 49 PRKRIP1 * chr7 104338014 104338014 chr7 104924746 104924746 TCGA-G9-6369 INV 9 28 LHFPL3 LHFPL3-AS2 chr7 104338598 104338598 chr7 104965467 104965467 TCGA-G9-6369 DUP 21 33 LHFPL3 LINC01004 chr7 105088103 105088103 chr7 108628549 108628549 TCGA-G9-6369 DUP 26 44 KMT2E * chr7 105161901 105161901 chr7 105564758 105564758 TCGA-G9-6369 DUP 48 21 SRPK2 RINT1 chr7 108928971 108928971 chr7 112826766 112826766 TCGA-G9-6369 DUP 32 44 AC004014.1 BMT2 chr7 112381161 112381161 chr7 112884581 112884581 TCGA-G9-6369 DEL 50 5 AC004112.1 BMT2 chr7 112394221 112394222 chr5 111747596 111747597 TCGA-G9-6369 BND 12 19 AC004112.1 NREP chr7 112423778 112423778 chr5 111843000 111843000 TCGA-G9-6369 BND 38 47 IFRD1 NREP chr7 113468205 113468205 chr7 113599158 113599158 TCGA-G9-6369 DUP 46 14 * * chr7 114198614 114198614 chr7 114341862 114341862 TCGA-G9-6369 DUP 14 19 FOXP2 FOXP2 chr7 114866512 114866512 chr7 117990539 117990539 TCGA-G9-6369 DUP 50 28 * * chr7 116527013 116527013 chr7 116786602 116786602 TCGA-G9-6369 DUP 8 40 CAV1 MET chr7 126792710 126792710 chr3 33606991 33606991 TCGA-G9-6369 BND 37 19 GRM8 CLASP2 chr7 129965899 129965899 chr7 133074093 133074093 TCGA-G9-6369 DUP 49 48 AC073320.1 CHCHD3 chr7 130985965 130985965 chr7 135137651 135137651 TCGA-G9-6369 DUP 25 30 AC016831.6 AGBL3 chr7 131763646 131763646 chr7 132477585 132477585 TCGA-G9-6369 DUP 25 46 * PLXNA4 chr7 132650417 132650417 chr7 135858493 135858493 TCGA-G9-6369 DUP 19 45 FLJ40288 * chr7 136724770 136724770 chr7 138335050 138335050 TCGA-G9-6369 DUP 16 4 AC009264.1 * chr7 137141500 137141500 chr7 137313692 137313692 TCGA-G9-6369 DUP 37 50 AC009264.1 PTN chr7 140664081 140664081 chr7 141021306 141021306 TCGA-G9-6369 DUP 48 41 DENND2A * chr7 140792862 140792862 chr1 205670177 205670177 TCGA-G9-6369 BND 6 42 BRAF SLC45A3 chr7 141515997 141515997 chr7 141633361 141633361 TCGA-G9-6369 DUP 42 44 * AGK chr7 148070891 148070891 chr7 149440414 149440414 TCGA-G9-6369 DUP 14 14 CNTNAP2 ZNF777 chr7 148522136 148522136 chr7 149915318 149915318 TCGA-G9-6369 DUP 22 44 * * chr7 148532814 148532814 chr7 148838138 148838138 TCGA-G9-6369 DUP 50 24 * EZH2 chr7 150909954 150909954 chrX 68653605 68653605 TCGA-G9-6369 BND 9 49 * STARD8 chr7 152002017 152002017 chr7 152057245 152057245 TCGA-G9-6369 DUP 1 26 GALNTL5 GALNT11 chr7 152056479 152056479 chr7 152192792 152192792 TCGA-G9-6369 DUP 35 50 GALNT11 KMT2C chr7 154582876 154582876 chr7 154880037 154880037 TCGA-G9-6369 DUP 23 22 DPP6 DPP6 chr7 16551333 16551333 chr7 16678068 16678068 TCGA-G9-6369 DUP 12 26 LRRC72 BZW2 chr7 16625315 16625315 chr7 16836037 16836037 TCGA-G9-6369 DUP 29 30 ANKMY2 * chr7 18578040 18578040 chr7 18865283 18865283 TCGA-G9-6369 DUP 22 23 HDAC9 HDAC9 chr7 21593682 21593682 chr7 21761160 21761160 TCGA-G9-6369 DUP 49 50 DNAH11 DNAH11 chr7 2307563 2307563 chr7 2493251 2493251 TCGA-G9-6369 DUP 6 48 SNX8 * chr7 24978511 24978511 chr7 25577281 25577281 TCGA-G9-6369 DUP 31 28 OSBPL3 * chr7 29021133 29021133 chr7 29298685 29298685 TCGA-G9-6369 DUP 30 8 CPVL CHN2 chr7 33894959 33894959 chr7 34245493 34245493 TCGA-G9-6369 DUP 37 14 * AC009262.1 chr7 34748488 34748488 chr7 37609662 37609662 TCGA-G9-6369 DUP 8 47 NPSR1 * chr7 36654469 36654469 chr7 36654624 36654624 TCGA-G9-6369 INV 12 38 AOAH AOAH chr7 41172681 41172681 chr7 41211787 41211787 TCGA-G9-6369 DEL 42 38 * * chr7 54219297 54219297 chr7 54308287 54308306 TCGA-G9-6369 INV 34 19 * * chr7 55476094 55476094 chr7 55713216 55713216 TCGA-G9-6369 DUP 41 7 VOPP1 FKBP9P1 chr7 75742933 75742933 chr7 76006456 76006456 TCGA-G9-6369 DUP 17 4 * STYXL1 chr7 79112122 79112122 chr3 27486604 27486604 TCGA-G9-6369 BND 7 46 MAGI2 AC099535.1 chr7 79325244 79325244 chr7 79711397 79711397 TCGA-G9-6369 DUP 3 48 MAGI2 * chr7 79413432 79413432 chr7 79597948 79597948 TCGA-G9-6369 DUP 2 20 MAGI2 * chr7 79922636 79922636 chr20 24470075 24470075 TCGA-G9-6369 BND 23 29 GNAI1 SYNDIG1 chr7 81709675 81709675 chr3 35929482 35929482 TCGA-G9-6369 BND 10 37 HGF * chr7 81715854 81715854 chr3 74664483 74664483 TCGA-G9-6369 BND 28 50 HGF * chr7 86407309 86407309 chr7 87618978 87618978 TCGA-G9-6369 DUP 34 20 * ABCB1 chr7 86629998 86629998 chr7 89255458 89255458 TCGA-G9-6369 DUP 14 25 * ZNF804B chr7 86726409 86726409 chr7 86726461 86726461 TCGA-G9-6369 INV 42 1 GRM3 GRM3 chr7 87022093 87022093 chr7 87161850 87161850 TCGA-G9-6369 DUP 46 2 ELAPOR2 DMTF1 chr7 89573880 89573880 chr7 91708936 91708936 TCGA-G9-6369 DUP 31 17 * MTERF1 chr7 93265805 93265805 chr7 96112244 96112244 TCGA-G9-6369 DUP 45 34 VPS50 * chr7 95679218 95679218 chr12 30967796 30967796 TCGA-G9-6369 BND 16 35 * TSPAN11 chr7 97830801 97830801 chr7 101752581 101752581 TCGA-G9-6369 DUP 42 8 * * chr7 98757215 98757215 chr7 99490201 99490201 TCGA-G9-6369 DEL 41 9 * ZNF789 chr7 99387221 99387221 chr7 99869439 99869439 TCGA-G9-6369 DEL 23 42 AC004922.1 AC011904.1 chr8 101573751 101573751 chr8 102323750 102323750 TCGA-G9-6369 DUP 32 17 GRHL2 UBR5 chr8 103314456 103314456 chr8 103483910 103483910 TCGA-G9-6369 DUP 10 13 FZD6 AC012213.5 chr8 105464892 105464892 chr8 107914144 107914144 TCGA-G9-6369 DUP 26 26 ZFPM2 RSPO2 chr8 107201024 107201024 chr8 110427426 110427426 TCGA-G9-6369 DUP 5 6 * * chr8 112665159 112665159 chr8 114203529 114203529 TCGA-G9-6369 DUP 44 27 CSMD3 * chr8 11825696 11825696 chr8 39923037 39923037 TCGA-G9-6369 DEL 21 46 FDFT1 IDO1 chr8 118379975 118379975 chr8 118802806 118802806 TCGA-G9-6369 DUP 42 39 SAMD12 SAMD12-AS1 chr8 119078156 119078156 chr8 119274064 119274064 TCGA-G9-6369 DUP 40 38 COLEC10 * chr8 127426717 127426717 chr8 127545914 127545914 TCGA-G9-6369 DUP 46 41 CASC8 * chr8 128429714 128429714 chr8 128521640 128521640 TCGA-G9-6369 DUP 33 33 LINC00824 LINC00824 chr8 131125053 131125053 chr8 131326049 131326049 TCGA-G9-6369 DUP 28 18 * * chr8 131247538 131247538 chr8 135469885 135469885 TCGA-G9-6369 DUP 43 22 * KHDRBS3 chr8 131892375 131892375 chr8 135478296 135478296 TCGA-G9-6369 DUP 3 39 * KHDRBS3 chr8 142214498 142214498 chr8 143678272 143678272 TCGA-G9-6369 DUP 30 46 TSNARE1 * chr8 19786895 19786895 chr8 22532391 22532391 TCGA-G9-6369 DUP 38 9 * PPP3CC chr8 20914246 20914246 chr8 24843408 24843408 TCGA-G9-6369 DUP 5 10 * AC120193.1 chr8 23394842 23394842 chr8 24283882 24283882 TCGA-G9-6369 DUP 22 15 LOXL2 * chr8 23495349 23495349 chr8 23495814 23495814 TCGA-G9-6369 INV 22 9 AC104561.3 * chr8 23524924 23524924 chr8 23524946 23524946 TCGA-G9-6369 INV 6 41 * * chr8 23544435 23544435 chr8 23544507 23544507 TCGA-G9-6369 INV 40 29 SLC25A37 SLC25A37 chr8 23701735 23701735 chr8 23701767 23701767 TCGA-G9-6369 INV 36 47 * * chr8 23701831 23701831 chr8 23701868 23701868 TCGA-G9-6369 INV 34 26 * * chr8 24988479 24988479 chr8 25111156 25111156 TCGA-G9-6369 DUP 15 1 * * chr8 27047940 27047940 chr8 67317454 67317454 TCGA-G9-6369 INV 26 44 * ARFGEF1 chr8 30626377 30626377 chr8 30836210 30836210 TCGA-G9-6369 DUP 17 5 GTF2E2 TEX15 chr8 32276001 32276001 chr8 32369846 32369846 TCGA-G9-6369 DUP 45 3 NRG1 NRG1 chr8 40812348 40812348 chr8 40996739 40996739 TCGA-G9-6369 DUP 4 11 ZMAT4 * chr8 52440703 52440703 chr8 55278289 55278289 TCGA-G9-6369 DUP 9 25 ST18 XKR4 chr8 62606139 62606139 chr8 62750956 62750956 TCGA-G9-6369 DUP 3 39 NKAIN3 NKAIN3 chr8 6398696 6398696 chr8 6534117 6534117 TCGA-G9-6369 DUP 15 7 * MCPH1 chr8 64742688 64742688 chr8 64884715 64884715 TCGA-G9-6369 DUP 7 47 CYP7B1 * chr8 68943861 68943861 chr8 69137699 69137699 TCGA-G9-6369 DUP 37 30 LINC01592 * chr8 69821927 69821927 chr8 70152115 70152115 TCGA-G9-6369 DUP 41 24 SLCO5A1 NCOA2 chr8 69898646 69898646 chr8 70038978 70038978 TCGA-G9-6369 DUP 33 15 * * chr8 73218566 73218566 chr8 75631398 75631398 TCGA-G9-6369 DUP 12 5 * * chr8 76665369 76665369 chr8 77192130 77192130 TCGA-G9-6369 DUP 49 10 ZFHX4-AS1 * chr8 78353690 78353690 chr8 78482496 78482496 TCGA-G9-6369 DUP 38 1 * PKIA-AS1 chr8 79630727 79630727 chr8 79788415 79788415 TCGA-G9-6369 DUP 9 31 STMN2 LINC01607 chr8 8255761 8255761 chr8 10172435 10172435 TCGA-G9-6369 DUP 20 38 * MSRA chr8 82967528 82967528 chr8 83474693 83474693 TCGA-G9-6369 DUP 36 24 * * chr8 91244395 91244395 chr8 91405950 91405950 TCGA-G9-6369 DUP 49 32 SLC26A7 * chr8 94594552 94594552 chr8 97655281 97655281 TCGA-G9-6369 DUP 49 43 AC023632.4 MTDH chr8 94817804 94817804 chr8 95148459 95148459 TCGA-G9-6369 DUP 5 29 INTS8 PLEKHF2 chr8 95517064 95517064 chr8 95828437 95828437 TCGA-G9-6369 DUP 28 33 C8orf37-AS1 * chr8 97273713 97273713 chr8 101545901 101545901 TCGA-G9-6369 DUP 2 7 TSPYL5 GRHL2 chr8 97648422 97648422 chr8 97928389 97928389 TCGA-G9-6369 DUP 42 4 MTDH MATN2 chr9 101752033 101752033 chr9 102042075 102042075 TCGA-G9-6369 DUP 10 10 * * chr9 103909641 103909641 chr9 104070953 104070953 TCGA-G9-6369 DUP 50 11 * * chr9 104922981 104922981 chr9 105311945 105311945 TCGA-G9-6369 DUP 13 42 ABCA1 SLC44A1 chr9 108859188 108859188 chr9 111634319 111634319 TCGA-G9-6369 DUP 16 23 * DNAJC25 chr9 111093316 111093316 chr9 114563876 114563876 TCGA-G9-6369 DUP 22 16 * * chr9 11514763 11514763 chr9 11644410 11644410 TCGA-G9-6369 DUP 26 39 * AL353595.1 chr9 115857952 115857952 chr9 123636162 123636162 TCGA-G9-6369 DEL 18 49 * DENND1A chr9 117059894 117059894 chr9 120359820 120359820 TCGA-G9-6369 DUP 47 29 ASTN2 * chr9 118937507 118937507 chr9 119110921 119110921 TCGA-G9-6369 DUP 46 39 * * chr9 124753343 124753343 chr9 125950172 125950172 TCGA-G9-6369 DUP 26 18 NR6A1 PBX3 chr9 125477642 125477642 chr9 125477675 125477675 TCGA-G9-6369 INV 3 36 MAPKAP1 MAPKAP1 chr9 18184704 18184704 chr11 109872766 109872766 TCGA-G9-6369 BND 16 6 ADAMTSL1 RDX chr9 20957491 20957491 chr9 21103705 21103705 TCGA-G9-6369 DUP 14 30 FOCAD * chr9 28819931 28819931 chr9 29064536 29064536 TCGA-G9-6369 DUP 26 14 * * chr9 36353426 36353426 chr9 36870697 36870697 TCGA-G9-6369 DUP 17 18 RNF38 PAX5 chr9 71580403 71580406 chr13 24531913 24531916 TCGA-G9-6369 BND 43 28 * TPTE2P6 chr9 81967609 81967609 chr9 82067939 82067939 TCGA-G9-6369 DUP 36 38 AL158154.3 AL162726.3 chr9 87419802 87419802 chr9 87572157 87572157 TCGA-G9-6369 DUP 34 43 * DAPK1 chr9 92421675 92421675 chr9 92616742 92616742 TCGA-G9-6369 DUP 7 40 CENPP CENPP chr9 97540673 97540673 chr9 97541861 97541881 TCGA-G9-6369 INV 40 23 TMOD1 TMOD1 chr9 97541861 97541881 chr16 48654754 48654754 TCGA-G9-6369 BND 15 23 TMOD1 AC007611.1 chr9 99961857 99961857 chr9 100519543 100519543 TCGA-G9-6369 DUP 16 1 STX17 TMEFF1 chrX 101069932 101069932 chrX 103986891 103986891 TCGA-G9-6369 INV 21 34 TRMT2B-AS1 * chrX 109416704 109416704 chrX 112127169 112127169 TCGA-G9-6369 DUP 44 13 GUCY2F * chrX 116906843 116906843 chrX 119533768 119533768 TCGA-G9-6369 DUP 27 3 * * chrX 122338376 122338376 chrX 122517421 122517421 TCGA-G9-6369 DUP 48 20 * * chrX 12777308 12777308 chrX 15271067 15271067 TCGA-G9-6369 DUP 39 42 * ASB9 chrX 128737318 128737318 chrX 132229164 132229164 TCGA-G9-6369 DUP 27 41 * RAP2C-AS1 chrX 15066569 15066569 chrX 17654480 17654480 TCGA-G9-6369 DUP 50 43 * NHS chrX 152969794 152969794 chrX 155635052 155635052 TCGA-G9-6369 DUP 34 23 ZNF185 TMLHE chrX 153061672 153061672 chrX 153083555 153083555 TCGA-G9-6369 DEL 44 44 * * chrX 19751554 19751554 chrX 20129426 20129426 TCGA-G9-6369 DUP 42 2 SH3KBP1 EIF1AX chrX 24388395 24388395 chrX 143806010 143806010 TCGA-G9-6369 INV 1 38 * AL500522.1 chrX 33407539 33407539 chrX 33656995 33656995 TCGA-G9-6369 DUP 34 49 * * chrX 35691665 35691665 chrX 36185107 36185107 TCGA-G9-6369 DUP 27 47 * CFAP47 chrX 38139260 38139260 chrX 38873162 38873162 TCGA-G9-6369 DUP 49 37 AF241726.1 * chrX 44810979 44810979 chrX 45041253 45041253 TCGA-G9-6369 DUP 26 19 * KDM6A chrX 51647134 51647134 chrX 51928478 51928478 TCGA-G9-6369 DUP 39 29 * * chrX 55331801 55331801 chrX 147742997 147742997 TCGA-G9-6369 INV 24 29 * * chrX 57576059 57576059 chrX 149806067 149806067 TCGA-G9-6369 INV 17 27 * * chrX 57674587 57674587 chrX 149886640 149886640 TCGA-G9-6369 INV 5 3 * * chrX 57677656 57677656 chrX 149915285 149915285 TCGA-G9-6369 INV 43 19 NLRP2B * chrX 66699975 66699993 chrX 68125964 68125964 TCGA-G9-6369 DUP 43 47 * OPHN1 chrX 67919437 67919437 chrX 68084270 68084270 TCGA-G9-6369 DEL 12 38 * OPHN1 chrX 69226189 69226189 chrX 69475316 69475316 TCGA-G9-6369 DUP 40 32 * * chrX 71133440 71133440 chrX 71140055 71140055 TCGA-G9-6369 DEL 4 6 MED12 MED12 chrX 7654216 7654216 chrX 7730926 7730926 TCGA-G9-6369 DUP 24 6 * * chrX 76911514 76911514 chrX 78668012 78668012 TCGA-G9-6369 DUP 10 21 MIR325HG * chrX 77075576 77075576 chrX 77191413 77191413 TCGA-G9-6369 DUP 45 45 * * chrX 99263090 99263090 chrX 153027074 153027074 TCGA-G9-6369 DUP 41 42 * * chr10 101486820 101486820 chr10 101487047 101487047 TCGA-YL-A9WY INS 32 35 BTRC BTRC chr10 32027424 32027441 chr2 170933658 170933658 TCGA-YL-A9WY BND 20 27 KIF5B GORASP2 chr10 32037575 32037575 chr2 170920636 170920636 TCGA-YL-A9WY BND 48 11 KIF5B * chr10 34537224 34537224 chr10 34537502 34537502 TCGA-YL-A9WY DEL 41 20 PARD3 PARD3 chr10 70421601 70421601 chr10 70423908 70423908 TCGA-YL-A9WY DEL 10 26 EIF4EBP2 EIF4EBP2 chr10 92497212 92497212 chr10 93357809 93357809 TCGA-YL-A9WY DEL 15 37 IDE MYOF chr10 93664182 93664182 chr10 93674306 93674306 TCGA-YL-A9WY DEL 48 18 PDE6C FRA10AC1 chr10 93666575 93666575 chr3 163933163 163933163 TCGA-YL-A9WY BND 9 33 * * chr10 93673119 93673119 chr3 163932372 163932372 TCGA-YL-A9WY BND 42 44 FRA10AC1 * chr11 10772346 10772347 chr7 1152929 1152930 TCGA-YL-A9WY BND 47 20 CTR9 ZFAND2A chr11 10781102 10781102 chr7 1153000 1153000 TCGA-YL-A9WY BND 25 38 CTR9 ZFAND2A chr11 114316847 114316847 chr12 76164905 76164905 TCGA-YL-A9WY BND 26 19 AP002518.2 * chr11 47871586 47871586 chr11 47871820 47871820 TCGA-YL-A9WY INS 48 7 * * chr11 49166420 49166426 chr3 190872572 190872578 TCGA-YL-A9WY BND 47 46 FOLH1 GMNC chr11 62800298 62800298 chr11 114316562 114316562 TCGA-YL-A9WY DEL 13 31 NXF1 AP002518.2 chr12 67358557 67358557 chrX 12027487 12027487 TCGA-YL-A9WY BND 42 50 * * chr12 67363485 67363485 chrX 12016185 12016185 TCGA-YL-A9WY BND 3 28 * * chr12 78101277 78101277 chr12 78101362 78101362 TCGA-YL-A9WY INS 10 31 NAV3 NAV3 chr12 97007251 97007252 chrX 8941721 8941722 TCGA-YL-A9WY BND 39 41 AC007656.2 * chr13 23002275 23002286 chr17 7679514 7679514 TCGA-YL-A9WY BND 29 30 * TP53 chr13 23005820 23005820 chr14 37842428 37842428 TCGA-YL-A9WY BND 22 39 * TTC6 chr13 23586500 23586500 chr13 23650326 23650326 TCGA-YL-A9WY INS 44 30 TNFRSF19 TNFRSF19 chr13 68452000 68452000 chr13 68491584 68491584 TCGA-YL-A9WY DEL 40 41 * * chr13 95210375 95210375 chr13 95212797 95212797 TCGA-YL-A9WY DEL 48 5 ABCC4 ABCC4 chr14 37842686 37842686 chr3 40322120 40322120 TCGA-YL-A9WY BND 39 36 TTC6 ENTPD3-AS1 chr14 59369907 59369907 chr1 184803744 184803744 TCGA-YL-A9WY BND 32 12 DAAM1 NIBAN1 chr15 72480927 72480927 chr15 101646969 101646969 TCGA-YL-A9WY DEL 11 26 ARIH1 TM2D3 chr16 3774614 3774614 chr16 3774789 3774789 TCGA-YL-A9WY DEL 41 5 CREBBP CREBBP chr17 7679777 7679777 chr13 113451594 113451594 TCGA-YL-A9WY BND 30 25 TP53 ADPRHL1 chr18 58175764 58175764 chr18 58208791 58208791 TCGA-YL-A9WY DEL 4 50 NEDD4L NEDD4L chr18 58253725 58253725 chr18 58253794 58253794 TCGA-YL-A9WY INS 3 12 NEDD4L NEDD4L chr19 37357359 37357359 chr19 37357437 37357437 TCGA-YL-A9WY INS 22 43 ZNF875 ZNF875 chr19 50913590 50913590 chr19 50915352 50915352 TCGA-YL-A9WY DEL 39 31 * * chr19 57401181 57401182 chr5 72853973 72853974 TCGA-YL-A9WY BND 6 49 ZNF548 TNPO1 chr1 184781872 184781872 chr1 185220629 185220629 TCGA-YL-A9WY DEL 29 23 * SWT1 chr1 184804433 184804433 chr1 184808244 184808244 TCGA-YL-A9WY DEL 21 30 NIBAN1 NIBAN1 chr1 205660928 205660935 chr3 186069295 186069302 TCGA-YL-A9WY BND 30 5 SLC45A3 ETV5 chr1 229254357 229254357 chr3 68929089 68929089 TCGA-YL-A9WY BND 14 41 * TAFA4 chr1 229258053 229258054 chr3 45861407 45861408 TCGA-YL-A9WY BND 32 29 * LZTFL1 chr20 31540170 31540170 chr20 41541969 41541969 TCGA-YL-A9WY DEL 27 35 HM13 CHD6 chr20 64097064 64097064 chr4 48241050 48241050 TCGA-YL-A9WY BND 16 48 OPRL1 TEC chr20 8748450 8748450 chr20 8748604 8748604 TCGA-YL-A9WY INS 30 1 PLCB1 PLCB1 chr21 8986840 8986840 chr17 20886952 20886952 TCGA-YL-A9WY BND 16 36 MIR3648-2 CCDC144NL chr2 120028721 120028721 chr2 155329281 155329281 TCGA-YL-A9WY INS 1 25 EPB41L5 RNU6-546P chr2 120635504 120635504 chr2 154452469 154452469 TCGA-YL-A9WY DEL 28 45 * GALNT13 chr2 170926289 170926289 chr2 170926535 170926535 TCGA-YL-A9WY INS 10 48 * * chr2 172565643 172565643 chr2 173902567 173902567 TCGA-YL-A9WY DEL 10 43 PDK1 * chr2 172565962 172565962 chr2 173902538 173902538 TCGA-YL-A9WY INS 18 16 PDK1 * chr2 173125434 173125434 chr2 173905755 173905755 TCGA-YL-A9WY INS 40 45 MAP3K20 * chr2 175150075 175150075 chr2 190666821 190666821 TCGA-YL-A9WY DEL 21 17 ATF2 NAB1 chr2 175401313 175401313 chr2 177545118 177545118 TCGA-YL-A9WY DEL 28 46 AC093459.1 AGPS chr2 230812516 230812516 chr10 32037661 32037661 TCGA-YL-A9WY BND 33 4 CAB39 KIF5B chr2 230820436 230820454 chr10 32027424 32027441 TCGA-YL-A9WY BND 30 39 CAB39 KIF5B chr2 230820436 230820454 chr10 31964993 31964993 TCGA-YL-A9WY BND 34 4 CAB39 * chr2 96409452 96409453 chr2 97110070 97110070 TCGA-YL-A9WY DEL 10 38 * * chr2 9687752 9687752 chr2 9688382 9688382 TCGA-YL-A9WY INS 12 26 AC082651.4 AC082651.4 chr2 99559570 99559570 chr10 12071893 12071893 TCGA-YL-A9WY BND 28 27 AFF3 DHTKD1 chr3 116478624 116478624 chr3 116487623 116487623 TCGA-YL-A9WY DEL 6 17 LSAMP LSAMP chr3 131968473 131968473 chr3 131985735 131985735 TCGA-YL-A9WY DEL 21 32 CPNE4 CPNE4 chr3 15368474 15368474 chr3 15368604 15368604 TCGA-YL-A9WY DEL 42 44 * * chr3 186069324 186069324 chr1 205669658 205669658 TCGA-YL-A9WY BND 49 45 ETV5 SLC45A3 chr3 190870167 190870167 chr3 190872390 190872390 TCGA-YL-A9WY DEL 11 45 GMNC GMNC chr3 190872572 190872578 chr11 49166420 49166426 TCGA-YL-A9WY BND 21 40 GMNC FOLH1 chr3 40321846 40321846 chr13 23002275 23002286 TCGA-YL-A9WY BND 30 9 ENTPD3-AS1 * chr3 44226138 44226138 chr3 68928372 68928372 TCGA-YL-A9WY INS 17 20 * TAFA4 chr3 45861407 45861408 chr1 229258053 229258054 TCGA-YL-A9WY BND 38 46 LZTFL1 * chr3 46350211 46350211 chr3 46395532 46395532 TCGA-YL-A9WY DEL 13 12 * CCR5AS chr3 71469926 71469926 chr3 71585489 71585489 TCGA-YL-A9WY DEL 5 7 FOXP1 FOXP1 chr3 84777075 84777075 chr5 156011751 156011751 TCGA-YL-A9WY BND 11 42 LINC00971 SGCD chr3 84783397 84783399 chr5 150755549 150755551 TCGA-YL-A9WY BND 10 3 LINC00971 DCTN4 chr4 125294739 125294739 chr21 41467084 41467084 TCGA-YL-A9WY BND 50 3 * TMPRSS2 chr4 134611089 134611089 chr4 134611660 134611660 TCGA-YL-A9WY DEL 1 17 * * chr4 163473942 163473942 chr4 163482544 163482544 TCGA-YL-A9WY DEL 27 40 TKTL2 * chr4 30446304 30446304 chr4 30448743 30448743 TCGA-YL-A9WY DEL 25 31 * * chr5 132415814 132415814 chr5 173642635 173642635 TCGA-YL-A9WY INS 30 32 AC116366.2 LINC01863 chr5 132899480 132899480 chr5 155996954 155996954 TCGA-YL-A9WY DEL 8 16 AFF4 SGCD chr5 150755549 150755551 chr3 84783397 84783399 TCGA-YL-A9WY BND 23 6 DCTN4 LINC00971 chr5 151341039 151341039 chr5 173665164 173665164 TCGA-YL-A9WY INS 1 48 SLC36A2 * chr5 151341178 151341178 chr5 156011832 156011832 TCGA-YL-A9WY DEL 19 6 SLC36A2 SGCD chr6 18934571 18934571 chr6 50094426 50094426 TCGA-YL-A9WY INS 9 11 * AL138826.1 chr6 55577321 55577321 chrX 41534636 41534636 TCGA-YL-A9WY BND 22 34 HMGCLL1 CASK chr6 71014574 71014574 chr6 71014722 71014722 TCGA-YL-A9WY INS 34 20 * * chr7 104115835 104115835 chr7 104118259 104118259 TCGA-YL-A9WY DEL 31 8 * * chr7 104267835 104267835 chr7 104268125 104268125 TCGA-YL-A9WY DEL 25 3 * * chr7 1153000 1153000 chr11 10781102 10781102 TCGA-YL-A9WY BND 48 25 ZFAND2A CTR9 chr7 132248393 132248393 chr7 132248618 132248618 TCGA-YL-A9WY DEL 13 6 PLXNA4 PLXNA4 chr7 134518418 134518418 chr7 134519335 134519335 TCGA-YL-A9WY DEL 36 12 * * chr7 152213049 152213049 chr7 152215381 152215381 TCGA-YL-A9WY DEL 6 10 KMT2C KMT2C chr8 136404027 136404027 chr8 136404177 136404177 TCGA-YL-A9WY DEL 34 12 LINC02055 LINC02055 chrX 16803221 16803221 chrX 17829098 17829098 TCGA-YL-A9WY DEL 9 3 TXLNG RAI2 chrX 16807424 16807424 chrX 18498251 18498251 TCGA-YL-A9WY DEL 28 14 TXLNG CDKL5 chrX 17828676 17828676 chrX 18337384 18337384 TCGA-YL-A9WY DEL 40 29 RAI2 SCML2 chrX 18346430 18346430 chr12 97007226 97007226 TCGA-YL-A9WY BND 38 49 SCML2 AC007656.2 chrX 18498201 18498208 chr12 96963399 96963406 TCGA-YL-A9WY BND 12 19 CDKL5 * chrX 27737060 27737060 chrX 27737150 27737150 TCGA-YL-A9WY INS 29 17 DCAF8L2 DCAF8L2 chr10 109163631 109163631 chr10 109631012 109631012 TCGA-ZG-A8QX DEL 40 9 * * chr11 111598439 111598439 chr14 82083042 82083042 TCGA-ZG-A8QX BND 36 26 * * chr11 39618936 39618936 chr9 32181871 32181871 TCGA-ZG-A8QX BND 19 31 * * chr11 49064603 49064603 chr11 49076006 49076006 TCGA-ZG-A8QX DEL 34 29 * * chr11 7117822 7117822 chr11 7164326 7164326 TCGA-ZG-A8QX DEL 49 30 * * chr12 13816919 13816919 chr12 33565378 33565378 TCGA-ZG-A8QX INS 30 23 GRIN2B * chr12 14100840 14100840 chr12 33721086 33721086 TCGA-ZG-A8QX DEL 16 2 * * chr12 14449257 14449257 chr12 14481886 14481886 TCGA-ZG-A8QX DEL 18 41 ATF7IP ATF7IP chr13 61200787 61200787 chr13 61946594 61946594 TCGA-ZG-A8QX INS 9 8 MIR3169 * chr13 88414377 88414377 chr13 88415729 88415729 TCGA-ZG-A8QX DEL 6 3 * * chr14 28612877 28612877 chr14 28622540 28622540 TCGA-ZG-A8QX DEL 31 12 LINC02300 * chr17 10545032 10545032 chr12 94053429 94053429 TCGA-ZG-A8QX BND 19 41 MYHAS * chr18 55202720 55202720 chr18 55222309 55222309 TCGA-ZG-A8QX DEL 22 36 * * chr18 55393306 55393306 chr18 55436151 55436151 TCGA-ZG-A8QX DEL 15 23 TCF4 TCF4 chr1 192362095 192362095 chr1 192364900 192364900 TCGA-ZG-A8QX DEL 38 36 AL390957.1 AL390957.1 chr1 195826630 195826630 chr1 195828132 195828132 TCGA-ZG-A8QX DEL 33 43 * * chr1 85637137 85637137 chr1 96104413 96104413 TCGA-ZG-A8QX DEL 7 30 * * chr21 10518088 10518088 chr21 10525045 10525045 TCGA-ZG-A8QX DEL 49 40 AF254983.1 TPTE chr2 114069120 114069120 chr2 116496333 116496333 TCGA-ZG-A8QX DEL 9 10 * * chr2 116242942 116242942 chr2 116298914 116298914 TCGA-ZG-A8QX DEL 31 12 * * chr2 140190071 140190071 chr2 140207589 140207589 TCGA-ZG-A8QX DEL 29 22 * * chr2 154361021 154361021 chr2 154393213 154393214 TCGA-ZG-A8QX DEL 29 7 GALNT13 GALNT13 chr2 154401852 154401852 chr2 155704139 155704139 TCGA-ZG-A8QX DEL 16 24 GALNT13 * chr2 200015018 200015018 chr2 200031761 200031761 TCGA-ZG-A8QX DEL 48 50 * * chr2 52968092 52968092 chr2 52972879 52972879 TCGA-ZG-A8QX DEL 5 17 * * chr2 58295243 58295243 chr2 58303771 58303771 TCGA-ZG-A8QX DEL 42 46 LINC01795 * chr2 77880315 77880315 chr2 77898080 77898080 TCGA-ZG-A8QX DEL 42 3 * * chr2 78194634 78194634 chr2 78255644 78255644 TCGA-ZG-A8QX DEL 15 15 * * chr2 78208196 78208196 chr2 80572743 80572743 TCGA-ZG-A8QX INS 28 25 * CTNNA2 chr2 78244437 78244437 chr2 80573023 80573023 TCGA-ZG-A8QX DEL 42 2 * CTNNA2 chr3 2235385 2235385 chr3 2271004 2271004 TCGA-ZG-A8QX DEL 34 8 CNTN4 CNTN4 chr3 2340009 2340009 chr3 2348643 2348643 TCGA-ZG-A8QX DEL 10 37 CNTN4 CNTN4 chr3 75484779 75484779 chr3 78248121 78248121 TCGA-ZG-A8QX DEL 25 23 ENPP7P2 * chr3 77184490 77184490 chr3 78226080 78226080 TCGA-ZG-A8QX INS 16 28 ROBO2 * chr3 78097686 78097686 chr3 81989504 81989504 TCGA-ZG-A8QX INS 9 12 * LINC02008 chr3 90231592 90231592 chr3 90233769 90233769 TCGA-ZG-A8QX DEL 35 11 PROS2P PROS2P chr4 105203553 105203553 chr4 134496972 134496972 TCGA-ZG-A8QX DEL 47 20 TET2 * chr4 17985039 17985039 chr4 21831703 21831703 TCGA-ZG-A8QX DEL 9 16 LCORL KCNIP4 chr4 32676811 32676811 chr4 36256843 36256843 TCGA-ZG-A8QX DEL 28 38 * AC104078.1 chr4 35796802 35796802 chr2 133751586 133751586 TCGA-ZG-A8QX BND 38 26 * * chr4 8982276 8982276 chr4 41325998 41325998 TCGA-ZG-A8QX INS 47 46 AC073648.3 * chr5 101017053 101017053 chr5 101827782 101827782 TCGA-ZG-A8QX DEL 25 5 * * chr5 101884183 101884183 chr5 101916332 101916332 TCGA-ZG-A8QX DEL 23 17 * * chr5 40685483 40685483 chr5 40686251 40686251 TCGA-ZG-A8QX DEL 39 8 TTC33 TTC33 chr5 96302519 96302519 chr5 98392237 98392237 TCGA-ZG-A8QX DEL 26 31 AC104123.1 KRT8P32 chr5 98392891 98392891 chr5 100799173 100799173 TCGA-ZG-A8QX DEL 29 6 KRT8P32 * chr6 61196027 61196027 chr6 61200232 61200232 TCGA-ZG-A8QX DEL 19 30 * * chr6 65360240 65360240 chr6 65389315 65389315 TCGA-ZG-A8QX DEL 13 10 EYS EYS chr6 69403963 69403963 chr6 69404538 69404538 TCGA-ZG-A8QX DEL 9 10 * * chr6 73714536 73714536 chr6 74978580 74978580 TCGA-ZG-A8QX DEL 43 10 CD109 * chr6 73714618 73714618 chr6 75205880 75205880 TCGA-ZG-A8QX INS 35 22 CD109 COL12A1 chr6 73738861 73738861 chr6 73740145 73740145 TCGA-ZG-A8QX DEL 8 17 CD109 CD109 chr6 79597075 79597075 chr6 97877230 97877230 TCGA-ZG-A8QX DEL 15 49 * AL589740.1 chr8 111293836 111293836 chr8 111295378 111295378 TCGA-ZG-A8QX DEL 34 50 * * chr8 14337113 14337113 chr8 60785015 60785015 TCGA-ZG-A8QX INS 21 49 SGCZ CHD7 chr8 31739070 31739070 chr8 32098980 32098980 TCGA-ZG-A8QX INS 41 45 NRG1 NRG1 chr8 34951284 34951284 chr8 38825836 38825836 TCGA-ZG-A8QX DEL 28 28 * TACC1 chr8 47102032 47102032 chr8 60792984 60792984 TCGA-ZG-A8QX DEL 15 12 AC120036.1 CHD7 chr8 89004925 89004925 chr8 89185993 89185993 TCGA-ZG-A8QX DEL 46 38 * * chr9 62814083 62814084 chr9 63792846 63792846 TCGA-ZG-A8QX INS 41 42 * * chr9 9811052 9811052 chr9 9816442 9816442 TCGA-ZG-A8QX DEL 13 25 PTPRD PTPRD chr11 99259670 99259670 chr11 125506470 125506470 TCGA-VP-A87H DEL 3 32 CNTN5 FEZ1 chr1 106976710 106976710 chr5 11901812 11901812 TCGA-VP-A87H BND 47 22 * CTNND2 chr1 165118392 165118392 chr1 165141533 165141533 TCGA-VP-A87H DEL 24 6 * * chr1 172063485 172063485 chr1 172673373 172673373 TCGA-VP-A87H INS 30 33 DNM3 * chr2 138869708 138869708 chr2 141989730 141989730 TCGA-VP-A87H DEL 11 14 * LRP1B chr2 140372989 140372989 chr2 141324447 141324447 TCGA-VP-A87H INS 14 18 LRP1B LRP1B chr5 104686056 104686056 chr5 104709608 104709608 TCGA-VP-A87H DEL 16 38 AC099520.1 AC099520.1 chr5 163442393 163442393 chr5 163452044 163452044 TCGA-VP-A87H DEL 17 18 CCNG1 NUDCD2 chr6 87157849 87157849 chr6 115653505 115653505 TCGA-VP-A87H INS 38 37 ZNF292 * chr6 89315281 89315281 chr6 90558430 90558430 TCGA-VP-A87H DEL 30 29 GABRR2 MAP3K7 chr8 37553518 37553518 chr7 8903777 8903777 TCGA-VP-A87H BND 24 29 LINC01605 * chr10 16708347 16708347 chr10 18240185 18240185 TCGA-Y6-A8TL DEL 21 33 RSU1 CACNB2 chr12 26421591 26421591 chr12 26421645 26421645 TCGA-Y6-A8TL INS 3 35 ITPR2 ITPR2 chr15 22085128 22085128 chr15 22095703 22095703 TCGA-Y6-A8TL DEL 3 32 AC134980.2 AC134980.2 chr4 133368590 133368590 chr4 133879104 133879104 TCGA-Y6-A8TL DEL 49 24 * AC079380.1 chr8 107368450 107368450 chr8 107368851 107368851 TCGA-Y6-A8TL DEL 47 22 ANGPT1 ANGPT1 chr10 111305818 111305818 chr10 114453326 114453326 TCGA-2A-A8VX INS 13 6 * ABLIM1 chr10 11730173 11730173 chr10 14551544 14551544 TCGA-2A-A8VX INS 7 4 * FAM107B chr10 130236762 130236762 chr10 130602690 130602690 TCGA-2A-A8VX INS 29 1 LINC02646 * chr10 14074986 14074986 chr10 16232470 16232470 TCGA-2A-A8VX INS 31 31 FRMD4A * chr10 23517377 23517377 chr10 28414376 28414376 TCGA-2A-A8VX INS 47 31 * * chr10 28061167 28061167 chr10 28747566 28747566 TCGA-2A-A8VX INS 35 42 MPP7 LINC01517 chr10 32673484 32673484 chr10 32985294 32985294 TCGA-2A-A8VX INS 37 28 CCDC7 ITGB1 chr10 33458997 33458997 chr10 35902883 35902883 TCGA-2A-A8VX INS 11 31 * * chr10 52782975 52782975 chr10 54439264 54439264 TCGA-2A-A8VX INS 49 10 * PCDH15 chr10 63540094 63540094 chr10 64647565 64647565 TCGA-2A-A8VX INS 29 19 REEP3 * chr10 63562889 63562889 chr10 65914805 65914805 TCGA-2A-A8VX INS 28 49 REEP3 CTNNA3 chr10 6494855 6494855 chr10 8140541 8140541 TCGA-2A-A8VX INS 32 31 PRKCQ * chr10 69193962 69193962 chr10 69596395 69596395 TCGA-2A-A8VX INS 2 36 SUPV3L1 MTND2P15 chr10 70469346 70469346 chr10 73302396 73302396 TCGA-2A-A8VX INS 45 31 * CFAP70 chr10 8180473 8180473 chr10 8186837 8186837 TCGA-2A-A8VX DEL 5 21 * * chr10 84808477 84808477 chr10 87754678 87754678 TCGA-2A-A8VX INS 39 5 * ATAD1 chr10 8681795 8681795 chr10 12196889 12196889 TCGA-2A-A8VX INS 33 40 * NUDT5 chr10 8733727 8733727 chr10 12095179 12095179 TCGA-2A-A8VX DEL 17 9 * DHTKD1 chr10 95305338 95305338 chr10 99113577 99113577 TCGA-2A-A8VX INS 14 32 * HPSE2 chr11 106662161 106662161 chr11 106895114 106895114 TCGA-2A-A8VX INS 42 42 * GUCY1A2 chr11 126813849 126813849 chr11 127200080 127200080 TCGA-2A-A8VX INS 48 33 KIRREL3 AP003121.1 chr11 1888138 1888138 chr11 2067777 2067777 TCGA-2A-A8VX INS 45 24 LSP1 * chr11 26859497 26859497 chr11 27266137 27266137 TCGA-2A-A8VX INS 8 40 * * chr11 3361506 3361506 chr11 7826154 7826154 TCGA-2A-A8VX INS 36 20 ZNF195 AC044810.3 chr11 4570186 4570186 chr11 7261317 7261317 TCGA-2A-A8VX INS 13 14 * SYT9 chr11 54851444 54851448 chr3 161627656 161627660 TCGA-2A-A8VX BND 41 35 * * chr11 65367151 65367151 chr11 69097373 69097373 TCGA-2A-A8VX INS 32 27 AP000944.1 TPCN2 chr11 65394425 65394425 chr11 67782105 67782105 TCGA-2A-A8VX INS 50 22 FRMD8 OR7E11P chr11 65401331 65401331 chr11 65645146 65645146 TCGA-2A-A8VX INS 1 37 FRMD8 SIPA1 chr11 66932197 66932197 chr11 70229941 70229941 TCGA-2A-A8VX INS 22 24 PC * chr11 67607157 67607157 chr11 75051448 75051448 TCGA-2A-A8VX INS 47 39 C11orf72 * chr11 68181400 68181400 chr11 128621942 128621942 TCGA-2A-A8VX DEL 24 44 KMT5B AP001122.1 chr11 77001134 77001134 chr11 80538535 80538535 TCGA-2A-A8VX INS 35 10 ACER3 * chr11 77741420 77741420 chr11 78376814 78376814 TCGA-2A-A8VX INS 3 39 RSF1 GAB2 chr11 83012007 83012007 chr11 83970803 83970803 TCGA-2A-A8VX INS 42 33 RAB30 DLG2 chr11 97376680 97376680 chr11 97522551 97522551 TCGA-2A-A8VX INS 9 32 * * chr12 103389435 103389435 chr12 106168044 106168044 TCGA-2A-A8VX INS 11 40 C12orf42 * chr12 106516909 106516909 chr12 106782085 106782085 TCGA-2A-A8VX INS 25 12 AC079385.1 RIC8B chr12 115008792 115008792 chr12 118299867 118299867 TCGA-2A-A8VX INS 23 19 * TAOK3 chr12 121036422 121036422 chr12 121475439 121475439 TCGA-2A-A8VX INS 34 31 OASL KDM2B chr12 127054298 127054298 chr12 130793260 130793260 TCGA-2A-A8VX INS 30 19 LINC02405 STX2 chr12 33705982 33705982 chr12 34396816 34396816 TCGA-2A-A8VX INS 9 12 * * chr12 49059645 49059645 chr12 53046549 53046549 TCGA-2A-A8VX INS 25 29 KMT2D TNS2 chr12 54276106 54276106 chr12 56871193 56871193 TCGA-2A-A8VX INS 34 28 CBX5 AC121758.2 chr12 54705412 54705412 chr12 56341014 56341014 TCGA-2A-A8VX INS 18 30 * * chr12 5980667 5980667 chr12 6288476 6288476 TCGA-2A-A8VX INS 3 17 VWF * chr12 6311228 6311228 chr12 6793657 6793657 TCGA-2A-A8VX INS 43 11 PLEKHG6 CD4 chr12 74576168 74576168 chr12 118391873 118391873 TCGA-2A-A8VX DEL 46 12 * SUDS3 chr12 91012491 91012491 chr12 94271456 94271456 TCGA-2A-A8VX INS 9 37 * PLXNC1 chr12 92869200 92869200 chr12 94248527 94248527 TCGA-2A-A8VX INS 34 15 EEA1 PLXNC1 chr12 98158280 98158280 chr12 98733686 98733686 TCGA-2A-A8VX INS 19 11 AC016152.1 APAF1 chr13 101347068 101347068 chr13 104129929 104129929 TCGA-2A-A8VX INS 25 40 NALCN * chr13 105259382 105259382 chr13 109321997 109321997 TCGA-2A-A8VX INS 11 9 * * chr13 108660597 108660597 chr13 112432341 112432341 TCGA-2A-A8VX INS 16 30 MYO16 SPACA7 chr13 110412062 110412062 chr13 110658141 110658141 TCGA-2A-A8VX INS 4 42 COL4A2 CARS2 chr13 29556034 29556034 chr13 30178990 30178990 TCGA-2A-A8VX INS 30 45 SLC7A1 * chr13 72882580 72882580 chr13 90577024 90577024 TCGA-2A-A8VX INS 39 34 PIBF1 * chr13 90257759 90257759 chr13 90725580 90725580 TCGA-2A-A8VX INS 3 6 * * chr13 98279060 98279060 chr13 98294429 98294429 TCGA-2A-A8VX DEL 33 22 FARP1 FARP1 chr14 101043303 101043303 chr14 102285505 102285505 TCGA-2A-A8VX INS 5 49 MIR1185-2 MOK chr14 21802047 21802047 chr14 24927378 24927378 TCGA-2A-A8VX INS 30 26 * STXBP6 chr14 25705420 25705420 chr14 31469431 31469431 TCGA-2A-A8VX INS 42 31 LINC02306 * chr14 32969974 32969974 chr14 33655025 33655025 TCGA-2A-A8VX INS 31 4 NPAS3 NPAS3 chr14 46539752 46539752 chr14 47256013 47256013 TCGA-2A-A8VX INS 36 29 * MDGA2 chr14 65452773 65452773 chr14 65651234 65651234 TCGA-2A-A8VX INS 42 16 FUT8 FUT8 chr14 67033644 67033644 chr14 68060977 68060977 TCGA-2A-A8VX INS 2 46 GPHN RAD51B chr14 68747820 68747820 chr14 72226308 72226308 TCGA-2A-A8VX INS 13 20 * RGS6 chr14 72786034 72786034 chr14 73159005 73159005 TCGA-2A-A8VX INS 48 41 DPF3 PSEN1 chr15 54832010 54832010 chr15 55073264 55073264 TCGA-2A-A8VX INS 7 27 * AC025272.1 chr15 58326981 58326981 chr15 60741985 60741985 TCGA-2A-A8VX INS 49 30 ALDH1A2 RORA chr15 64590399 64590399 chr15 66979417 66979417 TCGA-2A-A8VX INS 16 39 ZNF609 * chr15 69629313 69629313 chr15 70194981 70194981 TCGA-2A-A8VX INS 30 37 DRAIC * chr15 79651005 79651005 chr15 83500727 83500727 TCGA-2A-A8VX DEL 10 49 * SH3GL3 chr15 85175867 85175867 chr15 87963506 87963506 TCGA-2A-A8VX INS 15 25 * NTRK3 chr15 87092659 87092659 chr15 87438635 87438635 TCGA-2A-A8VX INS 24 30 * AC020687.1 chr15 87693104 87693104 chr15 89287267 89287267 TCGA-2A-A8VX INS 14 7 AC020687.1 FANCI chr15 98974867 98974867 chr15 101462547 101462547 TCGA-2A-A8VX INS 24 28 PGPEP1L PCSK6 chr16 14669601 14669601 chr16 17622791 17622791 TCGA-2A-A8VX INS 36 6 * * chr16 24625972 24625972 chr16 25208199 25208199 TCGA-2A-A8VX INS 33 43 TNRC6A * chr16 46779561 46779561 chr16 47555255 47555255 TCGA-2A-A8VX INS 47 10 MYLK3 PHKB chr16 47332798 47332798 chr16 47359601 47359601 TCGA-2A-A8VX DEL 39 3 ITFG1 ITFG1 chr16 54139990 54139990 chr16 56335664 56335664 TCGA-2A-A8VX INS 44 17 FTO GNAO1 chr16 58092313 58092313 chr16 64003494 64003494 TCGA-2A-A8VX INS 9 24 AC012182.1 * chr16 5904141 5904141 chr16 9088272 9088272 TCGA-2A-A8VX INS 30 2 RBFOX1 * chr16 62805721 62805721 chr16 62965757 62965757 TCGA-2A-A8VX INS 50 41 * * chr17 56792730 56792746 chr4 102390862 102390862 TCGA-2A-A8VX BND 26 24 C17orf67 SLC39A8 chr17 59176961 59176961 chr17 59514648 59514648 TCGA-2A-A8VX INS 3 9 PRR11 LINC01476 chr17 63163030 63163030 chr17 67392733 67392733 TCGA-2A-A8VX INS 23 31 TANC2 PITPNC1 chr17 72453617 72453617 chr17 72458809 72458809 TCGA-2A-A8VX DEL 1 28 LINC00511 LINC00511 chr17 79245749 79245749 chr17 80276824 80276824 TCGA-2A-A8VX INS 24 17 RBFOX3 RNF213 chr17 8635400 8635400 chr17 8770067 8770067 TCGA-2A-A8VX INS 7 39 * * chr18 25022790 25022790 chr18 27080380 27080380 TCGA-2A-A8VX INS 37 24 * AQP4-AS1 chr18 26345092 26345092 chr18 32117912 32117912 TCGA-2A-A8VX INS 8 37 TAF4B RNF138 chr18 26425539 26425539 chr18 26559945 26559945 TCGA-2A-A8VX INS 29 38 LINC01543 KCTD1 chr18 26556776 26556776 chr18 26559188 26559188 TCGA-2A-A8VX INS 29 22 KCTD1 KCTD1 chr18 27950191 27950191 chr18 30972812 30972812 TCGA-2A-A8VX INS 5 1 * AC016382.1 chr18 36871203 36871203 chr18 39712189 39712189 TCGA-2A-A8VX INS 27 32 KIAA1328 MIR924HG chr18 55408083 55408083 chr18 55408558 55408558 TCGA-2A-A8VX DEL 32 10 TCF4 TCF4 chr18 55843005 55843005 chr18 59434656 59434656 TCGA-2A-A8VX INS 11 19 * CCBE1 chr18 58274803 58274803 chr18 60043168 60043168 TCGA-2A-A8VX INS 19 10 NEDD4L * chr18 58640954 58640954 chr18 59885665 59885665 TCGA-2A-A8VX INS 23 4 * * chr18 58703331 58703331 chr18 58706408 58706408 TCGA-2A-A8VX DEL 15 23 MALT1 MALT1 chr19 16014117 16014117 chr19 19370169 19370169 TCGA-2A-A8VX INS 19 35 LINC00661 * chr19 18372121 18372121 chr19 19317285 19317285 TCGA-2A-A8VX INS 5 4 * SUGP1 chr19 47757961 47757961 chr19 49143897 49143897 TCGA-2A-A8VX INS 30 47 NOP53-AS1 PPFIA3 chr1 107698683 107698683 chr1 110849636 110849636 TCGA-2A-A8VX INS 24 41 VAV3 NRBF2P3 chr1 14449745 14449745 chr1 15250474 15250474 TCGA-2A-A8VX INS 16 50 KAZN FHAD1 chr1 150534812 150534812 chr1 153815847 153815847 TCGA-2A-A8VX INS 21 20 * GATAD2B chr1 159255874 159255874 chr1 159855186 159855186 TCGA-2A-A8VX INS 14 6 * SNHG28 chr1 166619413 166619413 chr1 169210743 169210743 TCGA-2A-A8VX INS 15 30 FMO9P NME7 chr1 173414140 173414140 chr1 173653690 173653690 TCGA-2A-A8VX INS 12 14 * ANKRD45 chr1 177289577 177289577 chr1 181069137 181069137 TCGA-2A-A8VX INS 11 14 * * chr1 180834199 180834199 chr1 181127308 181127308 TCGA-2A-A8VX INS 10 15 XPR1 * chr1 183534079 183534079 chr1 183537727 183537727 TCGA-2A-A8VX DEL 17 7 SMG7 SMG7 chr1 183910892 183910892 chr1 185131651 185131651 TCGA-2A-A8VX INS 21 44 RGL1 TRMT1L chr1 189435922 189435922 chr1 189621277 189621277 TCGA-2A-A8VX INS 34 44 * * chr1 206888376 206888376 chr1 238764933 238764933 TCGA-2A-A8VX DEL 4 31 * * chr1 206961041 206961041 chr1 211408872 211408872 TCGA-2A-A8VX INS 1 24 FCAMR LINC00467 chr1 210440299 210440299 chr1 212584873 212584873 TCGA-2A-A8VX INS 24 24 HHAT ATF3 chr1 216683561 216683561 chr1 216745702 216745702 TCGA-2A-A8VX DEL 31 3 ESRRG ESRRG chr1 235462378 235462378 chr1 235962417 235962417 TCGA-2A-A8VX INS 18 25 B3GALNT2 LINC02768 chr1 39231194 39231194 chr1 42908609 42908609 TCGA-2A-A8VX INS 37 21 MACF1 * chr1 56182864 56182864 chr1 62166244 62166244 TCGA-2A-A8VX INS 12 44 AC119674.1 PATJ chr1 71328467 71328467 chr1 71881837 71881837 TCGA-2A-A8VX INS 26 20 ZRANB2-AS2 NEGR1 chr1 94409265 94409265 chr1 97249291 97249291 TCGA-2A-A8VX INS 50 3 * DPYD chr1 96546864 96546864 chr1 96720343 96720343 TCGA-2A-A8VX INS 29 26 * PTBP2 chr1 9665406 9665406 chr1 10268358 10268358 TCGA-2A-A8VX INS 49 46 PIK3CD KIF1B chr20 46798903 46798903 chr20 47295351 47295351 TCGA-2A-A8VX INS 29 29 * ZMYND8 chr20 4747353 4747353 chr20 7417463 7417463 TCGA-2A-A8VX INS 28 49 * * chr20 7501860 7501860 chr20 8414522 8414522 TCGA-2A-A8VX INS 25 42 * PLCB1 chr20 7893670 7893670 chr20 8374618 8374618 TCGA-2A-A8VX INS 50 2 HAO1 PLCB1 chr20 9867426 9867426 chr20 12775727 12775727 TCGA-2A-A8VX INS 45 21 * * chr21 22256016 22256016 chr21 22494453 22494453 TCGA-2A-A8VX INS 27 24 AP000561.1 * chr22 23047654 23047654 chr22 25851498 25851498 TCGA-2A-A8VX INS 43 49 * MYO18B chr22 25420921 25420921 chr22 25650295 25650295 TCGA-2A-A8VX INS 39 31 * GRK3 chr22 28080569 28080569 chr22 28352848 28352848 TCGA-2A-A8VX INS 3 35 TTC28 TTC28 chr22 31537449 31537449 chr22 33517297 33517297 TCGA-2A-A8VX INS 15 27 SFI1 LARGE1 chr22 38957703 38957703 chr22 39151658 39151658 TCGA-2A-A8VX INS 35 47 APOBEC3A CBX7 chr22 44255493 44255493 chr22 47663134 47663134 TCGA-2A-A8VX INS 31 34 SHISAL1 AL117329.1 chr2 105086609 105086609 chr2 109281253 109281253 TCGA-2A-A8VX INS 25 38 MRPS9 SH3RF3 chr2 11168994 11168994 chr2 15932626 15932626 TCGA-2A-A8VX INS 2 6 SLC66A3 MYCNUT chr2 112576690 112576690 chr2 115242390 115242390 TCGA-2A-A8VX INS 36 11 POLR1B DPP10 chr2 116082320 116082320 chr2 116228703 116228703 TCGA-2A-A8VX INS 8 20 * * chr2 127233690 127233690 chr2 130944475 130944475 TCGA-2A-A8VX INS 14 23 * ARHGEF4 chr2 128892200 128892200 chr2 130905002 130905002 TCGA-2A-A8VX DEL 24 30 * ARHGEF4 chr2 136763210 136763210 chr2 136880628 136880628 TCGA-2A-A8VX INS 4 12 * THSD7B chr2 15385338 15385338 chr2 16075564 16075564 TCGA-2A-A8VX INS 22 43 NBAS GACAT3 chr2 159181103 159181103 chr2 159386491 159386491 TCGA-2A-A8VX INS 44 26 TANC1 BAZ2B chr2 15929285 15929285 chr2 15930639 15930639 TCGA-2A-A8VX DEL 8 5 MYCNUT MYCNUT chr2 181574962 181574962 chr2 183986237 183986237 TCGA-2A-A8VX INS 40 5 CERKL * chr2 193547487 193547487 chr2 197357129 197357129 TCGA-2A-A8VX INS 27 32 * * chr2 193787104 193787104 chr2 196586357 196586357 TCGA-2A-A8VX INS 25 48 * HECW2 chr2 203211104 203211104 chr2 207168678 207168678 TCGA-2A-A8VX INS 14 32 NBEAL1 KLF7 chr2 37766895 37766895 chr2 40367632 40367632 TCGA-2A-A8VX INS 36 5 * SLC8A1 chr2 51605738 51605738 chr2 52401510 52401510 TCGA-2A-A8VX INS 40 21 AC007402.1 AC007402.1 chr2 63557938 63557938 chr2 69932352 69932352 TCGA-2A-A8VX INS 13 19 WDPCP MXD1 chr2 64197057 64197057 chr2 64901905 64901905 TCGA-2A-A8VX INS 20 25 AC012368.1 LINC02245 chr2 72468477 72468477 chr2 73870357 73870357 TCGA-2A-A8VX INS 18 31 EXOC6B STAMBP chr2 81241435 81241435 chr2 81616752 81616752 TCGA-2A-A8VX INS 39 49 * * chr2 8512308 8512308 chr2 8881536 8881536 TCGA-2A-A8VX INS 16 21 LINC01814 MBOAT2 chr3 120925954 120925954 chr3 120930680 120930680 TCGA-2A-A8VX DEL 5 28 STXBP5L STXBP5L chr3 126491213 126491213 chr3 128778749 128778749 TCGA-2A-A8VX INS 31 29 UROC1 RAB7A chr3 128603313 128603313 chr3 129740627 129740627 TCGA-2A-A8VX INS 23 8 * TMCC1 chr3 13274000 13274000 chr3 18404361 18404361 TCGA-2A-A8VX INS 4 15 IQSEC1 TBC1D5 chr3 143579976 143579976 chr3 144117067 144117067 TCGA-2A-A8VX INS 22 16 SLC9A9 * chr3 151964887 151964887 chr3 153125995 153125995 TCGA-2A-A8VX INS 7 32 * * chr3 15618802 15618802 chr3 16108474 16108474 TCGA-2A-A8VX INS 49 20 BTD * chr3 166477372 166477379 chr3 166718100 166718100 TCGA-2A-A8VX INS 45 49 * * chr3 166586200 166586200 chr3 168588287 168588287 TCGA-2A-A8VX INS 6 5 * EGFEM1P chr3 166809593 166809593 chr3 169406493 169406493 TCGA-2A-A8VX INS 38 39 CBX1P5 MECOM chr3 175707076 175707076 chr3 175707210 175707210 TCGA-2A-A8VX DEL 17 6 NAALADL2 NAALADL2 chr3 177305085 177305085 chr3 177507189 177507189 TCGA-2A-A8VX INS 7 48 LINC00501 LINC00578 chr3 184341385 184341385 chr3 184784057 184784057 TCGA-2A-A8VX INS 9 32 FAM131A * chr3 184619095 184619095 chr3 187435260 187435260 TCGA-2A-A8VX INS 23 26 * * chr3 193771891 193771891 chr3 196320749 196320749 TCGA-2A-A8VX INS 36 23 * TM4SF19 chr3 30167043 30167043 chr3 33835861 33835861 TCGA-2A-A8VX INS 1 8 * PDCD6IP chr3 34072795 34072795 chr3 38178398 38178398 TCGA-2A-A8VX INS 11 36 * OXSR1 chr3 3563907 3563907 chr3 3565563 3565563 TCGA-2A-A8VX INS 37 28 AC034195.1 AC034195.1 chr3 70280651 70280651 chr3 74198908 74198908 TCGA-2A-A8VX INS 33 14 SAMMSON * chr3 76937269 76937269 chr3 80178701 80178701 TCGA-2A-A8VX INS 43 29 ROBO2 * chr3 80830799 80830799 chr3 82959089 82959089 TCGA-2A-A8VX INS 6 30 * * chr3 84487047 84487047 chr3 84791424 84791424 TCGA-2A-A8VX DEL 44 15 * LINC00971 chr3 85391531 85391531 chr3 87620123 87620123 TCGA-2A-A8VX INS 50 6 CADM2 * chr3 97418987 97418987 chr3 100390081 100390081 TCGA-2A-A8VX INS 31 10 EPHA6 TOMM70 chr4 104705119 104705119 chr4 105036869 105036869 TCGA-2A-A8VX INS 30 41 AC004053.1 AC096577.1 chr4 111772814 111772814 chr4 111824226 111824226 TCGA-2A-A8VX DEL 31 8 * AC139718.2 chr4 12595600 12595600 chr4 12605354 12605354 TCGA-2A-A8VX INS 12 18 * * chr4 127675027 127675027 chr4 130546548 130546548 TCGA-2A-A8VX INS 48 7 INTU * chr4 130091567 130091567 chr4 132099427 132099427 TCGA-2A-A8VX INS 16 28 * AC093916.1 chr4 136320460 136320460 chr20 48628862 48628862 TCGA-2A-A8VX BND 20 21 AC018680.1 PREX1 chr4 137852412 137852412 chr4 138025415 138025415 TCGA-2A-A8VX INS 8 49 * * chr4 140234963 140234963 chr4 146130919 146130919 TCGA-2A-A8VX INS 41 18 * * chr4 141763412 141763412 chr4 142136783 142136783 TCGA-2A-A8VX INS 36 12 * INPP4B chr4 164087403 164087403 chr4 164382648 164382648 TCGA-2A-A8VX INS 30 39 MARCHF1 MARCHF1 chr4 16759404 16759404 chr4 16981897 16981897 TCGA-2A-A8VX INS 28 25 LDB2 AC106894.1 chr4 168681923 168681923 chr4 168854633 168854633 TCGA-2A-A8VX INS 31 18 PALLD PALLD chr4 170493574 170493574 chr4 174121522 174121522 TCGA-2A-A8VX INS 41 25 * LINC02268 chr4 175429592 175429592 chr4 178696067 178696067 TCGA-2A-A8VX INS 25 47 * * chr4 181453940 181453940 chr4 181645504 181645504 TCGA-2A-A8VX INS 10 34 * * chr4 35602910 35602910 chr4 37665382 37665382 TCGA-2A-A8VX INS 37 24 * RELL1 chr4 42495208 42495208 chr4 42954568 42954568 TCGA-2A-A8VX INS 3 2 ATP8A1 GRXCR1 chr4 59851850 59851850 chr4 60057382 60057382 TCGA-2A-A8VX INS 37 24 * * chr4 61347970 61347970 chr4 63212129 63212129 TCGA-2A-A8VX INS 50 6 ADGRL3 * chr4 63349346 63349346 chr4 63396279 63396279 TCGA-2A-A8VX DEL 43 27 LARP1BP1 * chr4 65268129 65268129 chr4 65303259 65303259 TCGA-2A-A8VX DEL 5 25 * * chr4 65583666 65583666 chr4 65849927 65849927 TCGA-2A-A8VX INS 41 8 EPHA5 * chr4 70753237 70753237 chr4 71147517 71147517 TCGA-2A-A8VX INS 23 18 RUFY3 SLC4A4 chr4 70753703 70753703 chr4 70903797 70903797 TCGA-2A-A8VX DEL 6 26 RUFY3 MOB1B chr4 73393577 73393577 chr4 73866491 73866491 TCGA-2A-A8VX INS 42 41 * * chr4 8182579 8182579 chr4 8403911 8403911 TCGA-2A-A8VX INS 18 46 SH3TC1 ACOX3 chr4 83294720 83294720 chr4 87916854 87916854 TCGA-2A-A8VX INS 10 33 HPSE * chr4 88747826 88747826 chr4 89992647 89992647 TCGA-2A-A8VX INS 46 49 FAM13A * chr4 9711359 9711359 chr4 10280198 10280198 TCGA-2A-A8VX INS 8 12 ALG1L3P * chr5 113268879 113268879 chr5 113713954 113713954 TCGA-2A-A8VX INS 8 37 MCC * chr5 152053480 152053480 chr5 154499684 154499684 TCGA-2A-A8VX INS 23 25 LINC01933 * chr5 153501696 153501696 chr5 154170557 154170557 TCGA-2A-A8VX INS 25 46 GRIA1 MFAP3 chr5 174434969 174434969 chr5 178185973 178185973 TCGA-2A-A8VX INS 23 50 LINC01411 GMCL2 chr5 18430237 18430237 chr5 21800743 21800743 TCGA-2A-A8VX INS 13 3 * CDH12 chr5 26160213 26160213 chr5 26419751 26419751 TCGA-2A-A8VX INS 31 7 * * chr5 3714087 3714087 chr5 3838221 3838221 TCGA-2A-A8VX INS 15 45 * * chr5 51728826 51728826 chr5 56110680 56110680 TCGA-2A-A8VX INS 11 31 * AC008892.1 chr5 57626391 57626391 chr5 59833620 59833620 TCGA-2A-A8VX INS 19 16 * PDE4D chr5 60998993 60998993 chr5 65425679 65425679 TCGA-2A-A8VX INS 33 33 NDUFAF2 ADAMTS6 chr6 119391170 119391170 chr6 119534757 119534757 TCGA-2A-A8VX INS 8 19 * * chr6 11986016 11986016 chr6 18444401 18444401 TCGA-2A-A8VX INS 25 21 * RNF144B chr6 121299269 121299269 chr6 121646707 121646707 TCGA-2A-A8VX INS 31 11 TBC1D32 * chr6 124570972 124570972 chr6 125044659 125044659 TCGA-2A-A8VX INS 19 28 NKAIN2 RNF217 chr6 13829169 13829169 chr6 14462076 14462076 TCGA-2A-A8VX INS 41 27 * * chr6 139162197 139162197 chr6 139743067 139743067 TCGA-2A-A8VX INS 6 37 HECA FILNC1 chr6 144355855 144355855 chr6 144821713 144821713 TCGA-2A-A8VX INS 2 19 UTRN UTRN chr6 146658601 146658601 chr6 148288181 148288181 TCGA-2A-A8VX INS 9 5 ADGB SASH1 chr6 147135386 147135386 chr6 147382980 147382980 TCGA-2A-A8VX INS 41 8 STXBP5-AS1 STXBP5 chr6 28500858 28500858 chr6 34075001 34075001 TCGA-2A-A8VX INS 15 17 * GRM4 chr6 42739053 42739053 chr6 45445857 45445857 TCGA-2A-A8VX INS 26 14 * RUNX2 chr6 43320096 43320096 chr6 46978882 46978882 TCGA-2A-A8VX INS 45 39 ZNF318 * chr6 44885057 44885057 chr6 45038967 45038967 TCGA-2A-A8VX DEL 37 7 SUPT3H SUPT3H chr6 56513028 56513028 chr6 58452223 58452229 TCGA-2A-A8VX INS 16 25 DST * chr6 77223517 77223517 chr6 78134186 78134186 TCGA-2A-A8VX INS 47 13 * * chr6 84407636 84407636 chr6 85534073 85534073 TCGA-2A-A8VX INS 8 16 * SNX14 chr6 8593098 8593098 chr6 9504737 9504737 TCGA-2A-A8VX INS 46 5 AL355499.2 * chr6 90250799 90250799 chr6 93135815 93135815 TCGA-2A-A8VX INS 1 37 BACH2 * chr6 93646765 93646765 chr6 93684631 93684631 TCGA-2A-A8VX INS 20 37 * * chr7 110144012 110144012 chr7 111204154 111204154 TCGA-2A-A8VX INS 26 16 * IMMP2L chr7 111063832 111063832 chr7 113526205 113526205 TCGA-2A-A8VX INS 41 3 IMMP2L * chr7 120177464 120177464 chr7 121879097 121879097 TCGA-2A-A8VX INS 4 1 AC004946.2 PTPRZ1 chr7 129428867 129428867 chr7 129854944 129854944 TCGA-2A-A8VX INS 36 4 AHCYL2 UBE2H chr7 130050046 130050047 chr7 130505534 130505534 TCGA-2A-A8VX INS 3 35 ZC3HC1 MEST chr7 48627534 48627534 chr7 48867604 48867604 TCGA-2A-A8VX INS 6 14 ABCA13 * chr7 48628266 48628266 chr7 48628562 48628562 TCGA-2A-A8VX DEL 38 20 ABCA13 ABCA13 chr7 86214212 86214212 chr7 89316327 89316327 TCGA-2A-A8VX INS 6 44 * ZNF804B chr7 86238371 86238371 chr7 88520940 88520940 TCGA-2A-A8VX INS 35 39 * * chr8 103982523 103982523 chr8 104933096 104933096 TCGA-2A-A8VX INS 2 2 RIMS2 ZFPM2 chr8 109329336 109329336 chr8 112325464 112325464 TCGA-2A-A8VX INS 24 16 NUDCD1 CSMD3 chr8 113624038 113624038 chr8 117604376 117604376 TCGA-2A-A8VX INS 6 37 * * chr8 114347135 114347135 chr8 117357083 117357083 TCGA-2A-A8VX INS 36 23 * * chr8 117866676 117866676 chr8 118249148 118249148 TCGA-2A-A8VX INS 25 23 EXT1 SAMD12 chr8 118590828 118590828 chr8 120157960 120157960 TCGA-2A-A8VX INS 1 21 SAMD12 COL14A1 chr8 119755922 119755922 chr8 121496847 121496847 TCGA-2A-A8VX INS 24 3 TAF2 * chr8 119756505 119756505 chr8 121470751 121470752 TCGA-2A-A8VX DEL 8 8 TAF2 * chr8 124547862 124547862 chr8 124885683 124885683 TCGA-2A-A8VX INS 43 25 NDUFB9 LINC00964 chr8 124756411 124756411 chr8 127219627 127219627 TCGA-2A-A8VX INS 42 37 * PCAT1 chr8 129731256 129731256 chr8 133181285 133181285 TCGA-2A-A8VX INS 10 16 * * chr8 130214882 130214882 chr8 130343443 130343443 TCGA-2A-A8VX INS 28 47 ASAP1 ASAP1 chr8 13894058 13894058 chr8 18685387 18685387 TCGA-2A-A8VX INS 29 9 * PSD3 chr8 14163034 14163034 chr8 14524442 14524442 TCGA-2A-A8VX INS 5 11 SGCZ SGCZ chr8 142443856 142443856 chr8 144610076 144610076 TCGA-2A-A8VX INS 48 42 * * chr8 17856845 17856845 chr8 18166228 18166228 TCGA-2A-A8VX INS 22 37 AC027117.2 * chr8 31975969 31975969 chr8 32184653 32184653 TCGA-2A-A8VX INS 12 31 NRG1 NRG1 chr8 32102636 32102636 chr8 32105110 32105110 TCGA-2A-A8VX DEL 4 41 NRG1 NRG1 chr8 34250108 34250108 chr8 36301365 36301365 TCGA-2A-A8VX INS 23 4 AC090993.1 * chr8 39799843 39799843 chr8 40099031 40099031 TCGA-2A-A8VX INS 9 38 ADAM2 * chr8 48983121 48983121 chr8 49630830 49630830 TCGA-2A-A8VX INS 46 12 * * chr8 63992306 63992306 chr8 67244075 67244075 TCGA-2A-A8VX INS 24 21 LINC01414 ARFGEF1 chr8 69336556 69336556 chr8 75865591 75865591 TCGA-2A-A8VX INS 26 29 * * chr8 73495248 73495248 chr8 74800591 74800591 TCGA-2A-A8VX INS 7 22 STAU2 MIR2052HG chr8 74321859 74321859 chr8 74780756 74780756 TCGA-2A-A8VX INS 33 41 JPH1 MIR2052HG chr8 82475419 82475419 chr8 84896333 84896333 TCGA-2A-A8VX INS 15 25 * RALYL chr8 95458382 95458382 chr8 99242161 99242161 TCGA-2A-A8VX INS 16 42 C8orf37-AS1 VPS13B chr9 102003721 102003721 chr9 106017200 106017200 TCGA-2A-A8VX INS 19 12 * LINC01505 chr9 109212304 109212304 chr9 113008224 113008224 TCGA-2A-A8VX INS 44 21 EPB41L4B ZNF883 chr9 131661101 131661101 chr9 131964240 131964240 TCGA-2A-A8VX INS 3 8 RAPGEF1 MED27 chr9 18240150 18240150 chr9 18997704 18997704 TCGA-2A-A8VX INS 21 12 ADAMTSL1 SAXO1 chr9 5428604 5428604 chr9 9749068 9749068 TCGA-2A-A8VX INS 47 20 PLGRKT PTPRD chr9 80570009 80570009 chr9 80753543 80753543 TCGA-2A-A8VX INS 50 14 * * chr9 86773760 86773760 chr9 87076936 87076936 TCGA-2A-A8VX INS 46 31 * * chrX 107555018 107555018 chrX 107942536 107942536 TCGA-2A-A8VX INS 6 4 FRMPD3 * chrX 120731966 120731966 chrX 121149950 121149950 TCGA-2A-A8VX INS 45 33 GLRX5P1 * chrX 125740551 125740551 chrX 128964830 128964830 TCGA-2A-A8VX INS 7 27 * * chrX 143364490 143364490 chrX 143667365 143667365 TCGA-2A-A8VX INS 25 12 AC239727.1 * chrX 65738337 65738337 chrX 66099972 66099972 TCGA-2A-A8VX INS 32 19 MSN * chrX 95128196 95128196 chrX 95463147 95463147 TCGA-2A-A8VX INS 48 5 * * chr10 10285086 10285086 chr10 10511668 10511668 TCGA-G9-6338 INV 21 10 * * chr10 119070016 119070016 chr10 119080764 119080764 TCGA-G9-6338 INV 46 48 EIF3A EIF3A chr10 119070016 119070016 chr10 119081043 119081043 TCGA-G9-6338 DUP 40 35 EIF3A EIF3A chr10 124039038 124039038 chr3 41227681 41227681 TCGA-G9-6338 BND 11 42 CHST15 CTNNB1 chr10 128219465 128219465 chr11 1169322 1169322 TCGA-G9-6338 BND 27 25 LINC01163 MUC5AC chr10 133028276 133028276 chr11 1106550 1106550 TCGA-G9-6338 BND 46 38 * MUC2 chr10 133065828 133065828 chr16 57729025 57729025 TCGA-G9-6338 BND 5 44 * DRC7 chr10 133066057 133066057 chr16 57730349 57730349 TCGA-G9-6338 BND 26 11 * DRC7 chr10 17411962 17411962 chr10 17417852 17417852 TCGA-G9-6338 INV 38 25 ST8SIA6 ST8SIA6 chr10 24514727 24514727 chr10 25601613 25601613 TCGA-G9-6338 DUP 47 41 KIAA1217 GPR158 chr10 26053809 26053809 chr10 26071796 26071796 TCGA-G9-6338 DEL 6 19 MYO3A MYO3A chr10 51780362 51780362 chr3 98460528 98460528 TCGA-G9-6338 BND 30 29 PRKG1 * chr10 52532181 52532181 chr10 52558975 52558975 TCGA-G9-6338 DEL 47 34 LNCAROD LNCAROD chr10 57802238 57802238 chr10 58123021 58123021 TCGA-G9-6338 DEL 9 18 * * chr10 65353088 65353088 chr10 65359644 65359644 TCGA-G9-6338 DEL 22 50 * * chr10 82983675 82983675 chr10 84223682 84223682 TCGA-G9-6338 DEL 13 35 NRG3 LRIT2 chr10 86600240 86600240 chr10 101166634 101166634 TCGA-G9-6338 DEL 48 26 * * chr10 87877809 87877809 chr10 88270194 88270194 TCGA-G9-6338 DEL 41 41 PTEN * chr11 117103567 117103567 chr11 117209790 117209790 TCGA-G9-6338 DUP 46 31 AP000936.1 PCSK7 chr11 121509633 121509633 chr11 121740073 121740073 TCGA-G9-6338 DUP 13 20 SORL1 * chr11 1861580 1861580 chr19 3235487 3235487 TCGA-G9-6338 BND 23 48 LSP1 CELF5 chr11 1894606 1894606 chr11 1939829 1939829 TCGA-G9-6338 DEL 23 5 * * chr11 2201283 2201283 chr14 104203642 104203642 TCGA-G9-6338 BND 42 42 * * chr11 69110863 69110863 chr22 27325298 27325298 TCGA-G9-6338 BND 30 18 TPCN2 * chr11 69291422 69291422 chr22 45080511 45080511 TCGA-G9-6338 BND 16 45 * * chr11 69291676 69291676 chr22 49595508 49595508 TCGA-G9-6338 BND 11 14 * C22orf34 chr11 92546352 92546352 chr11 100968678 100968678 TCGA-G9-6338 DEL 45 33 FAT3 ARHGAP42 chr12 100143056 100143056 chr12 101164927 101164927 TCGA-G9-6338 INS 42 38 UHRF1BP1L SLC5A8 chr12 131187826 131187826 chr12 131191173 131191173 TCGA-G9-6338 INV 40 36 LINC01257 LINC01257 chr12 131199470 131199470 chr12 131439139 131439139 TCGA-G9-6338 DUP 38 29 LINC01257 * chr12 40942958 40942958 chr15 78974768 78974768 TCGA-G9-6338 BND 39 47 CNTN1 RASGRF1 chr12 41124687 41124687 chr12 41126801 41126801 TCGA-G9-6338 DEL 14 50 * * chr12 41776244 41776244 chr12 45838077 45838077 TCGA-G9-6338 INV 7 23 * ARID2 chr12 56007765 56007765 chr12 56364421 56364421 TCGA-G9-6338 DUP 23 49 IKZF4 * chr12 59414274 59414274 chr12 59447576 59447576 TCGA-G9-6338 DEL 48 15 * * chr12 62006416 62006416 chr12 62007406 62007406 TCGA-G9-6338 DEL 22 11 TAFA2 TAFA2 chr12 69058353 69058353 chr12 71139944 71139944 TCGA-G9-6338 DUP 18 34 * TSPAN8 chr12 7003543 7003543 chr5 99154887 99154887 TCGA-G9-6338 BND 39 9 LPCAT3 * chr12 71490675 71490675 chr12 71493501 71493501 TCGA-G9-6338 DEL 3 29 LGR5 LGR5 chr12 72741150 72741150 chr12 72744255 72744255 TCGA-G9-6338 DEL 1 38 * * chr13 28125465 28125465 chr13 78281263 78281263 TCGA-G9-6338 DEL 19 31 * OBI1-AS1 chr13 36867527 36867527 chr13 36994731 36994731 TCGA-G9-6338 DEL 12 23 SMAD9 ALG5 chr13 38979928 38979928 chr13 58506360 58506360 TCGA-G9-6338 INS 11 50 STOML3 * chr13 39669119 39669119 chr13 83209678 83209678 TCGA-G9-6338 INS 16 46 COG6 * chr13 53066785 53066785 chr13 60311346 60311346 TCGA-G9-6338 DEL 39 18 * * chr13 60309229 60309229 chr13 83576490 83576490 TCGA-G9-6338 DEL 35 27 * * chr13 60631344 60631344 chr13 60635077 60635077 TCGA-G9-6338 DEL 43 15 * * chr14 105570734 105570734 chr14 105700395 105700395 TCGA-G9-6338 INV 36 4 * * chr14 89325213 89325213 chr14 104300906 104300906 TCGA-G9-6338 INV 3 41 FOXN3 * chr15 20101753 20101753 chr15 21112833 21112833 TCGA-G9-6338 DUP 26 42 * * chr15 20534095 20534095 chr15 28560647 28560647 TCGA-G9-6338 INV 49 7 GOLGA6L6 AC138749.1 chr15 20535365 20535365 chr15 28559315 28559315 TCGA-G9-6338 DEL 39 9 GOLGA6L6 AC138749.1 chr15 22465198 22465198 chr15 28561333 28561336 TCGA-G9-6338 DUP 3 27 GOLGA6L22 AC138749.1 chr15 22466989 22466989 chr15 28560647 28560647 TCGA-G9-6338 DEL 32 40 GOLGA6L22 AC138749.1 chr15 23129845 23129845 chr15 28561543 28561543 TCGA-G9-6338 INV 10 7 GOLGA6L1 * chr15 23327888 23327888 chr15 28561491 28561491 TCGA-G9-6338 INV 39 29 AC100756.2 * chr15 23371344 23371344 chr15 23393379 23393379 TCGA-G9-6338 DEL 31 44 * * chr15 53117309 53117309 chr21 14476201 14476201 TCGA-G9-6338 BND 38 48 LINC02490 * chr15 73697709 73697709 chr15 74316398 74316398 TCGA-G9-6338 DUP 43 48 CD276 CCDC33 chr16 13415692 13415692 chr16 13415984 13415984 TCGA-G9-6338 DEL 35 33 U91319.1 U91319.1 chr16 1738387 1738387 chr16 5452087 5452087 TCGA-G9-6338 DUP 12 9 MAPK8IP3 RBFOX1 chr16 53949785 53949785 chr16 55274292 55274292 TCGA-G9-6338 DUP 25 45 FTO AC109462.1 chr16 58564242 58564242 chr16 60312735 60312735 TCGA-G9-6338 DEL 21 2 CNOT1 * chr16 58567853 58567853 chr16 60276189 60276189 TCGA-G9-6338 INS 10 26 CNOT1 * chr16 60200918 60200918 chr16 65143619 65143619 TCGA-G9-6338 DEL 29 18 * LINC02126 chr16 85187870 85187870 chr16 86671005 86671005 TCGA-G9-6338 DEL 25 13 GSE1 * chr16 9226155 9226155 chrX 4681943 4681943 TCGA-G9-6338 BND 47 39 * * chr17 43082914 43082914 chr19 5984180 5984180 TCGA-G9-6338 BND 13 37 BRCA1 AC011444.1 chr17 45449291 45449291 chr17 64796828 64796828 TCGA-G9-6338 DUP 22 21 PLEKHM1 PLEKHM1P1 chr17 45604154 45604154 chr17 46242081 46242081 TCGA-G9-6338 INV 11 13 * * chr17 46282512 46282512 chr17 64919750 64919750 TCGA-G9-6338 INV 16 15 ARL17B LRRC37A3 chr17 65916199 65916199 chr17 66572134 66572134 TCGA-G9-6338 DUP 45 46 CEP112 PRKCA chr17 7665625 7665625 chr17 7671497 7671497 TCGA-G9-6338 DEL 8 12 TP53 TP53 chr17 78060584 78060584 chr17 78201861 78201861 TCGA-G9-6338 DUP 38 41 TNRC6C AFMID chr18 25033703 25033703 chr18 47982631 47982631 TCGA-G9-6338 DEL 44 28 * * chr18 3796056 3796056 chr18 12377274 12377274 TCGA-G9-6338 DEL 6 16 DLGAP1 AFG3L2 chr18 46391724 46391724 chr18 46397458 46397458 TCGA-G9-6338 INV 35 39 RNF165 RNF165 chr18 79634168 79634168 chr21 46090893 46090901 TCGA-G9-6338 BND 47 23 * * chr19 3333009 3333009 chr19 10758278 10758278 TCGA-G9-6338 DEL 15 50 NFIC DNM2 chr19 47769819 47769819 chr19 47818178 47818178 TCGA-G9-6338 DEL 7 27 NOP53-AS1 TPRX1 chr19 48675180 48675180 chr19 49127502 49127502 TCGA-G9-6338 DEL 25 31 SEC1P PPFIA3 chr19 51469893 51469893 chr19 51486145 51486145 TCGA-G9-6338 DUP 37 19 AC020914.3 CEACAM18 chr19 57674529 57674529 chr19 58236949 58236949 TCGA-G9-6338 DUP 45 34 ZSCAN4 ZNF544 chr1 161242374 161242374 chr1 172340660 172340660 TCGA-G9-6338 DEL 34 26 * DNM3 chr1 161486605 161486605 chr1 162918318 162918318 TCGA-G9-6338 DEL 42 32 * * chr1 162077587 162077587 chr1 167769516 167769516 TCGA-G9-6338 DEL 38 47 NOS1AP MPZL1 chr1 162394377 162394377 chr1 166815922 166815922 TCGA-G9-6338 INS 18 43 * * chr1 162544767 162544767 chr1 164629390 164629390 TCGA-G9-6338 INS 50 47 * PBX1 chr1 162732348 162732348 chr1 167318509 167318509 TCGA-G9-6338 INS 1 10 DDR2 POU2F1 chr1 164275654 164275654 chr1 165033467 165033467 TCGA-G9-6338 INS 49 5 * * chr1 165070885 165070885 chr1 167863352 167863352 TCGA-G9-6338 DEL 22 33 * ADCY10 chr1 165093310 165093310 chr1 166055984 166055984 TCGA-G9-6338 INS 50 20 * * chr1 165504565 165504565 chr1 168513498 168513498 TCGA-G9-6338 DEL 19 27 LRRC52-AS1 * chr1 169217381 169217381 chr1 170011586 170011586 TCGA-G9-6338 DEL 27 27 NME7 KIFAP3 chr1 184003851 184003851 chr10 132224983 132224983 TCGA-G9-6338 BND 49 33 COLGALT2 STK32C chr1 185568514 185568514 chr1 186001372 186001372 TCGA-G9-6338 DUP 30 26 LINC01350 HMCN1 chr1 194644248 194644248 chr1 194650096 194650096 TCGA-G9-6338 DEL 41 25 * * chr1 199569659 199569659 chr1 199579872 199579872 TCGA-G9-6338 DEL 45 46 * * chr1 21576328 21576328 chr19 47818439 47818439 TCGA-G9-6338 BND 41 15 ALPL TPRX1 chr1 240351905 240351905 chr1 240374517 240374517 TCGA-G9-6338 DEL 10 48 FMN2 FMN2 chr1 37443055 37443055 chr15 95080437 95080437 TCGA-G9-6338 BND 11 2 * AC087633.2 chr1 72907326 72907326 chr1 73058245 73058245 TCGA-G9-6338 DUP 18 31 * * chr1 73219842 73219842 chr3 180370695 180370695 TCGA-G9-6338 BND 21 36 * * chr1 77114936 77114936 chr1 80259197 80259197 TCGA-G9-6338 DEL 3 22 PIGK * chr1 85868444 85868444 chr1 86053024 86053024 TCGA-G9-6338 DEL 3 32 COL24A1 COL24A1 chr1 97812808 97812808 chr3 191537084 191537084 TCGA-G9-6338 BND 12 3 DPYD AC073365.1 chr21 38464289 38464289 chr21 41498438 41498438 TCGA-G9-6338 DEL 6 7 ERG TMPRSS2 chr21 38500378 38500378 chr21 41506180 41506180 TCGA-G9-6338 DEL 44 18 ERG TMPRSS2 chr22 27324962 27324962 chr22 46648995 46648995 TCGA-G9-6338 DUP 32 5 * GRAMD4 chr2 117338794 117338794 chr2 153425998 153425998 TCGA-G9-6338 DEL 36 9 * AC012501.2 chr2 141484408 141484408 chr18 7188887 7188887 TCGA-G9-6338 BND 21 31 LRP1B * chr2 143645865 143645865 chr2 143645974 143645974 TCGA-G9-6338 DEL 31 28 ARHGAP15 ARHGAP15 chr2 154538835 154538835 chr2 155772730 155772730 TCGA-G9-6338 DEL 49 31 * * chr2 154577140 154577140 chr2 154654956 154654956 TCGA-G9-6338 INV 46 27 * * chr2 154577305 154577305 chr2 154655083 154655083 TCGA-G9-6338 INV 11 24 * * chr2 157319669 157319669 chr2 157638633 157638633 TCGA-G9-6338 DUP 36 20 ERMN * chr2 160269429 160269429 chr2 160623827 160623827 TCGA-G9-6338 DUP 36 8 AC092153.1 * chr2 172826456 172826456 chr2 173272125 173272125 TCGA-G9-6338 DEL 46 40 RAPGEF4 MAP3K20-AS1 chr2 180430166 180430166 chr2 180826919 180826919 TCGA-G9-6338 DUP 45 12 * SCHLAP1 chr2 184554007 184554007 chr2 191176054 191176054 TCGA-G9-6338 DEL 36 45 * * chr2 184659142 184659142 chr2 184663460 184663460 TCGA-G9-6338 DEL 41 29 ZNF804A ZNF804A chr2 206823282 206823282 chr11 36625005 36625005 TCGA-G9-6338 BND 21 32 AC008269.2 IFTAP chr2 231820615 231820615 chr2 232172719 232172719 TCGA-G9-6338 DUP 31 23 * DIS3L2 chr2 233014611 233014620 chr19 3235866 3235866 TCGA-G9-6338 BND 9 15 NGEF CELF5 chr2 233014611 233014620 chr9 134003357 134003357 TCGA-G9-6338 BND 12 22 NGEF * chr2 240233487 240233487 chr9 87040694 87040694 TCGA-G9-6338 BND 44 42 AC124861.1 AL513318.1 chr2 60340828 60340828 chr2 61758898 61758898 TCGA-G9-6338 DUP 43 47 MIR4432HG * chr2 87428980 87428980 chr2 90291370 90291370 TCGA-G9-6338 INV 14 10 * * chr2 94740645 94740645 chr2 94753849 94753849 TCGA-G9-6338 DUP 49 28 * * chr2 9776849 9776849 chr19 1550207 1550207 TCGA-G9-6338 BND 28 27 * * chr2 9776988 9776990 chr2 233014611 233014620 TCGA-G9-6338 DEL 25 22 * NGEF chr2 9776988 9776990 chr2 233015572 233015572 TCGA-G9-6338 INV 1 12 * AC106876.1 chr2 9776988 9776990 chr16 88423314 88423314 TCGA-G9-6338 BND 47 9 * * chr3 102423980 102423980 chr3 104417903 104417903 TCGA-G9-6338 DEL 15 37 ZPLD1 * chr3 102424712 102424712 chr8 50254739 50254739 TCGA-G9-6338 BND 29 16 ZPLD1 SNTG1 chr3 102425877 102425877 chr10 18671925 18671925 TCGA-G9-6338 BND 50 37 ZPLD1 ARL5B chr3 105698713 105698713 chr3 105701097 105701097 TCGA-G9-6338 DEL 43 37 CBLB CBLB chr3 125336101 125336101 chr3 129221191 129221191 TCGA-G9-6338 DUP 18 34 ZNF148 * chr3 126567775 126567775 chr3 126567815 126567815 TCGA-G9-6338 INV 13 13 * * chr3 128727585 128727585 chr3 128727683 128727683 TCGA-G9-6338 INV 7 40 RAB7A RAB7A chr3 132359344 132359344 chr19 41240993 41240993 TCGA-G9-6338 BND 18 41 ACP3 AXL chr3 148588896 148588896 chr3 148591265 148591265 TCGA-G9-6338 DEL 13 40 AC069410.1 AC069410.1 chr3 1569637 1569637 chr3 1570627 1570627 TCGA-G9-6338 DEL 49 6 * * chr3 166831737 166831737 chr8 49842254 49842254 TCGA-G9-6338 BND 19 18 * * chr3 180368597 180368597 chr1 73259412 73259412 TCGA-G9-6338 BND 26 48 * * chr3 194645492 194645495 chr8 1751750 1751750 TCGA-G9-6338 BND 16 31 LSG1 * chr3 194645492 194645495 chr12 2720779 2720796 TCGA-G9-6338 BND 14 42 LSG1 ITFG2-AS1 chr3 194645626 194645626 chr8 1751972 1751972 TCGA-G9-6338 BND 44 38 LSG1 * chr3 194706162 194706162 chrX 152872495 152872495 TCGA-G9-6338 BND 36 7 AC106706.1 * chr3 194706436 194706436 chrX 152872792 152872792 TCGA-G9-6338 BND 15 22 AC106706.1 * chr3 196541314 196541314 chr3 197497992 197497992 TCGA-G9-6338 DEL 24 38 * * chr3 28320399 28320399 chr3 38321953 38321953 TCGA-G9-6338 DEL 24 14 CMC1 * chr3 39148325 39148325 chr3 39148514 39148514 TCGA-G9-6338 INV 3 19 CSRNP1 CSRNP1 chr3 50146338 50146338 chr3 72668307 72668307 TCGA-G9-6338 INV 14 17 SEMA3F-AS1 * chr3 50266170 50266170 chr7 27171281 27171281 TCGA-G9-6338 BND 38 6 * HOXA9 chr3 72657070 72657070 chr7 27171158 27171158 TCGA-G9-6338 BND 41 29 * HOXA9 chr3 75563725 75563725 chr3 125782744 125782744 TCGA-G9-6338 DUP 31 12 AC133041.1 AC092902.4 chr3 82302759 82302759 chr3 82361142 82361142 TCGA-G9-6338 DEL 40 47 LINC02008 LINC02008 chr3 82348791 82348791 chr3 82383612 82383612 TCGA-G9-6338 DEL 50 46 LINC02008 LINC02008 chr3 83583562 83583562 chr3 83584671 83584671 TCGA-G9-6338 DEL 49 18 * * chr3 96627107 96627107 chr10 57350592 57350592 TCGA-G9-6338 BND 7 10 * * chr3 99676463 99676463 chr3 99683025 99683025 TCGA-G9-6338 DEL 46 8 COL8A1 COL8A1 chr4 102154307 102154307 chr4 102263469 102263469 TCGA-G9-6338 DUP 3 26 * SLC39A8 chr4 106548712 106548712 chr19 13618988 13618988 TCGA-G9-6338 BND 34 35 * CACNA1A chr4 106548936 106548936 chr19 13619168 13619168 TCGA-G9-6338 BND 30 32 * CACNA1A chr4 123640772 123640772 chr6 69100943 69100943 TCGA-G9-6338 BND 7 15 * ADGRB3 chr4 129941139 129941139 chr4 130199730 130199730 TCGA-G9-6338 DEL 39 14 LINC02465 * chr4 136430673 136430673 chr6 136878665 136878665 TCGA-G9-6338 BND 38 38 * PEX7 chr4 138935138 138935138 chr4 151351817 151351817 TCGA-G9-6338 DEL 16 2 AC109927.1 AC104819.3 chr4 144157205 144157205 chr4 144157901 144157901 TCGA-G9-6338 DEL 5 8 AC107223.1 AC107223.1 chr4 151353311 151353311 chr4 169384768 169384768 TCGA-G9-6338 DEL 30 15 AC104819.3 * chr4 153808787 153808787 chr19 2639817 2639817 TCGA-G9-6338 BND 48 20 * GNG7 chr4 153808960 153808960 chr19 2639817 2639817 TCGA-G9-6338 BND 36 38 * GNG7 chr4 161821097 161821097 chr4 170878901 170878901 TCGA-G9-6338 INS 38 21 FSTL5 * chr4 16229222 16229222 chr4 17105493 17105493 TCGA-G9-6338 DEL 6 44 TAPT1-AS1 * chr4 169309083 169309083 chr19 2185534 2185534 TCGA-G9-6338 BND 16 10 * DOT1L chr4 170810473 170810473 chr4 170892389 170892389 TCGA-G9-6338 DEL 3 14 * * chr4 17702984 17702984 chr4 17917077 17917077 TCGA-G9-6338 DEL 8 14 FAM184B LCORL chr4 17725665 17725665 chr4 17976051 17976051 TCGA-G9-6338 INS 11 21 FAM184B LCORL chr4 17842873 17842873 chr4 19060402 19060402 TCGA-G9-6338 DEL 8 36 NCAPG * chr4 17949763 17949763 chr4 47888124 47888124 TCGA-G9-6338 DEL 33 45 LCORL AC107068.2 chr4 17957423 17957423 chr4 44919442 44919442 TCGA-G9-6338 INS 32 49 LCORL * chr4 19935053 19935053 chr4 19954356 19954356 TCGA-G9-6338 DEL 21 49 * * chr4 20917732 20917732 chr4 21007469 21007469 TCGA-G9-6338 DEL 28 8 KCNIP4 KCNIP4 chr4 21741006 21741006 chr4 21770583 21770583 TCGA-G9-6338 DEL 15 27 KCNIP4 KCNIP4 chr4 30039518 30039518 chr4 30058280 30058280 TCGA-G9-6338 DEL 18 28 * * chr4 63124752 63124752 chr4 132361315 132361315 TCGA-G9-6338 INS 47 47 * * chr4 7262241 7262241 chr9 130373758 130373758 TCGA-G9-6338 BND 8 46 SORCS2 HMCN2 chr4 7262437 7262437 chr9 130373556 130373556 TCGA-G9-6338 BND 4 12 SORCS2 HMCN2 chr4 7449490 7449490 chr4 60423851 60423851 TCGA-G9-6338 INV 10 33 SORCS2 * chr5 102531105 102531105 chr5 102541068 102541068 TCGA-G9-6338 DEL 45 27 * * chr5 10835187 10835193 chr8 111490046 111490052 TCGA-G9-6338 BND 39 44 * LINC02237 chr5 10864249 10864249 chr5 18893794 18893794 TCGA-G9-6338 DEL 24 29 * * chr5 110973210 110973210 chr5 110974601 110974601 TCGA-G9-6338 DEL 12 1 AC010395.1 AC010395.1 chr5 124727547 124727547 chr5 124740429 124740429 TCGA-G9-6338 DEL 32 27 ZNF608 ZNF608 chr5 170704612 170704612 chr6 163954320 163954320 TCGA-G9-6338 BND 13 24 KCNIP1 * chr5 17350874 17350874 chr5 17354518 17354518 TCGA-G9-6338 DEL 46 32 * FTH1P10 chr5 18870539 18870539 chr8 23265344 23265344 TCGA-G9-6338 BND 45 18 * * chr5 19468469 19468469 chr5 20158810 20158810 TCGA-G9-6338 DEL 2 50 * CDH18 chr5 51693863 51693863 chr5 85652586 85652586 TCGA-G9-6338 DEL 29 40 * * chr5 697089 697089 chr5 788123 788123 TCGA-G9-6338 DEL 4 38 * * chr5 88969087 88969087 chr5 91303253 91303253 TCGA-G9-6338 DUP 7 48 MEF2C-AS1 LUCAT1 chr6 127730202 127730202 chr6 127759668 127759668 TCGA-G9-6338 INV 44 30 THEMIS THEMIS chr6 153721044 153721044 chr6 153721166 153721166 TCGA-G9-6338 DEL 13 11 * * chr6 160668795 160668795 chr6 160749365 160749365 TCGA-G9-6338 INV 17 11 AL109933.2 PLG chr6 160669217 160669217 chr6 160749699 160749699 TCGA-G9-6338 INV 48 33 AL109933.2 PLG chr6 16099557 16099557 chr18 50325138 50325138 TCGA-G9-6338 BND 5 1 * * chr6 162306962 162306962 chr6 162319189 162319189 TCGA-G9-6338 DEL 50 46 PRKN PRKN chr6 167169093 167169093 chr6 167385385 167385385 TCGA-G9-6338 INV 40 41 TCP10L2 TCP10L3 chr6 167169589 167169589 chr6 167389377 167389377 TCGA-G9-6338 INV 6 48 TCP10L2 * chr6 167170094 167170094 chr6 167387148 167387148 TCGA-G9-6338 INV 17 46 TCP10L2 * chr6 41203150 41203150 chr6 41242230 41242230 TCGA-G9-6338 INV 50 8 * * chr6 48028153 48028153 chr6 48042323 48042323 TCGA-G9-6338 DEL 44 22 PTCHD4 PTCHD4 chr6 53957490 53957490 chr6 54629099 54629099 TCGA-G9-6338 DEL 29 36 MLIP * chr6 54998611 54998611 chr6 55042391 55042391 TCGA-G9-6338 DEL 35 1 * * chr6 69981367 69981367 chr6 90795342 90795342 TCGA-G9-6338 DEL 35 48 COL19A1 * chr6 77434849 77434849 chr6 121137079 121137079 TCGA-G9-6338 DEL 5 10 * TBC1D32 chr6 89515590 89515590 chr6 89515862 89515862 TCGA-G9-6338 DEL 24 24 ANKRD6 ANKRD6 chr7 102512768 102512788 chr7 102611418 102611418 TCGA-G9-6338 DEL 34 28 RASA4B RASA4 chr7 111446346 111446346 chr8 126985913 126985913 TCGA-G9-6338 BND 7 45 IMMP2L PCAT1 chr7 117755409 117755409 chr7 117755894 117755894 TCGA-G9-6338 DEL 47 43 CTTNBP2 CTTNBP2 chr7 118501525 118501525 chr7 118530088 118530088 TCGA-G9-6338 DEL 35 40 * * chr7 13983698 13983698 chr7 26195272 26195272 TCGA-G9-6338 DEL 35 24 ETV1 HNRNPA2B1 chr7 1506515 1506515 chr11 995934 995934 TCGA-G9-6338 BND 17 17 * AP2A2 chr7 27196088 27196088 chr7 27197755 27197755 TCGA-G9-6338 DEL 46 43 HOXA13 HOXA13 chr7 42268014 42268014 chr19 6070135 6070135 TCGA-G9-6338 BND 15 17 * RFX2 chr7 74868420 74868420 chr7 75076183 75076183 TCGA-G9-6338 INV 15 26 * * chr7 81853052 81853052 chr7 81854667 81854667 TCGA-G9-6338 DEL 30 25 * * chr7 86544115 86544115 chr7 86587632 86587632 TCGA-G9-6338 DEL 3 31 * * chr8 101561598 101561598 chr8 101663902 101663902 TCGA-G9-6338 DEL 13 13 GRHL2 GRHL2 chr8 105332601 105332601 chr8 106095927 106095927 TCGA-G9-6338 DEL 30 42 ZFPM2 * chr8 105534714 105534714 chr9 28189421 28189421 TCGA-G9-6338 BND 42 20 ZFPM2 LINGO2 chr8 107049869 107049869 chr18 51414595 51414595 TCGA-G9-6338 BND 20 28 * LINC01630 chr8 109580676 109580676 chr8 109580809 109580809 TCGA-G9-6338 INV 42 4 SYBU SYBU chr8 111488181 111488181 chr5 19331857 19331857 TCGA-G9-6338 BND 18 34 LINC02237 * chr8 112495412 112495412 chr8 112774340 112774340 TCGA-G9-6338 DEL 4 22 CSMD3 CSMD3 chr8 113510573 113510573 chr8 113534250 113534250 TCGA-G9-6338 DEL 9 39 * * chr8 115435823 115435823 chr8 115435869 115435869 TCGA-G9-6338 INV 14 2 TRPS1 TRPS1 chr8 115768479 115768479 chrX 66077360 66077360 TCGA-G9-6338 BND 15 17 TRPS1 EIF4BP9 chr8 118732979 118732979 chr8 118733035 118733035 TCGA-G9-6338 INV 20 18 SAMD12-AS1 SAMD12-AS1 chr8 118733138 118733138 chr8 118733240 118733240 TCGA-G9-6338 INV 21 47 SAMD12-AS1 SAMD12-AS1 chr8 125806851 125806851 chr8 125806917 125806917 TCGA-G9-6338 INV 24 3 * * chr8 126093558 126093558 chr8 126093609 126093609 TCGA-G9-6338 INV 9 14 * * chr8 126121055 126121055 chr8 126121107 126121107 TCGA-G9-6338 INV 1 32 * * chr8 126121258 126121258 chr8 126121333 126121333 TCGA-G9-6338 INV 14 29 * * chr8 126212900 126212900 chr8 126213011 126213011 TCGA-G9-6338 INV 18 23 * * chr8 126293546 126293546 chr8 126293902 126293902 TCGA-G9-6338 INV 6 15 * * chr8 127926891 127926891 chr8 127926945 127926945 TCGA-G9-6338 INV 13 48 PVT1 PVT1 chr8 128039906 128039906 chr8 128039996 128039996 TCGA-G9-6338 INV 48 47 PVT1 PVT1 chr8 128115795 128115795 chr8 128115857 128115857 TCGA-G9-6338 INV 28 20 * * chr8 128333936 128333936 chr8 128334122 128334122 TCGA-G9-6338 INV 9 22 * * chr8 12835874 12835874 chr9 29150149 29150149 TCGA-G9-6338 BND 35 21 * * chr8 128798164 128798164 chr8 128798204 128798204 TCGA-G9-6338 INV 41 41 CCDC26 CCDC26 chr8 129181896 129181896 chr8 132748406 132748406 TCGA-G9-6338 DEL 29 9 CCDC26 TMEM71 chr8 130428477 130428477 chrX 3426978 3426978 TCGA-G9-6338 BND 26 38 ASAP1 * chr8 130560259 130560259 chr18 68464172 68464172 TCGA-G9-6338 BND 24 1 * * chr8 132943380 132943380 chr8 132943476 132943476 TCGA-G9-6338 INV 5 3 TG TG chr8 139219265 139219265 chr8 139222099 139222099 TCGA-G9-6338 DEL 6 42 * * chr8 139694424 139694424 chr8 139694675 139694675 TCGA-G9-6338 INV 41 43 KCNK9 KCNK9 chr8 139694804 139694804 chr8 139694862 139694862 TCGA-G9-6338 INV 28 39 KCNK9 KCNK9 chr8 141269598 141269598 chr8 141270061 141270061 TCGA-G9-6338 INV 43 34 SLC45A4 SLC45A4 chr8 14194373 14194373 chr8 15129814 15129814 TCGA-G9-6338 DEL 11 7 SGCZ SGCZ chr8 142272620 142272620 chr16 17239408 17239408 TCGA-G9-6338 BND 49 6 TSNARE1 XYLT1 chr8 144734288 144734288 chr8 144734362 144734362 TCGA-G9-6338 INV 15 4 ZNF251 ZNF251 chr8 144734493 144734493 chr8 144734568 144734568 TCGA-G9-6338 INV 28 44 ZNF251 ZNF251 chr8 17641428 17641428 chr9 24689449 24689449 TCGA-G9-6338 BND 49 37 PDGFRL * chr8 22394409 22394409 chr8 23044792 23044792 TCGA-G9-6338 INS 13 6 SLC39A14 TNFRSF10B chr8 22994429 22994429 chr8 23419294 23419294 TCGA-G9-6338 DEL 40 17 PEBP4 LOXL2 chr8 23516730 23516730 chr5 9678983 9678983 TCGA-G9-6338 BND 43 39 * TAS2R1 chr8 2670589 2670589 chr8 2682670 2682670 TCGA-G9-6338 DEL 29 47 AC246817.2 AC246817.2 chr8 32151672 32151672 chr9 24686039 24686039 TCGA-G9-6338 BND 46 18 NRG1 * chr8 32159208 32159208 chr9 24758845 24758845 TCGA-G9-6338 BND 50 1 NRG1 * chr8 33083520 33083520 chr8 33512576 33512576 TCGA-G9-6338 DEL 38 31 * TTI2 chr8 33957512 33957512 chr5 18928991 18928991 TCGA-G9-6338 BND 43 17 AF279873.3 * chr8 34179364 34179364 chr9 28127597 28127597 TCGA-G9-6338 BND 37 36 AC087855.2 LINGO2 chr8 34199935 34199935 chr8 41282176 41282176 TCGA-G9-6338 DEL 6 39 * SFRP1 chr8 34466443 34466443 chr8 41036314 41036314 TCGA-G9-6338 INV 22 4 * * chr8 36277380 36277380 chr5 20165849 20165849 TCGA-G9-6338 BND 6 46 * CDH18 chr8 36464540 36464540 chr8 110773220 110773220 TCGA-G9-6338 INS 43 48 * * chr8 3788994 3788994 chr8 108240954 108240954 TCGA-G9-6338 INS 19 7 CSMD1 EIF3E chr8 3943270 3943270 chr8 111255030 111255030 TCGA-G9-6338 DEL 3 30 CSMD1 * chr8 4046278 4046278 chr8 46314363 46314363 TCGA-G9-6338 INS 20 39 CSMD1 * chr8 40738015 40738015 chr9 29995571 29995571 TCGA-G9-6338 BND 42 35 ZMAT4 * chr8 40742230 40742230 chr9 28259435 28259435 TCGA-G9-6338 BND 38 30 ZMAT4 LINGO2 chr8 40805791 40805791 chr8 41028603 41028603 TCGA-G9-6338 INV 21 1 ZMAT4 * chr8 40885655 40885655 chr8 41071073 41071073 TCGA-G9-6338 DUP 24 26 ZMAT4 * chr8 40890359 40890359 chr8 41203138 41203138 TCGA-G9-6338 DUP 46 19 ZMAT4 * chr8 40928440 40928440 chr9 27722048 27722048 TCGA-G9-6338 BND 12 4 * * chr8 41126987 41126987 chr9 29977993 29977993 TCGA-G9-6338 BND 31 15 * * chr8 41231115 41231115 chr8 41496133 41496133 TCGA-G9-6338 INV 22 1 * GOLGA7 chr8 42710968 42710968 chr9 31707272 31707272 TCGA-G9-6338 BND 6 5 CHRNB3 * chr8 42754804 42754804 chr9 30437037 30437037 TCGA-G9-6338 BND 23 29 CHRNA6 LINC01242 chr8 46048422 46048422 chr8 46048529 46048529 TCGA-G9-6338 INV 19 6 * * chr8 46272156 46272156 chr8 46272387 46272387 TCGA-G9-6338 INV 14 16 * * chr8 47131524 47131524 chr8 121764200 121764200 TCGA-G9-6338 INV 17 46 AC120036.1 HAS2-AS1 chr8 50769221 50769221 chr8 114938334 114938334 TCGA-G9-6338 INV 16 38 SNTG1 * chr8 50823025 50823025 chr8 122347429 122347429 TCGA-G9-6338 DEL 38 40 * * chr8 56501896 56501896 chr8 56504700 56504700 TCGA-G9-6338 DEL 35 26 AC012349.1 AC012349.1 chr8 57453279 57453279 chr8 57473792 57473792 TCGA-G9-6338 DEL 36 7 * * chr8 58034584 58034584 chr8 58034671 58034671 TCGA-G9-6338 INV 3 18 FAM110B FAM110B chr8 6218460 6218460 chr8 112507688 112507688 TCGA-G9-6338 DEL 5 39 AC009435.1 CSMD3 chr8 6225674 6225674 chr8 32920089 32920089 TCGA-G9-6338 INS 21 23 AC009435.1 * chr8 64551300 64551300 chr8 124391411 124391411 TCGA-G9-6338 INV 7 17 * * chr8 65384508 65384508 chr8 65384704 65384704 TCGA-G9-6338 INV 45 8 * * chr8 65797975 65797975 chr8 65798222 65798222 TCGA-G9-6338 INV 7 8 PDE7A PDE7A chr8 65843969 65843969 chr8 65844026 65844026 TCGA-G9-6338 INV 39 43 * * chr8 68019338 68019338 chr8 68019428 68019428 TCGA-G9-6338 INV 2 26 PREX2 PREX2 chr8 68455222 68455222 chr8 68455410 68455410 TCGA-G9-6338 INV 30 37 C8orf34 C8orf34 chr8 71031910 71031910 chr8 71031962 71031962 TCGA-G9-6338 INV 43 47 AC015687.1 AC015687.1 chr8 71415989 71415989 chr8 71416165 71416165 TCGA-G9-6338 INV 37 5 EYA1 EYA1 chr8 72075093 72075093 chr8 72075349 72075349 TCGA-G9-6338 INV 15 24 MSC-AS1 MSC-AS1 chr8 72258292 72258292 chr8 75923778 75923778 TCGA-G9-6338 DEL 37 17 * * chr8 72258388 72258388 chr18 67606013 67606013 TCGA-G9-6338 BND 3 47 * AC114689.3 chr8 72909670 72909670 chr8 72909757 72909757 TCGA-G9-6338 INV 16 18 KCNB2 KCNB2 chr8 72917104 72917104 chr8 72917156 72917156 TCGA-G9-6338 INV 36 18 KCNB2 KCNB2 chr8 73212460 73212460 chr8 81637641 81637641 TCGA-G9-6338 INV 20 44 * * chr8 73355020 73355020 chr8 73355260 73355260 TCGA-G9-6338 INV 26 5 RDH10-AS1 RDH10-AS1 chr8 74648644 74648644 chr8 74648687 74648687 TCGA-G9-6338 INV 47 39 MIR2052HG MIR2052HG chr8 74656509 74656509 chr8 74656565 74656565 TCGA-G9-6338 INV 38 30 MIR2052HG MIR2052HG chr8 7497875 7497875 chr8 7507336 7507351 TCGA-G9-6338 INS 50 21 DEFB107B DEFB107B chr8 75605139 75605139 chr8 82874391 82874391 TCGA-G9-6338 INV 20 49 * AC105031.2 chr8 75924000 75924000 chr8 83163082 83163082 TCGA-G9-6338 INV 21 3 * * chr8 76040641 76040641 chr8 76040747 76040747 TCGA-G9-6338 INV 4 26 * * chr8 77510385 77510385 chr8 78485256 78485256 TCGA-G9-6338 INV 12 28 AC062004.1 PKIA-AS1 chr8 77604069 77604069 chr8 83509373 83509373 TCGA-G9-6338 INV 25 30 * * chr8 79696805 79696805 chr8 106525863 106525863 TCGA-G9-6338 INV 9 21 * OXR1 chr8 81184650 81184650 chr8 81184846 81184846 TCGA-G9-6338 INV 36 34 * * chr8 82622920 82622920 chr8 132751688 132751688 TCGA-G9-6338 INV 41 16 AC060765.1 TMEM71 chr8 83202301 83202301 chr8 122410871 122410871 TCGA-G9-6338 DEL 17 50 AC090132.1 * chr8 83208831 83208831 chr8 122472517 122472517 TCGA-G9-6338 INV 46 6 * * chr8 83208973 83208973 chr8 105659359 105659359 TCGA-G9-6338 INV 8 29 * ZFPM2 chr8 84604513 84604513 chr8 84604633 84604633 TCGA-G9-6338 INV 45 39 RALYL RALYL chr8 8702467 8702467 chr9 24685243 24685243 TCGA-G9-6338 BND 27 17 CLDN23 * chr8 8702629 8702629 chr8 32147958 32147958 TCGA-G9-6338 DEL 44 3 CLDN23 NRG1 chr8 88801636 88801636 chr8 88802147 88802147 TCGA-G9-6338 INV 10 14 AC090578.1 AC090578.1 chr8 88851920 88851920 chr8 89703753 89703753 TCGA-G9-6338 DUP 8 8 AC090578.1 AF117829.1 chr8 89285660 89285660 chr8 89285697 89285697 TCGA-G9-6338 INV 42 36 * * chr8 90790463 90790463 chr8 90790521 90790521 TCGA-G9-6338 INV 2 30 TMEM64 TMEM64 chr8 93042757 93042757 chr8 93042940 93042940 TCGA-G9-6338 INV 50 31 * * chr8 93338462 93338462 chr8 93338605 93338605 TCGA-G9-6338 INV 20 34 LINC00535 LINC00535 chr8 98176160 98176160 chr8 98176276 98176276 TCGA-G9-6338 INV 33 13 * * chr9 113678721 113678721 chr9 113687138 113687138 TCGA-G9-6338 INV 24 14 AL157702.2 * chr9 134003166 134003166 chr16 88980726 88980726 TCGA-G9-6338 BND 47 2 * * chr9 137229947 137229947 chr9 137477045 137477045 TCGA-G9-6338 DEL 8 50 SLC34A3 PNPLA7 chr9 23221940 23221940 chr9 23383235 23383235 TCGA-G9-6338 DEL 10 30 AL391117.1 AL391117.1 chr9 23222183 23222183 chr9 23223903 23223903 TCGA-G9-6338 INV 19 21 AL391117.1 AL391117.1 chr9 23222348 23222350 chr9 23383810 23383821 TCGA-G9-6338 INV 23 18 AL391117.1 AL391117.1 chr9 23255655 23255655 chr9 24759973 24759973 TCGA-G9-6338 INV 24 9 AL391117.1 * chr9 24544300 24544300 chr9 24544421 24544421 TCGA-G9-6338 INV 13 18 IZUMO3 IZUMO3 chr9 25810991 25810991 chr9 25811083 25811083 TCGA-G9-6338 INV 38 4 LINC01241 LINC01241 chr9 26050352 26050352 chr9 26050438 26050438 TCGA-G9-6338 INV 24 15 * * chr9 26973867 26973867 chr9 29202641 29202641 TCGA-G9-6338 DUP 34 18 IFT74 * chr9 27469417 27469417 chr9 27469634 27469634 TCGA-G9-6338 INV 26 27 MOB3B MOB3B chr9 27736873 27736873 chr9 31686820 31686820 TCGA-G9-6338 DUP 4 31 * * chr9 31696082 31696082 chr9 32378000 32378000 TCGA-G9-6338 INV 47 3 * * chr9 39964563 39964563 chr9 41440583 41440583 TCGA-G9-6338 INV 14 2 FGF7P3 * chr9 41757299 41757299 chr9 61970419 61970419 TCGA-G9-6338 INV 22 28 * * chr9 41758267 41758267 chr9 61557683 61557683 TCGA-G9-6338 INV 16 23 * * chr9 41758267 41758267 chr9 61969344 61969344 TCGA-G9-6338 DUP 47 46 * * chr9 61534765 61534765 chr9 61992506 61992506 TCGA-G9-6338 DEL 30 41 * * chr9 89671753 89671753 chr12 118708065 118708065 TCGA-G9-6338 BND 25 2 UNQ6494 * chr9 95937135 95937135 chr9 96386700 96386700 TCGA-G9-6338 DUP 33 1 ERCC6L2 ZNF367 chrX 125574595 125574595 chrX 127149084 127149084 TCGA-G9-6338 INV 36 3 * * chrX 142914156 142914156 chrX 142928674 142928674 TCGA-G9-6338 DEL 1 21 * * chrX 4681832 4681832 chrX 6621806 6621806 TCGA-G9-6338 INV 17 38 * * chrX 4682148 4682148 chrX 6622111 6622111 TCGA-G9-6338 INV 35 34 * * chrX 48381325 48381325 chrX 48413875 48413875 TCGA-G9-6338 INV 39 50 * AL606490.5 chrX 48381548 48381548 chrX 48414103 48414103 TCGA-G9-6338 INV 29 41 * AL606490.5 chr12 16440845 16440845 chr12 16440936 16440936 TCGA-EJ-7782 DEL 50 23 MGST1 MGST1 chr12 34584220 34584220 chr12 34584389 34584389 TCGA-EJ-7782 DEL 21 14 * * chr12 98945237 98945237 chr12 98950463 98950463 TCGA-EJ-7782 DEL 18 15 ANKS1B ANKS1B chr13 23695682 23695682 chr13 23868389 23868389 TCGA-EJ-7782 INS 23 49 * MIPEP chr14 64504421 64504421 chr14 64566132 64566132 TCGA-EJ-7782 INS 2 26 ZBTB25 PPP1R36 chr17 16538672 16538672 chr17 16539693 16539693 TCGA-EJ-7782 DEL 19 49 * * chr1 98367933 98367934 chr1 98370158 98370158 TCGA-EJ-7782 DEL 5 36 * * chr20 25238267 25238267 chr20 25238433 25238433 TCGA-EJ-7782 DEL 3 27 * * chr2 116934283 116934283 chr2 117089659 117089659 TCGA-EJ-7782 DEL 10 37 * * chr2 116944662 116944662 chr2 119265998 119265998 TCGA-EJ-7782 INS 13 2 * * chr2 118013360 118013360 chr2 118015000 118015000 TCGA-EJ-7782 DEL 7 11 CCDC93 CCDC93 chr2 118342268 118342268 chr2 118351455 118351455 TCGA-EJ-7782 DEL 45 30 * * chr2 119404598 119404598 chr2 119411650 119411650 TCGA-EJ-7782 DEL 14 39 * * chr3 98634349 98634349 chr3 98634479 98634479 TCGA-EJ-7782 DEL 17 41 * * chr4 132404893 132404893 chr4 132405159 132405159 TCGA-EJ-7782 DEL 6 12 * * chr4 18419074 18419074 chr4 20709387 20709387 TCGA-EJ-7782 DEL 24 22 * PACRGL chr4 188349732 188349732 chr8 88294542 88294542 TCGA-EJ-7782 BND 40 47 AC093789.1 MMP16 chr4 49144213 49144213 chr4 49161901 49161901 TCGA-EJ-7782 DEL 24 37 * * chr4 92911061 92911067 chr2 125600019 125600024 TCGA-EJ-7782 BND 25 28 GRID2 * chr5 104573138 104573138 chr5 108606609 108606609 TCGA-EJ-7782 DEL 13 26 AC099520.1 * chr5 109613032 109613032 chr5 116534983 116534983 TCGA-EJ-7782 DEL 1 36 * SEMA6A chr5 111294035 111294035 chr5 117683941 117683941 TCGA-EJ-7782 INS 33 31 CAMK4 * chr5 113351923 113351923 chr5 113383330 113383330 TCGA-EJ-7782 DEL 27 40 MCC MCC chr5 116527215 116527217 chr5 132727180 132727180 TCGA-EJ-7782 DEL 25 4 SEMA6A KIF3A chr5 154250875 154250875 chr5 154255109 154255109 TCGA-EJ-7782 DEL 42 49 GALNT10 GALNT10 chr5 41261062 41261062 chr5 41261226 41261226 TCGA-EJ-7782 DEL 28 39 C6 C6 chr5 42757785 42757785 chr5 42813818 42813818 TCGA-EJ-7782 DEL 5 39 CCDC152 SELENOP chr6 162663688 162663688 chr6 162664479 162664479 TCGA-EJ-7782 DEL 2 47 PRKN PRKN chr6 75488212 75488212 chr6 125700604 125700604 TCGA-EJ-7782 DEL 18 17 FILIP1 AL365259.1 chr7 122018796 122018796 chr7 122087734 122087734 TCGA-EJ-7782 DEL 19 16 PTPRZ1 AASS chr7 122090079 122090079 chr7 122092968 122092968 TCGA-EJ-7782 DEL 27 49 AASS AASS chr7 33678539 33678539 chr7 33678934 33678938 TCGA-EJ-7782 DEL 25 26 * * chr8 105484178 105484178 chr8 105486669 105486669 TCGA-EJ-7782 DEL 48 14 ZFPM2 ZFPM2 chr8 109835499 109835499 chr8 109837051 109837051 TCGA-EJ-7782 DEL 36 22 * * chr8 110296849 110296849 chr8 110311282 110311282 TCGA-EJ-7782 DEL 4 46 * * chr8 111912559 111912559 chr8 111918513 111918513 TCGA-EJ-7782 DEL 27 1 * * chr8 46697583 46697583 chr8 46731119 46731119 TCGA-EJ-7782 DEL 12 46 ASNSP4 * chr8 50265255 50265255 chr8 50268140 50268140 TCGA-EJ-7782 DEL 41 5 SNTG1 SNTG1 chr8 76274992 76274992 chr8 78628939 78628939 TCGA-EJ-7782 INS 45 10 * * chr8 76368224 76368224 chr8 76603969 76603969 TCGA-EJ-7782 DEL 38 42 * ZFHX4-AS1 chr8 76372052 76372052 chr8 77125170 77125170 TCGA-EJ-7782 INS 11 18 * * chr8 77133758 77133758 chr8 111733239 111733239 TCGA-EJ-7782 INS 25 13 * LINC02237 chr8 77233388 77233388 chr8 77300224 77300224 TCGA-EJ-7782 DEL 1 46 * * chr8 77407391 77407391 chr8 78395708 78395708 TCGA-EJ-7782 DEL 16 4 AC062004.1 * chr8 79532142 79532142 chr8 111775833 111775833 TCGA-EJ-7782 DEL 34 20 * * chr8 86962025 86962025 chr8 88279543 88279543 TCGA-EJ-7782 INS 6 50 CNBD1 MMP16 chr8 87111957 87111959 chr4 188359238 188359240 TCGA-EJ-7782 BND 35 27 CNBD1 * chr9 10357453 10357453 chr9 11092224 11092224 TCGA-EJ-7782 INS 21 19 PTPRD * chr9 12931075 12931076 chr9 12957356 12957356 TCGA-EJ-7782 DEL 24 6 * * chr9 62814083 62814084 chr9 63792846 63792846 TCGA-EJ-7782 INS 40 18 * * chrX 83398332 83398332 chrX 83398897 83398897 TCGA-EJ-7782 DEL 2 5 * * chrX 98005935 98005935 chrX 99488574 99488574 TCGA-EJ-7782 DEL 48 50 * * chr10 116487775 116487775 chr10 116677708 116677708 TCGA-KK-A8IA INS 11 39 * HSPA12A chr10 127722208 127722208 chr10 129908620 129908620 TCGA-KK-A8IA INS 27 39 * EBF3 chr10 17626398 17626398 chr16 70494575 70494575 TCGA-KK-A8IA BND 43 21 * COG4 chr10 19125258 19125258 chr12 114640795 114640795 TCGA-KK-A8IA BND 16 44 MALRD1 * chr10 46489845 46489845 chr10 46490343 46490343 TCGA-KK-A8IA DEL 43 28 AC244230.2 AC244230.2 chr10 58102500 58102500 chr10 58271593 58271593 TCGA-KK-A8IA INS 25 29 * CISD1 chr10 87841417 87841417 chr10 89223722 89223722 TCGA-KK-A8IA DEL 4 21 ATAD1 LIPA chr10 87853197 87853197 chr10 98871726 98871726 TCGA-KK-A8IA INV 27 34 * HPSE2 chr11 128339879 128339879 chr11 128479388 128479388 TCGA-KK-A8IA DEL 38 27 * ETS1 chr11 134168153 134168153 chr11 134588402 134588402 TCGA-KK-A8IA INS 48 36 NCAPD3 * chr11 13984545 13984545 chr11 14299346 14299346 TCGA-KK-A8IA INS 4 16 SPON1 RRAS2 chr11 14209433 14209433 chr11 14587750 14587750 TCGA-KK-A8IA INS 2 17 SPON1 PSMA1 chr11 16347386 16347386 chr11 16708769 16708769 TCGA-KK-A8IA INS 23 1 SOX6 SOX6 chr11 27160985 27160985 chr11 27822289 27822289 TCGA-KK-A8IA INS 46 19 BBOX1-AS1 AC103796.1 chr11 29688800 29688800 chr11 39073080 39073080 TCGA-KK-A8IA DEL 26 36 * AC021723.2 chr11 36329342 36329342 chr11 36598711 36598711 TCGA-KK-A8IA INS 14 16 PRR5L RAG2 chr11 47949706 47949706 chr11 48014141 48014141 TCGA-KK-A8IA DEL 29 49 * PTPRJ chr11 79898931 79898931 chr11 82320733 82320733 TCGA-KK-A8IA INS 14 14 * MIR4300HG chr11 80935212 80935212 chr11 80940141 80940141 TCGA-KK-A8IA DEL 11 7 * * chr11 96702055 96702055 chr11 98587240 98587240 TCGA-KK-A8IA INS 33 10 AP003066.1 * chr12 103964914 103964914 chr12 109011695 109011695 TCGA-KK-A8IA INS 45 17 C12orf73 SVOP chr12 109010838 109010838 chr12 109011997 109011997 TCGA-KK-A8IA INS 20 10 SVOP SVOP chr12 116552579 116552579 chr12 118563860 118563860 TCGA-KK-A8IA INS 33 7 MAP1LC3B2 * chr12 123111557 123111557 chr12 123147453 123147453 TCGA-KK-A8IA DUP 24 35 PITPNM2 PITPNM2 chr12 124093074 124093074 chr12 132464298 132464308 TCGA-KK-A8IA INV 29 39 RFLNA * chr12 19117361 19117361 chr12 19570768 19570768 TCGA-KK-A8IA INS 24 36 * AEBP2 chr12 19263721 19263721 chr13 48669715 48669715 TCGA-KK-A8IA BND 33 42 PLEKHA5 CYSLTR2 chr12 19263822 19263822 chr12 66252697 66252697 TCGA-KK-A8IA INV 43 33 PLEKHA5 IRAK3 chr12 22857881 22857881 chr14 52497299 52497299 TCGA-KK-A8IA BND 20 3 AC084816.1 TXNDC16 chr12 49271991 49271991 chr12 59395313 59395313 TCGA-KK-A8IA DUP 47 19 TUBA1C AC108721.1 chr12 54171845 54171845 chr12 57918888 57918888 TCGA-KK-A8IA INS 39 24 SMUG1 ATP23 chr12 62812130 62812130 chr12 63418279 63418279 TCGA-KK-A8IA INV 22 29 PPM1H * chr12 62821071 62821071 chr12 62927618 62927618 TCGA-KK-A8IA DUP 10 41 PPM1H PPM1H chr12 62822129 62822129 chr14 54969344 54969344 TCGA-KK-A8IA BND 32 30 PPM1H WDHD1 chr12 62849483 62849483 chr14 52394834 52394834 TCGA-KK-A8IA BND 40 7 PPM1H * chr12 62849783 62849783 chr13 30567631 30567631 TCGA-KK-A8IA BND 43 48 PPM1H HMGB1 chr12 66015084 66015084 chr13 52089782 52089782 TCGA-KK-A8IA BND 29 46 * NEK5 chr12 66252509 66252509 chr13 48669935 48669935 TCGA-KK-A8IA BND 49 37 IRAK3 CYSLTR2 chr12 95787274 95787274 chr12 97300410 97300410 TCGA-KK-A8IA INS 26 48 NTN4 * chr12 97807196 97807196 chr12 98772305 98772305 TCGA-KK-A8IA DUP 22 4 * ANKS1B chr13 100557316 100557316 chr13 100602878 100602878 TCGA-KK-A8IA DUP 40 5 GGACT * chr13 108438666 108438666 chr13 111035166 111035166 TCGA-KK-A8IA DUP 41 12 AL138694.1 * chr13 38422691 38422691 chr13 51695121 51695121 TCGA-KK-A8IA INV 29 39 * WDFY2 chr13 47743858 47743858 chr13 56098139 56098139 TCGA-KK-A8IA INV 6 29 * * chr13 48868757 48868757 chr14 52396919 52396919 TCGA-KK-A8IA BND 29 34 * * chr14 106335782 106335782 chr14 106360088 106360088 TCGA-KK-A8IA DEL 39 46 IGHV3-30 IGHV3-33 chr14 25206887 25206887 chr14 92700111 92700111 TCGA-KK-A8IA INV 32 38 * * chr14 35875549 35875549 chr14 36867168 36867168 TCGA-KK-A8IA INS 23 29 BRMS1L SLC25A21 chr14 36910277 36910277 chr14 37591857 37591857 TCGA-KK-A8IA INV 30 45 SLC25A21 FOXA1 chr15 20534301 20534319 chr15 28560396 28560396 TCGA-KK-A8IA INV 46 32 GOLGA6L6 AC138749.1 chr15 25001129 25001129 chr15 29414260 29414260 TCGA-KK-A8IA INS 44 7 SNHG14 FAM189A1 chr15 31742581 31742581 chr15 45802514 45802514 TCGA-KK-A8IA DEL 37 8 OTUD7A AC068722.1 chr15 57122368 57122368 chr15 57218935 57218935 TCGA-KK-A8IA DEL 29 6 TCF12 TCF12 chr15 70753095 70753095 chr15 70814030 70814030 TCGA-KK-A8IA INS 2 13 UACA * chr15 77570806 77570806 chr15 77796489 77796489 TCGA-KK-A8IA INS 50 15 AC046168.2 LINGO1 chr15 82042713 82042713 chr15 82737117 82737117 TCGA-KK-A8IA INV 16 37 MEX3B ACTG1P17 chr16 1362246 1362246 chr16 29777663 29777663 TCGA-KK-A8IA DUP 38 24 GNPTG ZG16 chr16 16327319 16327319 chr16 16370802 16370802 TCGA-KK-A8IA DEL 16 41 PKD1P1 PKD1P2 chr16 50470951 50470951 chr16 50951231 50951231 TCGA-KK-A8IA INS 47 10 AC007493.1 * chr16 73806465 73806465 chr2 29376259 29376259 TCGA-KK-A8IA BND 33 42 ZFHX3 ALK chr17 21349419 21349419 chr17 21438810 21438810 TCGA-KK-A8IA DEL 45 15 * LINC02693 chr17 39907990 39907990 chr17 40119573 40119573 TCGA-KK-A8IA DUP 16 27 GSDMB * chr17 50350193 50350193 chr17 50350576 50350576 TCGA-KK-A8IA DEL 22 2 XYLT2 XYLT2 chr17 58059717 58059717 chr17 58061482 58061482 TCGA-KK-A8IA INV 35 7 AC015813.8 AC015813.8 chr17 58060778 58060778 chrX 75271243 75271243 TCGA-KK-A8IA BND 9 32 AC015813.8 * chr17 59162798 59162798 chr17 63100544 63100544 TCGA-KK-A8IA INS 47 25 PRR11 TANC2 chr17 7684646 7684648 chr1 225278499 225278499 TCGA-KK-A8IA BND 41 40 TP53 DNAH14 chr18 22711825 22711825 chr18 23282542 23282542 TCGA-KK-A8IA INS 46 31 AC090912.1 TMEM241 chr18 66004627 66004627 chr18 66291013 66291013 TCGA-KK-A8IA INS 50 5 * * chr19 44818352 44818352 chr19 44819987 44819987 TCGA-KK-A8IA INV 44 24 BCAM BCAM chr1 102712126 102712126 chr1 113722267 113722267 TCGA-KK-A8IA DEL 46 50 * PHTF1 chr1 154961048 154961048 chr1 155415581 155415581 TCGA-KK-A8IA INS 14 19 PYGO2 ASH1L chr1 172913634 172913634 chr1 173249103 173249103 TCGA-KK-A8IA INS 10 48 AL031599.1 * chr1 193494641 193494641 chr1 193494845 193494845 TCGA-KK-A8IA DEL 33 41 * * chr1 194226381 194226381 chr1 194350878 194350878 TCGA-KK-A8IA DEL 45 38 * AL513348.1 chr1 205653232 205653232 chr7 13782187 13782187 TCGA-KK-A8IA BND 30 19 * * chr1 205666418 205666418 chr7 13951293 13951293 TCGA-KK-A8IA BND 48 15 SLC45A3 ETV1 chr1 218970605 218970605 chr1 222458714 222458714 TCGA-KK-A8IA DEL 50 28 * * chr1 223783346 223783346 chr2 239150782 239150782 TCGA-KK-A8IA BND 14 23 TP53BP2 HDAC4 chr1 228308889 228308889 chr1 228319522 228319522 TCGA-KK-A8IA DEL 49 25 OBSCN OBSCN chr1 235619547 235619547 chr1 235658759 235658759 TCGA-KK-A8IA DUP 13 41 GNG4 * chr1 236468725 236468725 chr1 236861976 236861976 TCGA-KK-A8IA INS 45 19 EDARADD MTR chr1 25762367 25762367 chr6 86316138 86316138 TCGA-KK-A8IA BND 19 42 MAN1C1 * chr1 25763641 25763641 chr9 123279651 123279651 TCGA-KK-A8IA BND 15 24 MAN1C1 * chr1 72223795 72223795 chr1 73758746 73758746 TCGA-KK-A8IA INS 27 2 NEGR1 * chr1 8548407 8548407 chr22 33874156 33874156 TCGA-KK-A8IA BND 27 6 RERE LARGE1 chr20 15442455 15442455 chr20 15937148 15937148 TCGA-KK-A8IA INS 15 20 MACROD2 MACROD2 chr20 35777699 35777699 chr20 36216507 36216507 TCGA-KK-A8IA INS 44 26 PHF20 EPB41L1 chr21 13341528 13341528 chr21 13370411 13370411 TCGA-KK-A8IA DUP 18 4 * * chr21 38459675 38459675 chr21 41494647 41494647 TCGA-KK-A8IA DEL 33 38 ERG TMPRSS2 chr21 38513749 38513749 chr21 41502621 41502621 TCGA-KK-A8IA DEL 17 50 ERG TMPRSS2 chr21 43336982 43336982 chr21 46091405 46091405 TCGA-KK-A8IA INV 8 20 * * chr22 16878277 16878277 chr22 35549570 35549570 TCGA-KK-A8IA INV 19 8 AC007064.1 RASD2 chr2 102588146 102588146 chr2 102595310 102595310 TCGA-KK-A8IA INS 27 27 * * chr2 125741411 125741411 chr12 110624041 110624041 TCGA-KK-A8IA BND 46 28 LINC01889 TCTN1 chr2 170543138 170543138 chr2 170794473 170794473 TCGA-KK-A8IA INS 26 50 MYO3B ERICH2 chr2 19469506 19469506 chr2 19911633 19911633 TCGA-KK-A8IA INS 15 14 AC010096.1 WDR35 chr2 206845064 206845064 chr2 206846255 206846255 TCGA-KK-A8IA INV 42 23 * * chr2 219794391 219794391 chr2 220031187 220031187 TCGA-KK-A8IA INV 16 18 * * chr2 219794591 219794591 chr2 234542537 234542537 TCGA-KK-A8IA DUP 44 5 * * chr2 220031130 220031130 chr8 141655704 141655704 TCGA-KK-A8IA BND 25 44 * * chr2 220039085 220039085 chr2 238782451 238782451 TCGA-KK-A8IA INV 17 42 * * chr2 230754768 230754768 chr2 230783327 230783327 TCGA-KK-A8IA DUP 4 28 CAB39 CAB39 chr2 237138844 237138844 chr6 25723253 25723253 TCGA-KK-A8IA BND 24 5 * * chr2 239445827 239445827 chr14 33538182 33538182 TCGA-KK-A8IA BND 40 35 * NPAS3 chr2 29374464 29374464 chr2 29814876 29814876 TCGA-KK-A8IA DEL 1 38 ALK ALK chr2 29799705 29799705 chr8 53125396 53125396 TCGA-KK-A8IA BND 7 37 ALK * chr2 30443400 30443400 chr2 30787405 30787405 TCGA-KK-A8IA DUP 8 7 * CAPN13 chr2 30470024 30470024 chr2 30734597 30734597 TCGA-KK-A8IA DUP 47 44 LCLAT1 CAPN13 chr2 36636858 36636858 chr2 43279747 43279747 TCGA-KK-A8IA DEL 49 6 FEZ2 THADA chr2 39218551 39218551 chr2 44895117 44895117 TCGA-KK-A8IA DEL 1 3 CDKL4 * chr2 4165087 4165087 chr2 4175888 4175888 TCGA-KK-A8IA DEL 20 33 * * chr2 6399712 6399712 chr19 10807260 10807260 TCGA-KK-A8IA BND 30 38 * DNM2 chr2 82765498 82765498 chr2 83075105 83075105 TCGA-KK-A8IA INS 20 50 * * chr3 113896857 113896857 chr3 118508744 118508744 TCGA-KK-A8IA INS 46 31 GRAMD1C AC068633.1 chr3 11887297 11887297 chr12 63470602 63470602 TCGA-KK-A8IA BND 26 35 FANCD2P2 * chr3 11890837 11890837 chr13 38552468 38552468 TCGA-KK-A8IA BND 47 31 FANCD2P2 * chr3 11989757 11989757 chr12 22857749 22857749 TCGA-KK-A8IA BND 14 41 * AC084816.1 chr3 12155155 12155155 chr13 30549713 30549713 TCGA-KK-A8IA BND 25 3 SYN2 HMGB1 chr3 128050206 128050206 chr3 128065356 128065356 TCGA-KK-A8IA DEL 6 3 MGLL SEC61A1 chr3 133079265 133079265 chr3 133097826 133097826 TCGA-KK-A8IA DEL 43 16 TMEM108 TMEM108 chr3 152381175 152381175 chr3 155447640 155447640 TCGA-KK-A8IA INV 26 21 MBNL1 PLCH1 chr3 152383418 152383418 chr3 155449765 155449765 TCGA-KK-A8IA INV 32 12 MBNL1 PLCH1 chr3 185692927 185692927 chr3 185877005 185877005 TCGA-KK-A8IA DEL 31 41 IGF2BP2 * chr3 189842997 189842997 chr13 40368681 40368681 TCGA-KK-A8IA BND 23 20 TP63 LINC00598 chr3 194290311 194290311 chr6 20557851 20557851 TCGA-KK-A8IA BND 41 23 * CDKAL1 chr3 26264288 26264288 chr3 29072205 29072205 TCGA-KK-A8IA INS 3 41 * AC098650.1 chr3 27452596 27452596 chr3 28136064 28136064 TCGA-KK-A8IA DUP 22 48 SLC4A7 * chr3 41896848 41896848 chr12 64504568 64504568 TCGA-KK-A8IA BND 9 49 ULK4 * chr3 41902982 41902982 chr13 48712062 48712062 TCGA-KK-A8IA BND 47 15 ULK4 * chr3 42012592 42012592 chr12 62843684 62843684 TCGA-KK-A8IA BND 47 35 TRAK1 PPM1H chr3 46563986 46563986 chr3 46835886 46835886 TCGA-KK-A8IA INS 6 37 LRRC2 * chr3 48933751 48933751 chr12 68402645 68402645 TCGA-KK-A8IA BND 30 37 ARIH2 LINC02384 chr3 48934903 48934903 chr3 85389461 85389461 TCGA-KK-A8IA DEL 24 18 ARIH2 CADM2 chr3 48937643 48937643 chr3 49008821 49008821 TCGA-KK-A8IA DUP 14 49 ARIH2 WDR6 chr3 48951669 48951669 chr3 50342745 50342745 TCGA-KK-A8IA DUP 21 19 ARIH2 ZMYND10 chr3 49019393 49019393 chr12 68406237 68406237 TCGA-KK-A8IA BND 20 35 DALRD3 LINC02384 chr3 49019419 49019419 chr3 85389540 85389540 TCGA-KK-A8IA DUP 48 5 DALRD3 CADM2 chr3 74963815 74963815 chr18 50878223 50878223 TCGA-KK-A8IA BND 33 33 * ME2 chr4 12238684 12238684 chr4 12896619 12896619 TCGA-KK-A8IA DUP 7 10 LINC02270 * chr4 137298453 137298453 chr4 137489183 137489183 TCGA-KK-A8IA INS 17 1 * * chr4 137895478 137895478 chr12 97987942 97987942 TCGA-KK-A8IA BND 29 46 * * chr4 146346154 146346154 chr4 146477845 146477845 TCGA-KK-A8IA DEL 32 48 SLC10A7 SLC10A7 chr4 146449399 146449399 chr4 146611784 146611784 TCGA-KK-A8IA INS 37 18 SLC10A7 * chr4 153672751 153672751 chr4 165609162 165609162 TCGA-KK-A8IA DUP 12 47 AC106865.1 * chr4 158469526 158469526 chr4 159497751 159497751 TCGA-KK-A8IA INS 49 5 RXFP1 * chr4 16741218 16741218 chr4 20426274 20426274 TCGA-KK-A8IA INS 24 42 LDB2 SLIT2 chr4 168275630 168275630 chr4 168781505 168781505 TCGA-KK-A8IA DUP 33 44 DDX60 PALLD chr4 179750605 179750605 chr6 18903215 18903215 TCGA-KK-A8IA BND 42 7 * * chr4 39219735 39219735 chr4 39248361 39248361 TCGA-KK-A8IA DUP 24 41 WDR19 WDR19 chr4 71314007 71314007 chr4 74324525 74324525 TCGA-KK-A8IA INS 26 24 SLC4A4 * chr5 112225747 112225747 chr5 112427365 112427365 TCGA-KK-A8IA DEL 5 17 EPB41L4A * chr5 128915244 128915244 chr5 132522072 132522072 TCGA-KK-A8IA INS 27 13 SLC27A6 AC116366.2 chr5 133881247 133881247 chr5 153417902 153417902 TCGA-KK-A8IA DUP 23 22 * * chr5 178358116 178358116 chr5 180670279 180670279 TCGA-KK-A8IA DEL 36 15 COL23A1 * chr5 44185311 44185311 chr8 4444410 4444410 TCGA-KK-A8IA BND 19 19 * CSMD1 chr5 51032505 51032505 chr5 51056065 51056065 TCGA-KK-A8IA DEL 37 1 * RNU6-480P chr5 51378821 51378821 chr5 57155888 57155888 TCGA-KK-A8IA INS 21 29 AC010478.1 * chr5 63822482 63822482 chr5 63824106 63824106 TCGA-KK-A8IA DEL 22 2 * * chr5 81872221 81872221 chr5 98874543 98874543 TCGA-KK-A8IA DEL 42 11 * CHD1 chr5 87411529 87411529 chr5 112213532 112213532 TCGA-KK-A8IA INV 28 16 CCNH EPB41L4A chr5 87414724 87414724 chr5 90624774 90624774 TCGA-KK-A8IA INV 3 35 AC018754.1 ADGRV1 chr5 87422719 87422719 chr5 112213377 112213377 TCGA-KK-A8IA DEL 5 32 AC018754.1 EPB41L4A chr6 101013834 101013841 chr10 44377565 44377583 TCGA-KK-A8IA BND 44 29 * CXCL12 chr6 108293166 108293166 chr6 108293519 108293519 TCGA-KK-A8IA DEL 39 29 * AFG1L chr6 115702386 115702386 chr6 115734023 115734023 TCGA-KK-A8IA DUP 23 27 * * chr6 133996857 133996857 chr6 134691541 134691541 TCGA-KK-A8IA INS 21 10 SLC2A12 * chr6 140072044 140072044 chr6 140075588 140075588 TCGA-KK-A8IA INV 29 21 AL357146.1 AL357146.1 chr6 143289073 143289073 chr6 143898556 143898556 TCGA-KK-A8IA INS 38 14 AIG1 AL049844.3 chr6 15374843 15374843 chr6 15584588 15584588 TCGA-KK-A8IA INS 46 49 JARID2 DTNBP1 chr6 154645746 154645746 chr6 155043179 155043179 TCGA-KK-A8IA INS 13 8 * TIAM2 chr6 18015169 18015169 chr6 19059735 19059735 TCGA-KK-A8IA INS 33 11 * * chr6 2642341 2642341 chr6 46021461 46021461 TCGA-KK-A8IA DEL 8 40 * CLIC5 chr6 46021573 46021573 chr9 97653029 97653029 TCGA-KK-A8IA BND 27 23 CLIC5 NCBP1 chr6 47357895 47357895 chr6 47725907 47725907 TCGA-KK-A8IA INS 7 22 * * chr6 60511987 60511987 chr9 92887928 92887928 TCGA-KK-A8IA BND 36 8 AC244258.1 ANKRD19P chr6 70814548 70814548 chr13 75474062 75474062 TCGA-KK-A8IA BND 48 27 SMAP1 TBC1D4 chr6 8068639 8068639 chr9 97653060 97653060 TCGA-KK-A8IA BND 4 45 EEF1E1-BLOC1S5 NCBP1 chr6 86301361 86301361 chr6 100927917 100927917 TCGA-KK-A8IA DEL 27 24 * * chr6 86560102 86560102 chr9 2081749 2081749 TCGA-KK-A8IA BND 22 1 * SMARCA2 chr7 13782159 13782159 chr7 13951007 13951007 TCGA-KK-A8IA DEL 1 27 * ETV1 chr7 150003941 150003941 chr7 154092964 154092964 TCGA-KK-A8IA DEL 47 14 AC092681.2 DPP6 chr7 150910544 150910545 chr8 141540964 141540964 TCGA-KK-A8IA BND 19 43 * * chr7 31919164 31919164 chr7 34064746 34064746 TCGA-KK-A8IA INV 43 42 PDE1C BMPER chr7 33127982 33127982 chr7 34062351 34062351 TCGA-KK-A8IA INV 39 2 * BMPER chr7 3940351 3940351 chr7 5440872 5440872 TCGA-KK-A8IA INS 46 16 SDK1 FBXL18 chr7 44268064 44268064 chr7 44279942 44279942 TCGA-KK-A8IA DEL 15 29 CAMK2B CAMK2B chr7 78805361 78805361 chr7 79013725 79013725 TCGA-KK-A8IA INS 20 32 MAGI2 MAGI2 chr7 8484757 8484757 chr7 11793713 11793713 TCGA-KK-A8IA INS 21 29 NXPH1 THSD7A chr8 127047074 127047074 chr8 127047449 127047449 TCGA-KK-A8IA INV 24 42 PCAT1 PCAT1 chr8 130017082 130017082 chr20 47063300 47063300 TCGA-KK-A8IA BND 15 21 CYRIB EYA2 chr8 132674063 132674063 chr8 134244063 134244063 TCGA-KK-A8IA DUP 5 33 LRRC6 AC105180.1 chr8 140667778 140667778 chr8 140908324 140908324 TCGA-KK-A8IA DUP 13 29 PTK2 PTK2 chr8 143036257 143036257 chr8 143036626 143036626 TCGA-KK-A8IA INV 38 16 * * chr8 38154480 38154480 chr10 70005146 70005146 TCGA-KK-A8IA BND 26 13 AC084024.3 LINC02636 chr8 41975198 41975198 chr8 69714306 69714306 TCGA-KK-A8IA INV 43 41 KAT6A SLCO5A1 chr8 66752438 66752438 chr8 66753624 66753624 TCGA-KK-A8IA INV 28 25 SGK3 SGK3 chr8 68305340 68305340 chr8 75835452 75835452 TCGA-KK-A8IA INV 34 19 C8orf34-AS1 * chr8 72656100 72656100 chr8 75075487 75075487 TCGA-KK-A8IA DUP 38 10 KCNB2 * chr8 7497830 7497830 chr8 7507336 7507351 TCGA-KK-A8IA INS 44 42 DEFB107B DEFB107B chr8 75320736 75320736 chr22 33971637 33971637 TCGA-KK-A8IA BND 49 5 CASC9 * chr8 75616069 75616069 chr8 78965900 78965900 TCGA-KK-A8IA INV 29 6 * * chr8 80754422 80754422 chr8 82589039 82589039 TCGA-KK-A8IA INS 34 11 ZNF704 AC060765.1 chr9 113644779 113644779 chr9 113645025 113645025 TCGA-KK-A8IA INV 11 19 * * chr9 129892224 129892224 chr9 132441724 132441724 TCGA-KK-A8IA INS 2 12 FNBP1 CFAP77 chr9 13704275 13704275 chr9 16252600 16252601 TCGA-KK-A8IA INS 27 36 * C9orf92 chr9 3295548 3295548 chr9 18255368 18255368 TCGA-KK-A8IA DEL 41 14 RFX3 ADAMTSL1 chr9 41780521 41780521 chr9 61534546 61534546 TCGA-KK-A8IA DEL 13 50 * * chr9 41781071 41781081 chr9 61992944 61992944 TCGA-KK-A8IA DEL 6 41 * * chr9 89022327 89022327 chr9 89022521 89022521 TCGA-KK-A8IA INS 23 17 SHC3 SHC3 chr9 9464483 9464483 chr9 9480729 9480729 TCGA-KK-A8IA DEL 35 20 PTPRD PTPRD chrX 139365832 139365832 chrX 140338847 140338847 TCGA-KK-A8IA DUP 33 5 * * chrX 148539063 148539063 chrX 149324064 149324064 TCGA-KK-A8IA DEL 11 16 AFF2 * chrX 452745 452745 chrX 456334 456334 TCGA-KK-A8IA INV 42 17 * * chrX 8169500 8169500 chrX 8467771 8467771 TCGA-KK-A8IA DUP 13 18 AC079142.1 * chr11 11154897 11154897 chr11 11179450 11179450 TCGA-VN-A88O DEL 12 3 LINC02752 LINC02752 chr11 2796259 2796259 chr11 49917524 49917524 TCGA-VN-A88O INS 38 33 KCNQ1 OR4A18P chr11 49949121 49949121 chr11 55695245 55695245 TCGA-VN-A88O INS 21 27 * * chr11 57916288 57916288 chr11 107278366 107278366 TCGA-VN-A88O INS 5 10 * * chr11 6420715 6420715 chr11 7643633 7643633 TCGA-VN-A88O DEL 36 35 APBB1 PPFIBP2 chr11 9608733 9608733 chr11 55719657 55719657 TCGA-VN-A88O DEL 44 10 * * chr11 9996503 9996503 chr11 111589117 111589117 TCGA-VN-A88O DEL 7 3 SBF2 * chr13 21176522 21176522 chr11 108715021 108715021 TCGA-VN-A88O BND 22 43 SKA3 DDX10 chr15 89103802 89103802 chr15 89372688 89372688 TCGA-VN-A88O INS 15 40 ABHD2 MIR9-3HG chr18 67294508 67294508 chr4 25495975 25495975 TCGA-VN-A88O BND 23 40 * * chr1 107084055 107084055 chr1 107085125 107085125 TCGA-VN-A88O DEL 2 4 * * chr20 15578655 15578655 chr20 15881467 15881467 TCGA-VN-A88O DEL 24 40 MACROD2 MACROD2 chr20 41970891 41970891 chr20 43193962 43193962 TCGA-VN-A88O DEL 45 31 * AL021395.1 chr2 59075665 59075665 chr2 59076428 59076428 TCGA-VN-A88O DEL 40 26 AC007092.1 AC007092.1 chr3 196131562 196131562 chr3 196260857 196260857 TCGA-VN-A88O DEL 6 25 * PCYT1A chr3 5637028 5637028 chr3 5647366 5647366 TCGA-VN-A88O DEL 7 16 * * chr3 79442526 79442526 chr3 80537458 80537458 TCGA-VN-A88O DEL 26 40 ROBO1 * chr3 80154917 80154917 chr3 86874694 86874694 TCGA-VN-A88O DEL 39 4 * * chr4 2599046 2599046 chr4 2724498 2724498 TCGA-VN-A88O INS 16 47 RNF4 FAM193A chr4 29192756 29192756 chr4 29193104 29193104 TCGA-VN-A88O DEL 42 33 AC109349.1 AC109349.1 chr4 48497917 48497917 chr4 48528970 48528970 TCGA-VN-A88O DEL 50 47 FRYL FRYL chr5 102475351 102475351 chr5 104035946 104035946 TCGA-VN-A88O DEL 44 43 SLCO6A1 * chr5 105539108 105539108 chr5 107456312 107456312 TCGA-VN-A88O DEL 50 12 * EFNA5 chr5 163074100 163074100 chr5 169626756 169626756 TCGA-VN-A88O INS 20 8 AC113414.1 * chr5 166494873 166494873 chr5 168152276 168152276 TCGA-VN-A88O INS 20 34 * TENM2 chr5 166795671 166795671 chr7 53550780 53550780 TCGA-VN-A88O BND 5 46 * * chr5 27985333 27985333 chr5 27986494 27986494 TCGA-VN-A88O DEL 12 42 * * chr5 61720501 61720501 chr5 108911209 108911209 TCGA-VN-A88O INS 14 2 C5orf64 FER chr5 63138462 63138462 chr5 83504760 83504760 TCGA-VN-A88O DEL 23 20 * VCAN chr5 63663555 63663555 chr5 82158801 82158801 TCGA-VN-A88O INS 42 8 * ATG10 chr5 63821175 63821175 chr5 63842707 63842707 TCGA-VN-A88O DEL 31 42 * * chr5 63907808 63907808 chr5 105303236 105303236 TCGA-VN-A88O DEL 10 23 * AC099520.1 chr5 81557471 81557471 chr5 109061620 109061620 TCGA-VN-A88O DEL 43 16 SSBP2 FER chr5 81562312 81562312 chr5 82167277 82167277 TCGA-VN-A88O DEL 47 34 SSBP2 ATG10 chr5 81574375 81574375 chr5 109024347 109024347 TCGA-VN-A88O INS 45 48 SSBP2 FER chr5 84396915 84396915 chr5 106504013 106504013 TCGA-VN-A88O DEL 11 42 EDIL3-DT * chr5 84401240 84401240 chr5 106456876 106456876 TCGA-VN-A88O INS 13 21 EDIL3-DT * chr5 84464071 84464071 chr5 85443042 85443042 TCGA-VN-A88O INS 12 37 EDIL3-DT * chr5 85014590 85014590 chr5 85464004 85464004 TCGA-VN-A88O DEL 11 1 * RPL5P17 chr5 90734875 90734875 chr5 95867881 95867881 TCGA-VN-A88O INS 27 13 ADGRV1 AC008592.1 chr5 91311569 91311569 chr5 91344210 91344210 TCGA-VN-A88O DEL 15 44 LUCAT1 * chr5 92211974 92211974 chr5 95822247 95822247 TCGA-VN-A88O INS 27 44 AC114316.1 RHOBTB3 chr5 92443330 92443330 chr5 99177484 99177484 TCGA-VN-A88O DEL 38 22 AC114316.1 * chr5 93146534 93146534 chr5 95198273 95198273 TCGA-VN-A88O INS 16 5 * MCTP1 chr5 94295381 94295381 chr5 102067767 102067767 TCGA-VN-A88O DEL 27 2 KIAA0825 * chr5 94603745 94603745 chr5 95070556 95070556 TCGA-VN-A88O DEL 18 15 KIAA0825 MCTP1 chr5 95117386 95117386 chr5 95219111 95219111 TCGA-VN-A88O DEL 10 44 MCTP1 MCTP1 chr5 95121228 95121228 chr5 99564723 99564723 TCGA-VN-A88O INS 11 28 MCTP1 LINC02113 chr6 2061210 2061210 chr6 2086143 2086143 TCGA-VN-A88O DEL 12 30 GMDS GMDS chr6 77736978 77736978 chr9 29603786 29603786 TCGA-VN-A88O BND 41 16 MEI4 * chr7 122121314 122121314 chr7 127395788 127395788 TCGA-VN-A88O INS 16 8 AASS ZNF800 chr7 122461992 122461992 chr7 122757630 122757630 TCGA-VN-A88O INS 27 25 CADPS2 CADPS2 chr7 125995888 125995888 chr7 126198827 126198827 TCGA-VN-A88O INS 12 20 * * chr7 146720732 146720732 chr7 147040487 147040487 TCGA-VN-A88O DEL 22 23 CNTNAP2 CNTNAP2 chr7 46960478 46960478 chr7 46979526 46979526 TCGA-VN-A88O DEL 48 8 AC004870.4 AC004870.4 chr8 63756857 63756857 chr8 63760513 63760513 TCGA-VN-A88O DEL 9 31 LINC01414 LINC01414 chr9 28042972 28042972 chr6 77298033 77298033 TCGA-VN-A88O BND 40 13 LINGO2 * chr9 29359467 29359467 chr6 78853110 78853110 TCGA-VN-A88O BND 21 38 * * chr10 113718923 113718923 chr10 120868043 120868043 TCGA-V1-A9OX DEL 33 27 CASP7 WDR11 chr10 75081718 75081718 chr10 77044105 77044105 TCGA-V1-A9OX DEL 29 17 * KCNMA1 chr10 89338374 89338374 chr10 89338810 89338810 TCGA-V1-A9OX DEL 24 16 LIPA LIPA chr12 22058413 22058413 chr12 22408256 22408256 TCGA-V1-A9OX DEL 48 18 CMAS ST8SIA1 chr12 81262026 81262027 chr4 124622172 124622189 TCGA-V1-A9OX BND 23 48 PPFIA2 * chr12 85223236 85223236 chr12 85223358 85223358 TCGA-V1-A9OX DEL 47 4 LRRIQ1 LRRIQ1 chr14 103043252 103043253 chr8 143904501 143904502 TCGA-V1-A9OX BND 28 38 CDC42BPB * chr14 54580763 54580764 chr8 106600898 106600899 TCGA-V1-A9OX BND 11 3 SAMD4A OXR1 chr14 54672510 54672519 chr8 136210903 136210912 TCGA-V1-A9OX BND 25 14 SAMD4A LINC02055 chr14 54697110 54697110 chr8 14637735 14637735 TCGA-V1-A9OX BND 44 20 SAMD4A SGCZ chr14 54709091 54709091 chr8 137289296 137289296 TCGA-V1-A9OX BND 3 21 SAMD4A * chr14 54709923 54709923 chr8 62158390 62158390 TCGA-V1-A9OX BND 13 40 SAMD4A * chr14 61378867 61378867 chr8 90636205 90636205 TCGA-V1-A9OX BND 29 12 PRKCH TMEM64 chr14 63310887 63310890 chr8 14242439 14242442 TCGA-V1-A9OX BND 40 11 * SGCZ chr14 72292467 72292467 chr8 59370633 59370633 TCGA-V1-A9OX BND 12 23 RGS6 * chr14 72300739 72300739 chr8 67358742 67358742 TCGA-V1-A9OX BND 21 5 RGS6 * chr14 72337333 72337333 chr8 14263375 14263375 TCGA-V1-A9OX BND 15 41 RGS6 SGCZ chr14 73349831 73349831 chr8 56945932 56945932 TCGA-V1-A9OX BND 42 50 NUMB * chr15 40532674 40532674 chr15 40532769 40532769 TCGA-V1-A9OX DEL 32 9 CCDC32 CCDC32 chr16 30923194 30923194 chr16 30923430 30923430 TCGA-V1-A9OX DEL 40 42 FBXL19 FBXL19 chr16 53477737 53477737 chr16 89241886 89241896 TCGA-V1-A9OX DEL 27 14 RBL2 * chr16 53479115 53479115 chr1 205654991 205654991 TCGA-V1-A9OX BND 47 1 RBL2 * chr16 53757228 53757248 chr1 205655022 205655026 TCGA-V1-A9OX BND 46 10 FTO * chr16 89241886 89241896 chr3 179805239 179805242 TCGA-V1-A9OX BND 32 42 * PEX5L chr1 114469951 114469951 chr1 114470134 114470134 TCGA-V1-A9OX INS 22 47 TRIM33 TRIM33 chr1 205617283 205617283 chr1 205633341 205633341 TCGA-V1-A9OX DEL 13 10 ELK4 ELK4 chr1 205654991 205654991 chr16 53479115 53479115 TCGA-V1-A9OX BND 6 31 * RBL2 chr1 205655022 205655026 chr16 53757228 53757248 TCGA-V1-A9OX BND 5 41 * FTO chr1 205675142 205675147 chr3 179805196 179805201 TCGA-V1-A9OX BND 12 9 SLC45A3 PEX5L chr20 32443514 32443518 chr9 110648391 110648395 TCGA-V1-A9OX BND 49 42 NOL4L * chr20 32444712 32444713 chr8 143900574 143900575 TCGA-V1-A9OX BND 35 13 NOL4L * chr2 33541554 33541554 chr2 33541999 33541999 TCGA-V1-A9OX DEL 12 18 RASGRP3 RASGRP3 chr2 79490557 79490557 chr2 79490650 79490650 TCGA-V1-A9OX DEL 7 22 CTNNA2 CTNNA2 chr3 131028728 131028728 chr3 131031189 131031189 TCGA-V1-A9OX DEL 12 24 ASTE1 NEK11 chr3 170348001 170348001 chr16 53757228 53757248 TCGA-V1-A9OX BND 24 45 AC073288.1 FTO chr3 179805239 179805242 chr16 89241886 89241896 TCGA-V1-A9OX BND 26 32 PEX5L * chr3 18845409 18845409 chr3 19512597 19512597 TCGA-V1-A9OX DEL 6 12 SATB1-AS1 KCNH8 chr3 260878 260878 chr3 19498659 19498659 TCGA-V1-A9OX INS 15 9 CHL1 KCNH8 chr4 124622172 124622189 chr12 81262318 81262318 TCGA-V1-A9OX BND 10 47 * PPFIA2 chr5 120790318 120790318 chr9 73201123 73201123 TCGA-V1-A9OX BND 47 6 AC114284.1 * chr5 95539384 95539384 chr5 95539570 95539570 TCGA-V1-A9OX DEL 4 38 TTC37 TTC37 chr8 106537807 106537807 chr14 72295825 72295825 TCGA-V1-A9OX BND 11 24 OXR1 RGS6 chr8 106600898 106600899 chr14 54580763 54580764 TCGA-V1-A9OX BND 42 23 OXR1 SAMD4A chr8 107505272 107505272 chr8 109594587 109594590 TCGA-V1-A9OX INS 7 28 * SYBU chr8 107558244 107558244 chr14 73337205 73337205 TCGA-V1-A9OX BND 8 1 * NUMB chr8 136210903 136210912 chr14 54672510 54672519 TCGA-V1-A9OX BND 29 32 LINC02055 SAMD4A chr8 14242439 14242442 chr14 63310887 63310890 TCGA-V1-A9OX BND 3 33 SGCZ * chr8 14319975 14319975 chr8 106584647 106584648 TCGA-V1-A9OX DEL 2 49 SGCZ OXR1 chr8 143900574 143900575 chr20 32444712 32444713 TCGA-V1-A9OX BND 19 7 * NOL4L chr8 144409424 144409424 chr9 111273221 111273221 TCGA-V1-A9OX BND 21 15 CPSF1 AL162414.1 chr8 14462675 14462675 chr8 90624754 90624754 TCGA-V1-A9OX INS 20 11 SGCZ TMEM64 chr8 14463964 14463964 chr8 137269998 137269998 TCGA-V1-A9OX DEL 50 39 SGCZ * chr8 14511573 14511574 chr8 59435684 59435684 TCGA-V1-A9OX DEL 8 45 SGCZ * chr8 14521593 14521593 chr8 59420891 59420891 TCGA-V1-A9OX INS 14 3 SGCZ * chr8 14593585 14593585 chr14 54585314 54585314 TCGA-V1-A9OX BND 35 43 SGCZ SAMD4A chr8 14635841 14635842 chr14 63312602 63312603 TCGA-V1-A9OX BND 34 4 SGCZ * chr8 24181974 24181974 chr8 24183981 24183981 TCGA-V1-A9OX DEL 40 48 * * chr8 59411560 59411560 chr8 110390782 110390782 TCGA-V1-A9OX INS 1 24 * * chr8 59445975 59445975 chr8 110355514 110355514 TCGA-V1-A9OX DEL 7 46 * * chr8 62472713 62472713 chr14 54674822 54674822 TCGA-V1-A9OX BND 43 17 NKAIN3 SAMD4A chr8 62489891 62489891 chr14 54591888 54591888 TCGA-V1-A9OX BND 12 46 NKAIN3 SAMD4A chr8 67909083 67909083 chr5 123365085 123365085 TCGA-V1-A9OX BND 42 32 * CEP120 chr8 70152939 70152939 chr9 71464985 71464985 TCGA-V1-A9OX BND 35 30 NCOA2 * chr8 70810705 70810705 chr8 91622621 91622621 TCGA-V1-A9OX INS 15 43 AC015687.1 AC103409.1 chr8 71101090 71101090 chr8 109261768 109261768 TCGA-V1-A9OX INS 15 45 AC015687.1 NUDCD1 chr9 110648075 110648075 chr9 111282299 111282299 TCGA-V1-A9OX DEL 20 50 * AL162414.1 chr9 111272993 111272993 chr20 32443160 32443160 TCGA-V1-A9OX BND 18 27 AL162414.1 NOL4L chr9 38228105 38228105 chr8 30724829 30724829 TCGA-V1-A9OX BND 45 47 * GSR chr9 71464985 71464985 chr8 70152939 70152939 TCGA-V1-A9OX BND 12 11 * NCOA2 chr10 105652746 105652746 chr10 111766127 111766127 TCGA-ZG-A9LB DEL 38 6 * * chr10 10791710 10791710 chr10 107997696 107997696 TCGA-ZG-A9LB DEL 28 48 SFTA1P LINC01435 chr10 109067382 109067382 chr10 111296741 111296741 TCGA-ZG-A9LB DEL 34 25 * * chr10 11592118 11592118 chr10 106127928 106127928 TCGA-ZG-A9LB DEL 7 43 USP6NL * chr10 12902016 12902016 chr10 108130654 108130654 TCGA-ZG-A9LB DEL 15 31 CCDC3 LINC01435 chr10 12905572 12905572 chr10 111765162 111765162 TCGA-ZG-A9LB INS 10 35 CCDC3 * chr10 20814640 20814640 chr7 78972962 78972962 TCGA-ZG-A9LB BND 44 13 NEBL MAGI2 chr10 8902364 8902364 chr10 10814117 10814117 TCGA-ZG-A9LB DEL 24 23 LINC02676 CELF2 chr10 8907884 8907884 chr10 11631463 11631463 TCGA-ZG-A9LB INS 36 1 LINC02676 * chr11 100820811 100820811 chr11 106333812 106333812 TCGA-ZG-A9LB INS 22 10 ARHGAP42 * chr11 101843336 101843336 chr11 106940488 106940488 TCGA-ZG-A9LB DEL 47 2 TRPC6 GUCY1A2 chr11 102411288 102411291 chr11 103737179 103737186 TCGA-ZG-A9LB DEL 23 2 TMEM123 AP002989.1 chr11 102798211 102798211 chr11 105927169 105927169 TCGA-ZG-A9LB DEL 15 12 WTAPP1 GRIA4 chr11 103943057 103943057 chr11 106738462 106738462 TCGA-ZG-A9LB DEL 38 27 PDGFD GUCY1A2 chr11 104429627 104429627 chr11 106761863 106761863 TCGA-ZG-A9LB INS 38 25 * GUCY1A2 chr11 105879693 105879693 chr11 106229414 106229414 TCGA-ZG-A9LB INS 14 31 GRIA4 * chr11 107970889 107970889 chr11 107977686 107977686 TCGA-ZG-A9LB DEL 2 18 * * chr11 108128316 108128316 chr11 110585213 110585213 TCGA-ZG-A9LB DEL 11 15 ACAT1 ARHGAP20 chr11 108663435 108663435 chr11 110194466 110194466 TCGA-ZG-A9LB INS 9 3 * RDX chr11 73100120 73100120 chr11 73779727 73779727 TCGA-ZG-A9LB INS 18 16 FCHSD2 * chr11 9096741 9096741 chr11 9550778 9550778 TCGA-ZG-A9LB INS 39 31 SCUBE2 * chr12 107608905 107608905 chr12 107608984 107608984 TCGA-ZG-A9LB DEL 8 48 BTBD11 BTBD11 chr12 13200142 13200142 chr12 13204060 13204060 TCGA-ZG-A9LB DEL 37 18 EMP1 EMP1 chr12 29225543 29225543 chr12 29683738 29683738 TCGA-ZG-A9LB DEL 45 36 FAR2 TMTC1 chr12 6957364 6957364 chr12 29658059 29658059 TCGA-ZG-A9LB INS 47 28 PTPN6 TMTC1 chr12 7579013 7579013 chr12 29658103 29658103 TCGA-ZG-A9LB DEL 11 2 * TMTC1 chr13 110642335 110642335 chr13 110646954 110646954 TCGA-ZG-A9LB DEL 15 32 CARS2 CARS2 chr13 48018541 48018541 chr13 103443310 103443310 TCGA-ZG-A9LB INS 25 11 SUCLA2 * chr13 56130161 56130161 chr13 80720414 80720414 TCGA-ZG-A9LB DEL 1 17 * * chr13 56136482 56136482 chr13 82476272 82476272 TCGA-ZG-A9LB INS 41 12 * * chr13 61196194 61196194 chr13 61197855 61197855 TCGA-ZG-A9LB DEL 20 14 * * chr13 62069692 62069692 chr13 62071597 62071597 TCGA-ZG-A9LB DEL 32 40 * * chr13 80238181 80238181 chr13 80239639 80239639 TCGA-ZG-A9LB DEL 48 8 * * chr13 80713488 80713488 chr13 82482145 82482145 TCGA-ZG-A9LB DEL 25 6 * * chr14 73079054 73079054 chr14 73080213 73080213 TCGA-ZG-A9LB DEL 33 6 RBM25 RBM25 chr16 61872188 61872188 chr16 61874059 61874059 TCGA-ZG-A9LB DEL 19 44 CDH8 CDH8 chr19 27441600 27441600 chr19 27442081 27442081 TCGA-ZG-A9LB DEL 5 1 * * chr19 28261020 28261020 chr19 28283659 28283659 TCGA-ZG-A9LB DEL 1 31 * * chr1 114244064 114244064 chr6 83908976 83908976 TCGA-ZG-A9LB BND 11 16 AL121999.1 CYB5R4 chr1 157037107 157037107 chr1 157930363 157930363 TCGA-ZG-A9LB DEL 32 27 ARHGEF11 AL139010.1 chr1 192135628 192135628 chr1 192136132 192136132 TCGA-ZG-A9LB DEL 8 34 * * chr1 193046287 193046287 chr1 196852322 196852322 TCGA-ZG-A9LB DEL 33 48 UCHL5 BX248415.1 chr1 205667866 205667866 chr1 228080637 228080637 TCGA-ZG-A9LB INS 23 11 SLC45A3 * chr1 226380858 226380858 chr1 228095751 228095751 TCGA-ZG-A9LB DEL 30 22 PARP1 ARF1 chr1 76052734 76052734 chr1 76062704 76062704 TCGA-ZG-A9LB DEL 15 5 AC092813.2 AC092813.2 chr1 77621459 77621459 chr1 79591803 79591803 TCGA-ZG-A9LB DEL 40 31 ZZZ3 * chr2 128222715 128222715 chr2 128287643 128287643 TCGA-ZG-A9LB DEL 20 16 * HS6ST1 chr2 128331260 128331260 chr2 132562039 132562039 TCGA-ZG-A9LB DEL 32 16 * GPR39 chr2 128939542 128939542 chr2 134385505 134385505 TCGA-ZG-A9LB DEL 39 28 * MGAT5 chr2 129759620 129759620 chr2 129782210 129782210 TCGA-ZG-A9LB DEL 5 42 * * chr2 133189630 133189630 chr2 135225894 135225894 TCGA-ZG-A9LB INS 50 36 NCKAP5 ZRANB3 chr2 134217504 134217504 chr2 134733980 134733980 TCGA-ZG-A9LB DEL 7 49 MGAT5 * chr2 56092556 56092556 chr2 57498543 57498543 TCGA-ZG-A9LB DEL 22 2 AC011306.1 * chr2 89147351 89147351 chr2 134723641 134723641 TCGA-ZG-A9LB INS 21 15 * * chr2 90054592 90054592 chr2 134486045 134486045 TCGA-ZG-A9LB INS 14 41 * TMEM163 chr2 90345452 90345452 chr2 133931668 133931668 TCGA-ZG-A9LB INS 27 44 * * chr2 90355779 90355779 chr2 132726179 132726179 TCGA-ZG-A9LB DEL 10 26 * NCKAP5 chr2 91618987 91618987 chr2 134233323 134233323 TCGA-ZG-A9LB DEL 47 46 LSP1P4 MGAT5 chr2 91633802 91633802 chr2 134151122 134151122 TCGA-ZG-A9LB INS 2 41 LSP1P4 MGAT5 chr3 112200086 112200086 chr3 147434568 147434568 TCGA-ZG-A9LB INS 5 49 SLC9C1 ZIC1 chr3 116011669 116011669 chr3 116012091 116012091 TCGA-ZG-A9LB DEL 16 36 LSAMP LSAMP chr3 146626793 146626793 chr3 147393323 147393323 TCGA-ZG-A9LB DEL 24 22 * ZIC4 chr3 163539620 163539622 chr3 163549894 163549894 TCGA-ZG-A9LB DEL 17 20 * * chr3 163765942 163765942 chr3 165810673 165810673 TCGA-ZG-A9LB DEL 28 17 * BCHE chr3 18894218 18894218 chr3 86383963 86383963 TCGA-ZG-A9LB DEL 15 37 SATB1-AS1 * chr3 20484165 20484165 chr3 21481539 21481539 TCGA-ZG-A9LB INS 36 28 SGO1-AS1 ZNF385D chr3 20504850 20504850 chr3 85955143 85955143 TCGA-ZG-A9LB DEL 5 5 SGO1-AS1 CADM2 chr3 20591615 20591615 chr3 20597140 20597140 TCGA-ZG-A9LB DEL 33 4 SGO1-AS1 SGO1-AS1 chr3 21934255 21934255 chr3 21960522 21960522 TCGA-ZG-A9LB DEL 34 32 ZNF385D ZNF385D chr3 2931849 2931849 chr3 2933167 2933167 TCGA-ZG-A9LB DEL 6 37 CNTN4 CNTN4 chr3 84836563 84836563 chr3 84836818 84836818 TCGA-ZG-A9LB DEL 42 5 LINC00971 LINC00971 chr3 86616699 86616699 chr3 86636866 86636866 TCGA-ZG-A9LB DEL 28 21 * * chr3 96853203 96853203 chr3 96888160 96888160 TCGA-ZG-A9LB DEL 15 1 EPHA6 EPHA6 chr3 96860670 96860670 chr3 96894901 96894901 TCGA-ZG-A9LB DEL 15 35 EPHA6 EPHA6 chr3 96908135 96908135 chr3 146926898 146926898 TCGA-ZG-A9LB DEL 25 4 EPHA6 AC092957.1 chr3 97227249 97227249 chr3 97367944 97367944 TCGA-ZG-A9LB INS 44 17 EPHA6 EPHA6 chr3 97292281 97292281 chr3 111045011 111045011 TCGA-ZG-A9LB DEL 16 11 EPHA6 NECTIN3-AS1 chr3 98057729 98057729 chr3 112181055 112181055 TCGA-ZG-A9LB INS 5 2 * SLC9C1 chr3 98166789 98166789 chr3 98346084 98346084 TCGA-ZG-A9LB DEL 18 48 OR5H15 AC117473.1 chr3 98907615 98907615 chr3 147357118 147357118 TCGA-ZG-A9LB DEL 26 14 AC091212.1 AC092957.1 chr4 112904843 112904843 chr4 112911732 112911732 TCGA-ZG-A9LB DEL 35 45 ANK2 ANK2 chr4 132016198 132016198 chr4 132070599 132070599 TCGA-ZG-A9LB DEL 50 32 AC093916.1 AC093916.1 chr4 136655065 136655065 chr4 138842734 138842734 TCGA-ZG-A9LB INS 15 31 * AC109927.1 chr4 137022596 137022613 chr4 138491967 138491967 TCGA-ZG-A9LB INS 23 37 LINC02511 * chr4 163425079 163425079 chr4 163434401 163434401 TCGA-ZG-A9LB DEL 28 37 * * chr4 166257767 166257767 chr4 166258162 166258162 TCGA-ZG-A9LB DEL 1 21 * * chr4 180548277 180548277 chr4 182722975 182722975 TCGA-ZG-A9LB INS 13 23 * TENM3 chr4 180885245 180885245 chr4 180885348 180885348 TCGA-ZG-A9LB DEL 30 9 * * chr4 180895719 180895719 chr4 181543669 181543669 TCGA-ZG-A9LB INS 20 41 * * chr4 181542709 181542709 chr4 183878628 183878628 TCGA-ZG-A9LB INS 34 16 * STOX2 chr4 181560860 181560860 chr4 183452892 183452892 TCGA-ZG-A9LB INS 31 32 * * chr4 182113859 182113859 chr4 184091937 184091937 TCGA-ZG-A9LB DEL 15 15 TENM3-AS1 ENPP6 chr4 182252617 182252617 chr4 182728744 182728744 TCGA-ZG-A9LB DEL 6 6 TENM3 TENM3 chr4 183070605 183070605 chr4 184085074 184085074 TCGA-ZG-A9LB INS 41 45 * * chr4 42748833 42748833 chr4 45412006 45412006 TCGA-ZG-A9LB DEL 50 26 * * chr4 45382068 45382068 chr4 45730876 45730876 TCGA-ZG-A9LB DEL 32 7 * * chr4 45468553 45468553 chr7 126629049 126629049 TCGA-ZG-A9LB BND 32 46 * GRM8 chr4 45680673 45680677 chr7 126644188 126644192 TCGA-ZG-A9LB BND 6 17 * GRM8 chr4 45761510 45761510 chr7 127555143 127555143 TCGA-ZG-A9LB BND 26 12 * * chr5 12635086 12635086 chr5 160968567 160968567 TCGA-ZG-A9LB DEL 36 24 LINC01194 * chr5 160950069 160950069 chr5 164339241 164339241 TCGA-ZG-A9LB DEL 26 29 * AC109466.1 chr5 162546973 162546973 chr5 162577266 162577266 TCGA-ZG-A9LB DEL 19 20 AC113414.1 AC113414.1 chr5 170149937 170149937 chr4 15824683 15824683 TCGA-ZG-A9LB BND 14 28 * CD38 chr5 25139288 25139288 chr5 26934512 26934512 TCGA-ZG-A9LB DEL 39 21 LINC02228 CDH9 chr5 28122734 28122734 chr5 28124621 28124621 TCGA-ZG-A9LB DEL 1 9 * * chr5 44827298 44827298 chr5 44830729 44830729 TCGA-ZG-A9LB DEL 42 44 AC093297.2 * chr5 50418464 50418464 chr5 82358509 82358509 TCGA-ZG-A9LB INS 17 50 EMB ATP6AP1L chr5 82374259 82374259 chr5 85210776 85210776 TCGA-ZG-A9LB INS 38 47 ATP6AP1L AC117522.3 chr5 84144664 84144664 chr5 84386902 84386902 TCGA-ZG-A9LB DEL 19 43 EDIL3 EDIL3-DT chr5 85316336 85316336 chr5 85326787 85326787 TCGA-ZG-A9LB DEL 28 12 * * chr5 85329342 85329342 chr5 85332858 85332858 TCGA-ZG-A9LB DEL 16 27 * * chr5 90123720 90123720 chr5 90124064 90124064 TCGA-ZG-A9LB DEL 50 36 * * chr5 98599506 98599506 chr5 98602613 98602613 TCGA-ZG-A9LB DEL 35 6 * * chr5 98822606 98822606 chr5 101842513 101842513 TCGA-ZG-A9LB DEL 23 25 * * chr6 120406318 120406318 chr6 120411108 120411108 TCGA-ZG-A9LB DEL 11 26 * * chr6 126271052 126271052 chr6 129137823 129137823 TCGA-ZG-A9LB DEL 50 46 * LAMA2 chr6 126557370 126557370 chr6 126800265 126800265 TCGA-ZG-A9LB DEL 15 20 * * chr6 68476563 68476563 chr6 68477024 68477024 TCGA-ZG-A9LB DEL 22 39 * * chr6 68856616 68856616 chr6 68884285 68884285 TCGA-ZG-A9LB DEL 43 48 ADGRB3 ADGRB3 chr6 71559414 71559414 chr6 72107239 72107239 TCGA-ZG-A9LB DEL 18 48 * RIMS1 chr6 77076080 77076080 chr6 127273352 127273352 TCGA-ZG-A9LB DEL 10 7 * RNF146 chr6 77414604 77414604 chr6 83621993 83621993 TCGA-ZG-A9LB DEL 44 11 * SNAP91 chr6 77435696 77435696 chr6 85215072 85215072 TCGA-ZG-A9LB INS 30 43 * * chr6 78250779 78250779 chr6 86247563 86247563 TCGA-ZG-A9LB DEL 35 19 * * chr6 78400807 78400807 chr6 86314587 86314587 TCGA-ZG-A9LB DEL 43 13 * * chr6 78486704 78486704 chr6 127744141 127744141 TCGA-ZG-A9LB INS 23 45 * THEMIS chr6 83843054 83843054 chr6 86286225 86286225 TCGA-ZG-A9LB INS 25 4 * * chr6 84142759 84142759 chr6 126761127 126761127 TCGA-ZG-A9LB DEL 21 27 CEP162 * chr6 84883084 84883084 chr6 84949152 84949152 TCGA-ZG-A9LB DEL 13 27 * * chr6 85007207 85007207 chr6 126577523 126577523 TCGA-ZG-A9LB DEL 1 7 * * chr6 86094139 86094139 chr6 127257728 127257728 TCGA-ZG-A9LB INS 45 5 * * chr7 123696301 123696301 chr7 123727119 123727119 TCGA-ZG-A9LB DEL 6 9 WASL WASL chr7 124212489 124212489 chr7 124212706 124212706 TCGA-ZG-A9LB DEL 33 13 AC006148.1 AC006148.1 chr7 125014004 125014004 chr7 125027553 125027553 TCGA-ZG-A9LB DEL 47 6 POT1-AS1 POT1-AS1 chr7 126026058 126026059 chr8 47969159 47969160 TCGA-ZG-A9LB BND 15 12 * MCM4 chr7 126353745 126353745 chr7 126362304 126362304 TCGA-ZG-A9LB DEL 24 32 * * chr7 127039672 127039672 chr4 45544237 45544237 TCGA-ZG-A9LB BND 6 13 GRM8 * chr7 127522034 127522035 chr4 46051799 46051800 TCGA-ZG-A9LB BND 30 13 * GABRG1 chr7 50178565 50178565 chr7 50590200 50590200 TCGA-ZG-A9LB DEL 48 5 * GRB10 chr7 57754314 57754314 chr7 57763565 57763565 TCGA-ZG-A9LB DEL 39 28 * * chr7 79099926 79099926 chr7 79101239 79101239 TCGA-ZG-A9LB DEL 26 7 MAGI2 MAGI2 chr7 84209160 84209160 chr7 84213301 84213301 TCGA-ZG-A9LB DEL 30 28 SEMA3A SEMA3A chr7 84247491 84247491 chr7 84249225 84249225 TCGA-ZG-A9LB DEL 7 33 SEMA3A SEMA3A chr7 85837272 85837272 chr7 85838083 85838083 TCGA-ZG-A9LB DEL 31 7 * * chr7 86273663 86273663 chr8 64557668 64557668 TCGA-ZG-A9LB BND 19 49 * * chr7 86274293 86274293 chr7 86436687 86436687 TCGA-ZG-A9LB INS 13 8 * * chr8 113809032 113809032 chr8 117545550 117545550 TCGA-ZG-A9LB DEL 39 19 * * chr8 114529042 114529042 chr8 114530519 114530519 TCGA-ZG-A9LB DEL 42 39 * * chr8 122234799 122234799 chr8 122235665 122235665 TCGA-ZG-A9LB DEL 8 3 * * chr8 13889935 13889935 chr8 14481915 14481915 TCGA-ZG-A9LB DEL 34 50 * SGCZ chr8 15360440 15360440 chr8 35464919 35464919 TCGA-ZG-A9LB INS 43 25 * UNC5D chr8 47810047 47810047 chr4 44304846 44304846 TCGA-ZG-A9LB BND 41 17 PRKDC KCTD8 chr8 47969159 47969160 chr7 126026058 126026059 TCGA-ZG-A9LB BND 3 37 MCM4 * chr8 51894128 51894128 chr8 52189141 52189141 TCGA-ZG-A9LB INS 24 1 PCMTD1 ST18 chr8 5625195 5625195 chr8 5627438 5627438 TCGA-ZG-A9LB DEL 2 49 * * chr8 87449087 87449087 chr8 91685930 91685930 TCGA-ZG-A9LB INS 44 15 CNBD1 AC103409.1 chr8 91646599 91646599 chr8 91653335 91653335 TCGA-ZG-A9LB DEL 33 23 AC103409.1 AC103409.1 chr8 9296601 9296601 chr2 153856249 153856249 TCGA-ZG-A9LB BND 39 22 AC022784.1 * chr9 103567135 103567135 chr9 105320299 105320299 TCGA-ZG-A9LB INS 46 45 * SLC44A1 chr9 103746148 103746148 chr9 105315736 105315736 TCGA-ZG-A9LB INS 5 35 * SLC44A1 chr9 11397852 11397852 chr9 11403922 11403922 TCGA-ZG-A9LB DEL 37 6 * * chr9 9283043 9283043 chr9 9299530 9299530 TCGA-ZG-A9LB DEL 41 5 PTPRD PTPRD chrX 128106426 128106426 chrX 149435254 149435254 TCGA-ZG-A9LB DEL 16 49 * * chrX 128106973 128106973 chrX 148508171 148508171 TCGA-ZG-A9LB INS 25 13 * AFF2 chrX 128507283 128507283 chrX 148485994 148485994 TCGA-ZG-A9LB DEL 28 50 AL008633.1 * chrX 128566324 128566324 chrX 129600136 129600136 TCGA-ZG-A9LB INS 41 36 AL008633.1 * chrX 129598825 129598825 chrX 148052198 148052198 TCGA-ZG-A9LB INS 49 23 * FTH1P8 chrX 147472723 147472723 chrX 148203994 148203994 TCGA-ZG-A9LB DEL 8 8 * * chrX 148182773 148182773 chrX 148494474 148494474 TCGA-ZG-A9LB DEL 7 40 * * chrX 148493332 148493332 chrX 148549187 148549187 TCGA-ZG-A9LB DEL 3 43 * AFF2 chrX 26950297 26950297 chrX 26951019 26951019 TCGA-ZG-A9LB DEL 5 31 * * chrX 83818233 83818233 chrX 89673913 89673913 TCGA-ZG-A9LB DEL 19 30 * * chrX 94473001 94473001 chrX 94475884 94475884 TCGA-ZG-A9LB DEL 9 5 * * chr10 12040313 12040313 chr10 88515683 88515683 TCGA-EJ-5510 DEL 4 16 UPF2 RNLS chr10 38507039 38507039 chr16 51017301 51017301 TCGA-EJ-5510 BND 49 50 * LINC02127 chr10 38507111 38507112 chr16 49842653 49842654 TCGA-EJ-5510 BND 41 41 * ZNF423 chr10 7991618 7991618 chr10 88454089 88454089 TCGA-EJ-5510 DEL 7 17 TAF3 RNLS chr11 84620467 84620467 chr11 84621760 84621760 TCGA-EJ-5510 DEL 28 18 DLG2 DLG2 chr13 92354807 92354807 chr10 88515639 88515639 TCGA-EJ-5510 BND 41 46 GPC5 RNLS chr15 68435348 68435348 chr15 68981088 68981088 TCGA-EJ-5510 DEL 25 5 * NOX5 chr15 70595926 70595926 chr15 70695236 70695236 TCGA-EJ-5510 DEL 31 27 * UACA chr16 49842653 49842654 chr10 38507111 38507112 TCGA-EJ-5510 BND 20 39 ZNF423 * chr16 50793452 50793452 chr16 50814145 50814145 TCGA-EJ-5510 INS 14 9 CYLD * chr16 50797993 50797993 chr16 50806137 50806137 TCGA-EJ-5510 DEL 12 38 CYLD LINC02168 chr16 50798027 50798027 chr16 53491729 53491729 TCGA-EJ-5510 INS 3 40 CYLD AKTIP chr16 50807652 50807652 chr16 50811270 50811270 TCGA-EJ-5510 INS 33 43 * * chr16 50808040 50808040 chr16 50812612 50812612 TCGA-EJ-5510 DEL 27 2 * * chr16 50819656 50819656 chr16 54320215 54320215 TCGA-EJ-5510 INS 36 20 * * chr16 51079425 51079425 chr5 134768300 134768300 TCGA-EJ-5510 BND 31 23 * DDX46 chr16 69578489 69578489 chr10 70203216 70203216 TCGA-EJ-5510 BND 4 27 NFAT5 PPA1 chr16 74433642 74433642 chr8 28440460 28440460 TCGA-EJ-5510 BND 9 49 AC009053.3 FBXO16 chr1 205667192 205667192 chr21 38493340 38493354 TCGA-EJ-5510 BND 50 37 SLC45A3 ERG chr1 42029541 42029541 chr1 55310919 55310919 TCGA-EJ-5510 INS 7 27 HIVEP3 MIR4422HG chr21 38493340 38493354 chr1 205667029 205667029 TCGA-EJ-5510 BND 42 31 ERG SLC45A3 chr22 34710620 34710621 chr6 10442020 10442021 TCGA-EJ-5510 BND 48 34 * MIR5689HG chr2 135045532 135045532 chr2 135069000 135069000 TCGA-EJ-5510 DEL 8 11 MAP3K19 RAB3GAP1 chr2 139384334 139384334 chr2 139386961 139386961 TCGA-EJ-5510 DEL 9 41 * * chr2 169969044 169969044 chr2 169975895 169975895 TCGA-EJ-5510 DEL 49 43 UBR3 UBR3 chr3 69982933 69982933 chr3 73408268 73408268 TCGA-EJ-5510 INS 3 49 * PDZRN3 chr3 73332423 73332423 chr3 73844539 73844539 TCGA-EJ-5510 INS 13 47 * LINC02005 chr6 10442020 10442021 chr22 34710620 34710621 TCGA-EJ-5510 BND 45 36 MIR5689HG * chr6 5633227 5633227 chr6 8099288 8099288 TCGA-EJ-5510 DEL 24 29 FARS2 EEF1E1 chr6 6861975 6861975 chr6 27156849 27156849 TCGA-EJ-5510 INS 43 18 * * chr6 8523528 8523528 chr6 25460067 25460067 TCGA-EJ-5510 DEL 5 19 AL355499.2 CARMIL1 chr7 35631442 35631442 chr7 35631663 35631663 TCGA-EJ-5510 DEL 18 20 * * chr8 28440460 28440460 chr16 74433642 74433642 TCGA-EJ-5510 BND 47 18 FBXO16 AC009053.3 chr8 48926083 48926083 chr8 48926321 48926321 TCGA-EJ-5510 DEL 5 44 * * chr8 48934743 48934743 chr8 102998605 102998605 TCGA-EJ-5510 DEL 41 43 * MAILR chr9 2547341 2547341 chr9 2548437 2548437 TCGA-EJ-5510 DEL 7 19 VLDLR-AS1 VLDLR-AS1 chrX 139217158 139217158 chrX 140110206 140110206 TCGA-EJ-5510 INS 11 21 FGF13 * chr11 40684926 40684926 chr11 40703101 40703101 TCGA-4L-AA1F DEL 19 2 LRRC4C LRRC4C chr11 41310250 41310250 chr11 41312278 41312278 TCGA-4L-AA1F DEL 38 22 LRRC4C LRRC4C chr11 41398809 41398809 chr11 41485646 41485646 TCGA-4L-AA1F DEL 50 45 LRRC4C * chr12 46563262 46563262 chr12 72030728 72030728 TCGA-4L-AA1F DEL 25 47 AC008014.1 TPH2 chr12 47535669 47535669 chr12 74166213 74166213 TCGA-4L-AA1F DEL 8 28 * LINC02882 chr12 72289772 72289772 chr12 82127733 82127733 TCGA-4L-AA1F DEL 48 37 TRHDE * chr12 98599363 98599363 chr12 99120400 99120400 TCGA-4L-AA1F INS 14 3 SLC25A3 ANKS1B chr17 17388755 17388755 chr17 17419341 17419341 TCGA-4L-AA1F INS 11 8 * * chr20 15435603 15435603 chr20 15535141 15535141 TCGA-4L-AA1F DEL 6 36 MACROD2 MACROD2 chr4 177608265 177608265 chr4 177710419 177710419 TCGA-4L-AA1F DEL 27 41 AC078881.1 * chr5 122700377 122700377 chr5 122701176 122701176 TCGA-4L-AA1F DEL 37 39 LINC02201 LINC02201 chr5 2893015 2893015 chr5 2896078 2896078 TCGA-4L-AA1F DEL 4 12 * * chr6 22713316 22713316 chr6 25756594 25756594 TCGA-4L-AA1F DEL 8 28 * SLC17A4 chr6 22719859 22719859 chr6 91571121 91571121 TCGA-4L-AA1F INS 10 12 * * chr6 22756781 22756781 chr6 24387994 24387994 TCGA-4L-AA1F INS 39 19 AL035401.1 * chr6 22782005 22782005 chr6 52848229 52848229 TCGA-4L-AA1F DEL 29 13 AL035401.1 GSTA11P chr6 23406334 23406334 chr6 84361168 84361168 TCGA-4L-AA1F INS 40 48 * * chr6 24397041 24397041 chr6 58425524 58425524 TCGA-4L-AA1F INS 31 50 * AL445250.1 chr6 26115252 26115252 chr6 85334124 85334124 TCGA-4L-AA1F DEL 3 40 H2BC4 * chr6 26151839 26151839 chr6 84380854 84380854 TCGA-4L-AA1F DEL 40 47 * * chr6 48611052 48611052 chr6 86824695 86824695 TCGA-4L-AA1F DEL 13 49 * * chr6 48957432 48957432 chr6 87599464 87599464 TCGA-4L-AA1F INS 22 11 * ORC3 chr6 50399828 50399828 chr6 84788503 84788503 TCGA-4L-AA1F DEL 6 12 * * chr6 50890658 50890658 chr6 84580206 84580206 TCGA-4L-AA1F INS 46 5 * * chr6 51269949 51269949 chr6 89844357 89844357 TCGA-4L-AA1F INS 16 12 * CASP8AP2 chr6 52546770 52546770 chr6 87246467 87246467 TCGA-4L-AA1F DEL 33 46 TRAM2 ZNF292 chr6 52559238 52559238 chr6 55042942 55042942 TCGA-4L-AA1F INS 4 11 TRAM2 * chr6 52613170 52613170 chr6 52615334 52615334 TCGA-4L-AA1F DEL 49 31 * * chr6 52790714 52790714 chr6 82260809 82260811 TCGA-4L-AA1F DEL 30 46 * * chr6 52842697 52842697 chr6 54644001 54644001 TCGA-4L-AA1F DEL 35 3 GSTA5 * chr6 52912723 52912723 chr6 83997529 83997529 TCGA-4L-AA1F INS 50 8 * AL034347.1 chr6 53395424 53395424 chr6 88430665 88430665 TCGA-4L-AA1F INS 29 46 * * chr6 54064144 54064144 chr6 83066158 83066158 TCGA-4L-AA1F INS 19 43 MLIP UBE3D chr6 54106074 54106074 chr6 58451598 58451598 TCGA-4L-AA1F DEL 1 38 MLIP * chr6 54414150 54414150 chr6 87241630 87241630 TCGA-4L-AA1F INS 23 43 * ZNF292 chr6 54510261 54510261 chr6 84587441 84587441 TCGA-4L-AA1F DEL 10 13 * * chr6 54514556 54514556 chr6 85375572 85375572 TCGA-4L-AA1F INS 36 9 * * chr6 55057875 55057875 chr6 58452223 58452229 TCGA-4L-AA1F INS 11 32 * * chr6 58310010 58310010 chr6 80807225 80807225 TCGA-4L-AA1F INS 31 50 AL445250.1 * chr6 58450552 58450552 chr6 60588574 60588574 TCGA-4L-AA1F DEL 35 46 * * chr6 58450575 58450575 chr6 81324750 81324750 TCGA-4L-AA1F INS 50 13 * * chr6 62131711 62131711 chr6 62133916 62133917 TCGA-4L-AA1F DEL 8 49 KHDRBS2 KHDRBS2 chr6 81061757 81061757 chr6 81297357 81297357 TCGA-4L-AA1F DEL 33 5 * * chr6 83459795 83459795 chr6 83824348 83824348 TCGA-4L-AA1F INS 19 35 * * chr6 87614998 87614998 chr6 89883425 89883425 TCGA-4L-AA1F INS 33 29 ORC3 * chr8 13824095 13824095 chr8 26348826 26348826 TCGA-4L-AA1F DEL 8 27 * PPP2R2A chr8 71755223 71755223 chr3 660988 660988 TCGA-4L-AA1F BND 4 28 * LINC01266 chr8 79034879 79034879 chr8 109287953 109287953 TCGA-4L-AA1F DEL 46 17 * NUDCD1 chr9 110128637 110128637 chr9 110128990 110128990 TCGA-4L-AA1F INS 11 9 PALM2AKAP2 PALM2AKAP2 chr9 128668502 128668502 chr9 128908855 128908855 TCGA-4L-AA1F INS 38 23 * LRRC8A chrX 140782639 140782639 chrX 140794082 140794082 TCGA-4L-AA1F DEL 28 16 LINC00632 * chr10 105107730 105107730 chr10 105367136 105367136 TCGA-KK-A6E0 DEL 29 13 SORCS3 * chr10 55748618 55748618 chr10 56893086 56893086 TCGA-KK-A6E0 DEL 8 2 * * chr10 57908483 57908483 chr10 58329768 58329768 TCGA-KK-A6E0 INV 42 29 * * chr10 58039367 58039367 chr10 58345943 58345943 TCGA-KK-A6E0 INV 43 1 * UBE2D1 chr10 87794519 87794519 chr10 88547626 88547626 TCGA-KK-A6E0 DEL 8 29 ATAD1 RNLS chr10 87849888 87849888 chr10 88559876 88559876 TCGA-KK-A6E0 DEL 28 46 * RNLS chr10 87915909 87915909 chr10 87940127 87940127 TCGA-KK-A6E0 DEL 20 20 PTEN PTEN chr11 113912639 113912639 chr11 114318028 114318028 TCGA-KK-A6E0 DUP 26 8 HTR3B AP002518.2 chr11 117324757 117324757 chr11 117778231 117778231 TCGA-KK-A6E0 DUP 39 9 CEP164 DSCAML1 chr11 58021161 58021161 chr11 109311354 109311354 TCGA-KK-A6E0 INS 46 25 * * chr11 58221646 58221646 chr11 101284578 101284578 TCGA-KK-A6E0 INS 16 40 * * chr11 58228391 58228391 chr11 68532858 68532858 TCGA-KK-A6E0 DEL 18 36 OR10Q1 PPP6R3 chr11 58229777 58229777 chr11 68534259 68534259 TCGA-KK-A6E0 INS 18 14 OR10Q1 PPP6R3 chr11 77192800 77192800 chr19 14596035 14596035 TCGA-KK-A6E0 BND 1 28 MYO7A CLEC17A chr11 82743229 82743229 chr11 82744340 82744340 TCGA-KK-A6E0 DEL 49 32 * * chr12 124092633 124092633 chr16 89069175 89069175 TCGA-KK-A6E0 BND 28 28 RFLNA * chr12 39811485 39811485 chr12 41052414 41052414 TCGA-KK-A6E0 INV 5 41 C12orf40 CNTN1 chr12 99613196 99613196 chr12 100607022 100607022 TCGA-KK-A6E0 DUP 8 36 ANKS1B GAS2L3 chr13 37977752 37977752 chr13 38049189 38049189 TCGA-KK-A6E0 DUP 1 41 LINC02334 * chr13 38684788 38684788 chr13 59110970 59110970 TCGA-KK-A6E0 DEL 36 4 * * chr13 38963516 38963516 chr13 86094079 86094079 TCGA-KK-A6E0 INV 19 36 * AL354994.1 chr13 39216728 39216728 chr13 84016089 84016089 TCGA-KK-A6E0 INV 27 38 AL354809.1 * chr13 56476178 56476178 chr13 59114869 59114869 TCGA-KK-A6E0 DEL 13 42 * * chr13 63251769 63251769 chr13 66757377 66757377 TCGA-KK-A6E0 DEL 18 39 LINC00376 PCDH9 chr13 63270673 63270673 chr13 65780048 65780048 TCGA-KK-A6E0 DUP 36 39 LINC00376 * chr13 64419501 64419501 chr13 66359205 66359205 TCGA-KK-A6E0 DEL 44 3 * PCDH9 chr13 64421096 64421096 chr13 64450831 64450831 TCGA-KK-A6E0 INV 42 47 * * chr13 64450591 64450591 chr13 66355990 66355990 TCGA-KK-A6E0 INV 43 37 * PCDH9 chr13 64901690 64901690 chr13 67041628 67041628 TCGA-KK-A6E0 INV 40 39 * PCDH9 chr13 64910827 64910827 chr13 65716896 65716896 TCGA-KK-A6E0 INV 38 16 * * chr13 65134414 65134414 chr13 66307421 66307421 TCGA-KK-A6E0 INV 32 9 * PCDH9 chr13 65782909 65782909 chr13 79091077 79091077 TCGA-KK-A6E0 INV 7 34 * NIPA2P5 chr13 66076256 66076256 chr13 66214910 66214910 TCGA-KK-A6E0 DEL 31 20 * * chr13 66320269 66320269 chr13 66757194 66757194 TCGA-KK-A6E0 DUP 43 50 PCDH9 PCDH9 chr13 84641016 84641016 chr13 86295356 86295356 TCGA-KK-A6E0 DEL 28 24 * * chr13 84647321 84647321 chr13 102078135 102078135 TCGA-KK-A6E0 INV 23 18 * FGF14 chr13 86286659 86286659 chr13 102070936 102070936 TCGA-KK-A6E0 INV 49 50 * FGF14 chr14 105571228 105571228 chr14 105683018 105683018 TCGA-KK-A6E0 DEL 34 19 * * chr14 36632609 36632609 chr14 37632856 37632856 TCGA-KK-A6E0 DUP 44 21 AL132857.1 TTC6 chr14 37520786 37520786 chr14 37589820 37589837 TCGA-KK-A6E0 INV 22 17 MIPOL1 * chr14 37583166 37583166 chr14 38748551 38748551 TCGA-KK-A6E0 DUP 16 49 * * chr14 94363814 94363814 chr14 94380415 94380415 TCGA-KK-A6E0 DUP 4 17 * SERPINA1 chr16 32317944 32317944 chr20 53862851 53862851 TCGA-KK-A6E0 BND 22 6 * * chr16 49946120 49946120 chr16 72635134 72635134 TCGA-KK-A6E0 DEL 19 10 * LINC01572 chr16 79193623 79193623 chr16 79507905 79507905 TCGA-KK-A6E0 DUP 8 20 WWOX AC084064.1 chr17 7671735 7671735 chr12 109215392 109215392 TCGA-KK-A6E0 BND 47 28 TP53 ACACB chr1 103158415 103158415 chr1 103172847 103172847 TCGA-KK-A6E0 DEL 19 12 * * chr1 121371686 121371686 chr5 89899891 89899891 TCGA-KK-A6E0 BND 13 12 SRGAP2C AC113167.1 chr1 143426084 143426084 chr1 143770042 143770042 TCGA-KK-A6E0 DUP 18 41 * * chr1 143496477 143496477 chr1 158956661 158956661 TCGA-KK-A6E0 DEL 19 18 AC239859.4 PYHIN1 chr1 143784963 143784963 chr5 89219557 89219557 TCGA-KK-A6E0 BND 46 26 * MEF2C-AS1 chr1 158493266 158493266 chr1 158524861 158524861 TCGA-KK-A6E0 DEL 6 14 AL365440.1 HSP90AA3P chr1 165475495 165475495 chr1 165475578 165475578 TCGA-KK-A6E0 INV 10 29 * * chr1 187218679 187218679 chr7 15396976 15396976 TCGA-KK-A6E0 BND 3 22 LINC01036 AGMO chr1 187254807 187254807 chr7 12293467 12293467 TCGA-KK-A6E0 BND 36 25 LINC01036 * chr1 188430714 188430714 chr1 189196563 189196563 TCGA-KK-A6E0 DUP 3 1 * * chr1 190872763 190872763 chr1 192051177 192051177 TCGA-KK-A6E0 INV 49 1 * * chr1 190911302 190911302 chr1 193132684 193132684 TCGA-KK-A6E0 DUP 23 11 AL138927.1 CDC73 chr1 190912755 190912755 chr1 194032798 194032798 TCGA-KK-A6E0 INV 43 7 AL138927.1 * chr1 190913037 190913037 chr1 193733536 193733536 TCGA-KK-A6E0 INV 42 46 AL138927.1 * chr1 191298319 191298319 chr1 194378156 194378156 TCGA-KK-A6E0 DEL 30 40 * * chr1 191422976 191422976 chr1 192646622 192646622 TCGA-KK-A6E0 INV 44 37 * AL390957.1 chr1 191978570 191978570 chr1 194342876 194342876 TCGA-KK-A6E0 INV 26 17 LINC02770 * chr1 192022572 192022572 chr1 194195909 194195909 TCGA-KK-A6E0 INV 28 23 * AL136456.1 chr1 192569174 192569174 chr1 193691109 193691109 TCGA-KK-A6E0 DUP 11 40 AL390957.1 AL357793.1 chr1 192629211 192629211 chr1 192790548 192790548 TCGA-KK-A6E0 DEL 11 6 AL390957.1 AL390957.1 chr1 192776621 192776621 chr7 45962236 45962236 TCGA-KK-A6E0 BND 20 50 AL390957.1 * chr1 193225932 193225932 chr1 194097564 194097564 TCGA-KK-A6E0 DUP 14 46 CDC73 * chr1 193483208 193483208 chr1 193583131 193583131 TCGA-KK-A6E0 DEL 48 17 * * chr1 194076006 194076006 chr1 194290474 194290474 TCGA-KK-A6E0 DUP 21 46 * * chr1 194319577 194319577 chr7 13970083 13970083 TCGA-KK-A6E0 BND 3 8 * ETV1 chr1 195920404 195920404 chr5 89060122 89060122 TCGA-KK-A6E0 BND 27 21 * MEF2C-AS1 chr1 195944286 195944286 chr5 90368081 90368081 TCGA-KK-A6E0 BND 12 23 * * chr1 206988242 206988242 chr1 206988455 206988455 TCGA-KK-A6E0 INV 50 7 * * chr1 208290073 208290073 chr1 240034671 240034671 TCGA-KK-A6E0 DEL 8 41 * FMN2 chr1 239747463 239747463 chr1 239751069 239751069 TCGA-KK-A6E0 INS 28 21 CHRM3 CHRM3 chr1 24266028 24266028 chr4 7181885 7181885 TCGA-KK-A6E0 BND 10 2 * * chr1 243793848 243793848 chr2 68295720 68295720 TCGA-KK-A6E0 BND 44 11 AKT3 CNRIP1 chr1 243843630 243843630 chr2 48214708 48214708 TCGA-KK-A6E0 BND 16 44 AKT3 AC092650.1 chr1 246605546 246605546 chr1 246635027 246635027 TCGA-KK-A6E0 DUP 50 34 CNST CNST chr1 48541291 48541291 chr1 49196700 49196700 TCGA-KK-A6E0 DUP 30 26 AGBL4 AGBL4 chr20 35670340 35670340 chr20 35869189 35869189 TCGA-KK-A6E0 DUP 19 30 AL109827.1 PHF20 chr21 38477671 38477671 chr21 41498171 41498171 TCGA-KK-A6E0 DEL 45 47 ERG TMPRSS2 chr21 38511451 38511451 chr21 41505415 41505422 TCGA-KK-A6E0 DEL 23 32 ERG TMPRSS2 chr2 107913622 107913622 chr2 108569160 108569160 TCGA-KK-A6E0 DUP 49 44 RPL22P8 LIMS1 chr2 12201587 12201587 chr2 44624083 44624083 TCGA-KK-A6E0 DEL 28 3 MIR3681HG CAMKMT chr2 12220732 12220732 chr2 14206235 14206235 TCGA-KK-A6E0 INV 9 50 MIR3681HG LINC00276 chr2 122453067 122453067 chr2 122776194 122776194 TCGA-KK-A6E0 DEL 15 2 * * chr2 135061400 135061400 chr2 135073836 135073836 TCGA-KK-A6E0 DEL 49 33 RAB3GAP1 RAB3GAP1 chr2 138001563 138001563 chr2 185334514 185334514 TCGA-KK-A6E0 INV 27 29 HNMT * chr2 14128465 14128465 chr2 53204760 53204760 TCGA-KK-A6E0 INV 32 26 LINC00276 * chr2 14215612 14215612 chr2 68217943 68217943 TCGA-KK-A6E0 INV 11 31 LINC00276 AC017083.3 chr2 143581208 143581208 chr2 184872116 184872116 TCGA-KK-A6E0 INV 12 10 ARHGAP15 ZNF804A chr2 145107021 145107021 chr2 188730531 188730531 TCGA-KK-A6E0 DEL 37 34 TEX41 AC092598.1 chr2 146070229 146070229 chr2 146138956 146138956 TCGA-KK-A6E0 INV 2 15 * * chr2 146081320 146081320 chr2 146154535 146154535 TCGA-KK-A6E0 INV 6 4 * * chr2 146418090 146418090 chr2 146431486 146431486 TCGA-KK-A6E0 DEL 15 17 * * chr2 15860271 15860271 chr2 48178557 48178557 TCGA-KK-A6E0 DUP 20 42 * AC092650.1 chr2 15863905 15863905 chr2 59515248 59515248 TCGA-KK-A6E0 INV 13 28 RNU5E-7P AC007100.1 chr2 15885143 15885143 chr2 45792047 45792047 TCGA-KK-A6E0 DUP 20 45 * PRKCE chr2 16313047 16313047 chr2 59517583 59517583 TCGA-KK-A6E0 DEL 41 37 AC010745.2 AC007100.1 chr2 167322182 167322182 chr2 168666202 168666202 TCGA-KK-A6E0 DEL 42 12 AC073050.1 CERS6 chr2 17438622 17438622 chr2 45823383 45823383 TCGA-KK-A6E0 DEL 1 24 * PRKCE chr2 17462978 17462978 chr2 24859350 24859350 TCGA-KK-A6E0 INV 34 18 * ADCY3 chr2 17649873 17649873 chr15 25591414 25591414 TCGA-KK-A6E0 BND 35 6 VSNL1 * chr2 17702994 17702994 chr2 56518608 56518608 TCGA-KK-A6E0 DUP 48 17 SMC6 * chr2 17708457 17708457 chr2 50800809 50800809 TCGA-KK-A6E0 INV 18 10 SMC6 NRXN1 chr2 17709980 17709980 chr2 24856554 24856554 TCGA-KK-A6E0 DUP 23 45 SMC6 ADCY3 chr2 17868417 17868417 chr2 52917300 52917300 TCGA-KK-A6E0 DEL 28 33 * * chr2 186640209 186640209 chr12 41052460 41052460 TCGA-KK-A6E0 BND 33 33 ITGAV CNTN1 chr2 186642293 186642293 chr12 39819458 39819458 TCGA-KK-A6E0 BND 30 38 ITGAV C12orf40 chr2 199574462 199574462 chr2 199590543 199590543 TCGA-KK-A6E0 DEL 5 7 * * chr2 205437831 205437831 chr2 206058270 206058270 TCGA-KK-A6E0 DUP 9 29 PARD3B INO80D chr2 212482945 212482945 chr2 212549155 212549155 TCGA-KK-A6E0 INV 25 42 ERBB4 * chr2 212531127 212531127 chr2 213310596 213310596 TCGA-KK-A6E0 INV 39 27 ERBB4 SPAG16 chr2 22243200 22243200 chr2 54016083 54016083 TCGA-KK-A6E0 DUP 15 47 AC096570.1 ACYP2 chr2 23269743 23269743 chr2 51927109 51927109 TCGA-KK-A6E0 DEL 14 50 * AC007402.1 chr2 23282144 23282144 chr2 50803663 50803663 TCGA-KK-A6E0 INV 3 13 * NRXN1 chr2 234042354 234042354 chr2 234112371 234112371 TCGA-KK-A6E0 DUP 18 16 * * chr2 23810766 23810766 chr15 23922200 23922200 TCGA-KK-A6E0 BND 5 39 ATAD2B * chr2 23847212 23847212 chr2 59006979 59006979 TCGA-KK-A6E0 DUP 14 38 ATAD2B LINC01122 chr2 241517532 241517532 chr5 11240186 11240186 TCGA-KK-A6E0 BND 35 33 * CTNND2 chr2 2457243 2457243 chr2 40349398 40349398 TCGA-KK-A6E0 INV 6 47 * SLC8A1 chr2 42162604 42162604 chr2 53143512 53143512 TCGA-KK-A6E0 DEL 48 30 EML4-AS1 * chr2 44587864 44587864 chr2 76478518 76478518 TCGA-KK-A6E0 DEL 32 37 CAMKMT * chr2 47045557 47045557 chr2 59072512 59072512 TCGA-KK-A6E0 INV 39 34 TTC7A AC007092.1 chr2 47306022 47306022 chr15 25506317 25506317 TCGA-KK-A6E0 BND 1 15 EPCAM-DT LINC02250 chr2 47624617 47624617 chr2 53875983 53875983 TCGA-KK-A6E0 DUP 24 16 MSH2 PSME4 chr2 51894761 51894761 chr2 57708101 57708101 TCGA-KK-A6E0 DEL 11 36 AC007402.1 * chr2 52234788 52234788 chr2 52850736 52850736 TCGA-KK-A6E0 INV 43 20 AC007402.1 AC010967.1 chr2 52255428 52255428 chr2 64159441 64159441 TCGA-KK-A6E0 INV 10 32 AC007402.1 AC012368.1 chr2 53228315 53228315 chr2 55801196 55801196 TCGA-KK-A6E0 DUP 41 42 * * chr2 53578136 53578136 chr2 57700511 57700511 TCGA-KK-A6E0 INV 37 1 ASB3 * chr2 53627157 53627157 chr2 55640366 55640366 TCGA-KK-A6E0 DUP 8 30 ASB3 PNPT1 chr2 53926945 53926945 chr2 54050875 54050875 TCGA-KK-A6E0 INV 12 24 PSME4 ACYP2 chr2 54757719 54757719 chr2 55655135 55655135 TCGA-KK-A6E0 DEL 41 6 EML6 PNPT1 chr2 55165014 55165014 chr2 55815986 55815986 TCGA-KK-A6E0 INV 46 47 * * chr2 58739873 58739873 chr2 58838816 58838816 TCGA-KK-A6E0 DEL 28 5 LINC01122 LINC01122 chr2 59464508 59464508 chr2 59580775 59580775 TCGA-KK-A6E0 INV 9 47 AC007100.1 AC007100.1 chr2 60728953 60728953 chr2 65859490 65859490 TCGA-KK-A6E0 INV 14 40 * AC007389.1 chr2 60732850 60732850 chr2 68194352 68194352 TCGA-KK-A6E0 INV 44 4 * AC017083.3 chr2 60744072 60744072 chr2 68217721 68217721 TCGA-KK-A6E0 DEL 40 30 * AC017083.3 chr2 60794117 60794117 chr2 76411911 76411911 TCGA-KK-A6E0 DUP 24 44 PAPOLG * chr2 64073243 64073243 chr15 23359114 23359114 TCGA-KK-A6E0 BND 37 19 * GOLGA8S chr2 65831898 65831898 chr15 23919832 23919832 TCGA-KK-A6E0 BND 12 12 AC007389.1 * chr2 68155452 68155452 chr2 68281275 68281275 TCGA-KK-A6E0 INV 35 18 WDR92 * chr2 80349641 80349641 chr2 80366103 80366103 TCGA-KK-A6E0 DEL 44 19 CTNNA2 CTNNA2 chr2 80462005 80462005 chr2 80479698 80479698 TCGA-KK-A6E0 DEL 46 22 CTNNA2 CTNNA2 chr3 107186379 107186379 chr3 107187915 107187915 TCGA-KK-A6E0 DEL 46 23 LINC00882 LINC00882 chr3 153687812 153687812 chr3 154259811 154259811 TCGA-KK-A6E0 DUP 26 44 LINC02006 * chr3 162274092 162274092 chr3 163201327 163201327 TCGA-KK-A6E0 INV 10 9 * AC128685.1 chr3 162285098 162285098 chr3 163202081 163202081 TCGA-KK-A6E0 INV 4 1 * AC128685.1 chr3 164675797 164675797 chr3 166182048 166182048 TCGA-KK-A6E0 INV 9 29 LINC01323 MCUR1P2 chr3 164676853 164676853 chr3 166938690 166938690 TCGA-KK-A6E0 DUP 33 8 LINC01323 * chr3 166191183 166191183 chr3 166942812 166942812 TCGA-KK-A6E0 INV 21 39 * * chr3 167628548 167628548 chr3 167653530 167653530 TCGA-KK-A6E0 DEL 12 18 WDR49 WDR49 chr3 167693457 167693457 chr5 161812186 161812186 TCGA-KK-A6E0 BND 16 6 PDCD10 * chr3 167860233 167860233 chr3 168449059 168449059 TCGA-KK-A6E0 INV 18 30 * EGFEM1P chr3 167943020 167943020 chr3 181592667 181592667 TCGA-KK-A6E0 INV 10 23 * SOX2-OT chr3 168752668 168752668 chr3 182272248 182272248 TCGA-KK-A6E0 INV 24 4 EGFEM1P * chr3 169461178 169461178 chr5 165148297 165148297 TCGA-KK-A6E0 BND 45 3 MECOM AC109466.1 chr3 169462994 169462994 chr5 166369989 166369989 TCGA-KK-A6E0 BND 41 30 MECOM * chr3 169683008 169683008 chr5 164338035 164338035 TCGA-KK-A6E0 BND 22 47 * AC109466.1 chr3 181589246 181589246 chr3 181882733 181882733 TCGA-KK-A6E0 DEL 36 26 SOX2-OT * chr3 181823185 181823185 chr3 182174644 182174644 TCGA-KK-A6E0 INV 19 31 SOX2-OT * chr3 185665482 185665482 chr12 126832317 126832317 TCGA-KK-A6E0 BND 3 23 IGF2BP2 * chr3 192567910 192567910 chr3 192590882 192590882 TCGA-KK-A6E0 DEL 30 28 FGF12 FGF12 chr3 69569445 69569445 chr3 69571978 69571978 TCGA-KK-A6E0 DEL 40 45 AC099328.2 AC099328.2 chr3 75460860 75460860 chr3 75570890 75570890 TCGA-KK-A6E0 DUP 35 43 ENPP7P2 AC133041.1 chr3 84463085 84463085 chr3 84706544 84706544 TCGA-KK-A6E0 DEL 1 37 * LINC00971 chr3 84684493 84684493 chr3 86205819 86205819 TCGA-KK-A6E0 INV 11 18 LINC00971 * chr3 94303211 94303211 chr3 94316134 94316134 TCGA-KK-A6E0 DEL 43 28 * * chr3 97159535 97159535 chr3 97577601 97577601 TCGA-KK-A6E0 DEL 36 29 EPHA6 EPHA6 chr4 101176587 101176587 chr4 101364983 101364983 TCGA-KK-A6E0 DUP 31 17 PPP3CA * chr4 115469487 115469487 chr4 117346829 117346829 TCGA-KK-A6E0 DUP 48 14 * LINC02262 chr4 129973506 129973506 chrX 28044678 28044678 TCGA-KK-A6E0 BND 23 23 * * chr4 129973886 129973886 chrX 27567095 27567098 TCGA-KK-A6E0 BND 29 40 * * chr4 170092534 170092534 chr4 170975489 170975489 TCGA-KK-A6E0 DEL 33 12 AADAT * chr4 170127146 170127146 chr4 170959972 170959972 TCGA-KK-A6E0 DUP 31 15 * * chr4 170867685 170867685 chr4 171705777 171705778 TCGA-KK-A6E0 INV 4 50 * * chr4 170868284 170868284 chr4 171726374 171726374 TCGA-KK-A6E0 DUP 31 48 * * chr4 171705777 171705778 chr4 171730672 171730672 TCGA-KK-A6E0 INV 39 19 * * chr4 26684107 26684107 chr4 30053868 30053868 TCGA-KK-A6E0 DUP 33 14 TBC1D19 * chr4 62681463 62681463 chr4 97696116 97696116 TCGA-KK-A6E0 INV 36 40 * STPG2 chr4 67849046 67849046 chr4 98017870 98017870 TCGA-KK-A6E0 INV 37 8 UBA6-AS1 STPG2 chr4 68580554 68580554 chr4 68675958 68675958 TCGA-KK-A6E0 DUP 4 18 * * chr5 110801014 110801014 chr5 112409849 112409849 TCGA-KK-A6E0 INV 37 5 * EPB41L4A chr5 110939281 110939281 chr5 113170267 113170267 TCGA-KK-A6E0 INV 5 36 * MCC chr5 110939571 110939571 chr5 111513243 111513243 TCGA-KK-A6E0 INV 8 50 * STARD4 chr5 130250767 130250767 chr5 130756484 130756484 TCGA-KK-A6E0 DEL 20 38 * * chr5 15435849 15435849 chr5 18536682 18536682 TCGA-KK-A6E0 DEL 16 5 * * chr5 15563274 15563274 chr7 147944785 147944785 TCGA-KK-A6E0 BND 15 19 FBXL7 CNTNAP2 chr5 161786477 161786477 chr5 164339564 164339564 TCGA-KK-A6E0 DEL 18 20 * AC109466.1 chr5 162844995 162844995 chr5 164130584 164130584 TCGA-KK-A6E0 DEL 49 40 AC113414.1 AC008662.1 chr5 164377645 164377645 chr5 165132728 165132728 TCGA-KK-A6E0 DEL 28 28 AC109466.1 AC109466.1 chr5 164573543 164573543 chr5 166404622 166404622 TCGA-KK-A6E0 INV 3 12 AC109466.1 * chr5 164590558 164590558 chr5 167970274 167970274 TCGA-KK-A6E0 INV 46 44 AC109466.1 TENM2 chr5 165147513 165147513 chr5 166370199 166370199 TCGA-KK-A6E0 DEL 14 6 AC109466.1 * chr5 16599933 16599933 chr7 123362520 123362520 TCGA-KK-A6E0 BND 41 42 RETREG1 * chr5 16635544 16635544 chr7 127129549 127129549 TCGA-KK-A6E0 BND 7 37 * GRM8 chr5 167234732 167234732 chr5 167262209 167262209 TCGA-KK-A6E0 DEL 16 25 * * chr5 16802388 16802388 chr7 145682683 145682683 TCGA-KK-A6E0 BND 38 10 MYO10 AC006007.1 chr5 16802519 16802519 chr7 149091375 149091375 TCGA-KK-A6E0 BND 1 36 MYO10 ZNF786 chr5 16813141 16813141 chr7 149229114 149229114 TCGA-KK-A6E0 BND 50 31 MYO10 * chr5 16814280 16814280 chr7 149019673 149019673 TCGA-KK-A6E0 BND 42 7 MYO10 PDIA4 chr5 17108978 17108978 chr7 124033254 124033254 TCGA-KK-A6E0 BND 34 5 BASP1 TMEM229A chr5 17158531 17158531 chr7 124035836 124035836 TCGA-KK-A6E0 BND 27 24 BASP1 AC006148.1 chr5 17370057 17370057 chr5 18232938 18232938 TCGA-KK-A6E0 INV 47 43 AC026785.3 * chr5 17422691 17422691 chr7 144918166 144918166 TCGA-KK-A6E0 BND 44 30 LINC02217 * chr5 17455204 17455204 chr7 149051001 149051001 TCGA-KK-A6E0 BND 3 21 LINC02218 * chr5 175918735 175918735 chr5 177960348 177960348 TCGA-KK-A6E0 DUP 17 18 THOC3 AC106795.3 chr5 17764163 17764163 chr7 127166617 127166617 TCGA-KK-A6E0 BND 14 22 LINC02223 GRM8 chr5 17767591 17767591 chr7 122857223 122857223 TCGA-KK-A6E0 BND 33 39 LINC02223 CADPS2 chr5 18172603 18172603 chr7 145668086 145668086 TCGA-KK-A6E0 BND 36 44 * * chr5 18428177 18428177 chr7 122100481 122100481 TCGA-KK-A6E0 BND 31 39 * AASS chr5 18496210 18496210 chr7 127359003 127359003 TCGA-KK-A6E0 BND 46 3 * ZNF800 chr5 18532750 18532750 chr7 123234560 123234561 TCGA-KK-A6E0 BND 20 12 * * chr5 19048587 19048587 chr5 19082889 19082889 TCGA-KK-A6E0 DEL 37 40 AC106744.1 AC106744.1 chr5 60348221 60348221 chr5 60978015 60978015 TCGA-KK-A6E0 DUP 22 13 PDE4D NDUFAF2 chr5 62708174 62708174 chr5 99467569 99467569 TCGA-KK-A6E0 INV 27 40 * * chr5 63678131 63678131 chr5 64345717 64345717 TCGA-KK-A6E0 INV 27 27 * RNF180 chr5 63679427 63679427 chr5 99434331 99434331 TCGA-KK-A6E0 DEL 26 22 * * chr5 63713164 63713164 chr5 64461155 64461155 TCGA-KK-A6E0 INV 17 14 * AC091862.1 chr5 64345973 64345973 chr5 99435626 99435626 TCGA-KK-A6E0 INV 42 24 RNF180 * chr5 64629830 64629830 chr5 99128054 99128054 TCGA-KK-A6E0 INV 24 40 * * chr5 81602271 81602271 chr5 112687333 112687333 TCGA-KK-A6E0 INV 20 5 SSBP2 * chr5 81630240 81630240 chr5 99167542 99167542 TCGA-KK-A6E0 INV 47 34 SSBP2 * chr5 82370265 82370265 chr5 112621951 112621951 TCGA-KK-A6E0 DEL 11 13 ATP6AP1L * chr5 83919157 83919157 chr5 112708025 112708025 TCGA-KK-A6E0 INV 25 21 * APC chr5 84345872 84345872 chr5 112375013 112375013 TCGA-KK-A6E0 INV 27 37 EDIL3 EPB41L4A chr5 84401966 84401966 chr5 110785752 110785752 TCGA-KK-A6E0 DUP 1 35 EDIL3-DT * chr5 84586277 84586277 chr5 112587397 112587397 TCGA-KK-A6E0 INV 15 10 * * chr5 86024653 86024653 chr5 86039564 86039564 TCGA-KK-A6E0 DEL 26 13 * * chr5 87520337 87520337 chr5 113172577 113172577 TCGA-KK-A6E0 INV 3 40 * MCC chr5 87936973 87936973 chr5 88745983 88745983 TCGA-KK-A6E0 INV 45 43 * MEF2C chr5 88691236 88691236 chr5 111489676 111489676 TCGA-KK-A6E0 DUP 5 28 LINC00461 CAMK4 chr5 88840826 88840826 chr5 97592113 97592113 TCGA-KK-A6E0 DUP 6 47 MEF2C LINC01340 chr5 89120034 89120034 chr5 97730684 97730684 TCGA-KK-A6E0 DUP 23 29 MEF2C-AS1 * chr5 89279081 89279081 chr5 89995042 89995042 TCGA-KK-A6E0 INV 6 1 MEF2C-AS1 * chr5 89709362 89709362 chr5 89793476 89793476 TCGA-KK-A6E0 DEL 46 37 * * chr5 90492234 90492234 chr5 99272189 99272189 TCGA-KK-A6E0 INV 1 45 POLR3G * chr5 97174309 97174309 chr5 99244408 99244408 TCGA-KK-A6E0 INV 8 1 LIX1-AS1 * chr5 97208473 97208473 chr5 97627666 97627666 TCGA-KK-A6E0 INV 20 27 LIX1-AS1 LINC01340 chr5 98907474 98907474 chr5 99052728 99052728 TCGA-KK-A6E0 DEL 7 10 CHD1 * chr6 125430651 125430651 chr22 28669977 28669987 TCGA-KK-A6E0 BND 48 18 AL450332.1 TTC28 chr6 161178370 161178370 chr6 161909005 161909005 TCGA-KK-A6E0 DUP 43 10 AGPAT4 PRKN chr6 32486351 32486351 chr6 32572370 32572370 TCGA-KK-A6E0 DUP 10 1 * * chr6 76629933 76629933 chr6 83855539 83855539 TCGA-KK-A6E0 DEL 39 25 * RIPPLY2 chr6 84632154 84632154 chr6 124940400 124940400 TCGA-KK-A6E0 DEL 27 20 * RNF217-AS1 chr6 98878152 98878152 chr6 98891115 98891115 TCGA-KK-A6E0 DEL 46 7 FBXL4 FBXL4 chr7 122224778 122224778 chr7 126291084 126291084 TCGA-KK-A6E0 INV 25 30 * * chr7 122341000 122341000 chr7 147928123 147928123 TCGA-KK-A6E0 DUP 29 7 CADPS2 CNTNAP2 chr7 122341226 122341226 chr7 148156258 148156258 TCGA-KK-A6E0 INV 38 46 CADPS2 CNTNAP2 chr7 122386782 122386782 chr7 149262513 149262513 TCGA-KK-A6E0 INV 15 22 CADPS2 ZNF783 chr7 122402693 122402693 chr7 126554958 126554958 TCGA-KK-A6E0 DUP 6 29 CADPS2 GRM8 chr7 122549230 122549230 chr7 122766254 122766254 TCGA-KK-A6E0 DUP 12 19 CADPS2 CADPS2 chr7 122559695 122559695 chr7 125905176 125905176 TCGA-KK-A6E0 DEL 1 18 CADPS2 * chr7 122562711 122562711 chr7 147448543 147448543 TCGA-KK-A6E0 DUP 40 41 CADPS2 CNTNAP2 chr7 122932619 122932619 chr7 123224440 123224440 TCGA-KK-A6E0 DUP 23 15 * * chr7 122994299 122994299 chr7 125610534 125610534 TCGA-KK-A6E0 INV 8 29 * * chr7 122999906 122999906 chr7 125419797 125419797 TCGA-KK-A6E0 DUP 46 46 * * chr7 123074414 123074414 chr7 123301263 123301263 TCGA-KK-A6E0 INV 28 33 AC073311.1 * chr7 123129799 123129799 chr7 149387241 149387241 TCGA-KK-A6E0 INV 33 33 SLC13A1 * chr7 123254537 123254537 chr7 126257713 126257713 TCGA-KK-A6E0 INV 2 21 * * chr7 123259892 123259892 chr7 126569668 126569668 TCGA-KK-A6E0 INV 41 22 * GRM8 chr7 12328399 12328399 chr7 13996183 13996183 TCGA-KK-A6E0 INV 2 17 * * chr7 123358353 123358353 chr7 149230568 149230568 TCGA-KK-A6E0 DUP 46 6 * * chr7 123520797 123520797 chr7 127344047 127344047 TCGA-KK-A6E0 INV 48 16 IQUB * chr7 123607592 123607592 chr7 126080141 126080141 TCGA-KK-A6E0 INV 17 9 ASB15 * chr7 124256972 124256972 chr7 148252911 148252911 TCGA-KK-A6E0 DEL 13 38 AC006148.1 CNTNAP2 chr7 124275252 124275252 chr7 146702317 146702317 TCGA-KK-A6E0 DUP 7 27 AC006148.1 CNTNAP2 chr7 124336906 124336906 chr7 148207244 148207244 TCGA-KK-A6E0 INV 23 30 AC006148.1 CNTNAP2 chr7 124348213 124348213 chr7 126732721 126732721 TCGA-KK-A6E0 DUP 32 14 AC006148.1 GRM8 chr7 124760693 124760693 chr7 149235918 149235918 TCGA-KK-A6E0 DEL 34 50 GPR37 * chr7 124954202 124954202 chr7 146267522 146267522 TCGA-KK-A6E0 INV 23 35 POT1-AS1 CNTNAP2 chr7 125258362 125258362 chr7 147993433 147993433 TCGA-KK-A6E0 DEL 49 6 AC019155.2 CNTNAP2 chr7 125272176 125272176 chr7 127625659 127625659 TCGA-KK-A6E0 INV 20 5 * * chr7 125423230 125423230 chr7 146738329 146738329 TCGA-KK-A6E0 INV 49 14 * CNTNAP2 chr7 126024739 126024739 chr7 147302314 147302314 TCGA-KK-A6E0 INV 6 24 * CNTNAP2 chr7 126775106 126775106 chr7 126962961 126962961 TCGA-KK-A6E0 INV 35 38 GRM8 GRM8 chr7 126960440 126960440 chr7 127573344 127573344 TCGA-KK-A6E0 INV 23 15 GRM8 * chr7 128104395 128104395 chr7 128154474 128154474 TCGA-KK-A6E0 DEL 50 17 * * chr7 128305184 128305184 chr7 149977744 149977744 TCGA-KK-A6E0 DUP 7 24 RBM28 * chr7 128465956 128465956 chr7 144546139 144546139 TCGA-KK-A6E0 INV 38 11 AC010655.4 TPK1 chr7 128488066 128488066 chr7 150018313 150018313 TCGA-KK-A6E0 INV 22 16 AC010655.4 * chr7 144598854 144598854 chr7 149716181 149716181 TCGA-KK-A6E0 INV 38 10 TPK1 KRBA1 chr7 145036518 145036518 chr7 147770912 147770912 TCGA-KK-A6E0 DEL 4 8 * CNTNAP2 chr7 145051998 145051998 chr7 147968454 147968454 TCGA-KK-A6E0 DUP 43 24 * CNTNAP2 chr7 145701027 145701027 chr7 147064955 147064955 TCGA-KK-A6E0 INV 39 39 * CNTNAP2 chr7 145776952 145776952 chr7 148794888 148794888 TCGA-KK-A6E0 DUP 43 12 * CUL1 chr7 146227784 146227784 chr7 147071914 147071914 TCGA-KK-A6E0 DEL 25 21 CNTNAP2 CNTNAP2 chr7 147307141 147307141 chr7 147880232 147880232 TCGA-KK-A6E0 DUP 30 47 CNTNAP2 CNTNAP2 chr7 149093944 149093944 chr7 149597654 149597654 TCGA-KK-A6E0 DUP 23 2 * ZNF767P chr7 149106652 149106652 chr7 149187169 149187169 TCGA-KK-A6E0 INV 22 41 ZNF425 * chr7 15406876 15406876 chr7 45973797 45973797 TCGA-KK-A6E0 INV 24 25 AGMO AC073115.2 chr7 37830261 37830261 chr7 37830416 37830416 TCGA-KK-A6E0 INV 10 19 GPR141 GPR141 chr7 49039600 49039600 chr7 50035252 50035252 TCGA-KK-A6E0 DEL 3 39 * ZPBP chr7 49076176 49076176 chr7 50530202 50530202 TCGA-KK-A6E0 INV 4 15 * FIGNL1 chr7 50034818 50034818 chr7 50374919 50374919 TCGA-KK-A6E0 DEL 6 24 ZPBP IKZF1 chr7 50314407 50314407 chr7 50527846 50527846 TCGA-KK-A6E0 DUP 42 38 IKZF1 FIGNL1 chr7 50350475 50350475 chr7 50528849 50528849 TCGA-KK-A6E0 INV 25 4 IKZF1 FIGNL1 chr7 53016929 53016929 chr7 53028965 53028965 TCGA-KK-A6E0 DEL 17 49 * * chr7 53496083 53496083 chr7 121636870 121636870 TCGA-KK-A6E0 INV 1 41 * * chr7 53497603 53497603 chr7 123234560 123234561 TCGA-KK-A6E0 DEL 23 3 * * chr7 53570510 53570510 chr7 121643712 121643712 TCGA-KK-A6E0 INV 5 10 * AC004875.1 chr7 79268518 79268518 chr7 79287253 79287253 TCGA-KK-A6E0 DEL 37 47 MAGI2 MAGI2 chr7 82109174 82109174 chr7 82180020 82180020 TCGA-KK-A6E0 DUP 4 36 CACNA2D1 CACNA2D1 chr7 87975750 87975750 chr7 91554753 91554753 TCGA-KK-A6E0 DEL 39 29 ADAM22 AC079760.1 chr7 95770681 95770681 chr7 95770784 95770784 TCGA-KK-A6E0 INV 12 23 * * chr7 98337760 98337760 chr7 98337974 98337974 TCGA-KK-A6E0 INV 9 38 BAIAP2L1 BAIAP2L1 chr8 104579051 104579051 chr8 105767930 105767930 TCGA-KK-A6E0 DEL 28 3 LRP12 ZFPM2 chr8 105892006 105892006 chr8 137832077 137832077 TCGA-KK-A6E0 INV 32 40 ZFPM2-AS1 AC046195.1 chr8 105893128 105893128 chr8 110092414 110092414 TCGA-KK-A6E0 INV 27 23 ZFPM2-AS1 * chr8 105913831 105913831 chr8 136371394 136371394 TCGA-KK-A6E0 DUP 18 4 ZFPM2-AS1 LINC02055 chr8 108059860 108059860 chr8 110101946 110101946 TCGA-KK-A6E0 DEL 33 26 RSPO2 * chr8 108844859 108844859 chr8 113451552 113451552 TCGA-KK-A6E0 INV 48 3 * * chr8 110036612 110036612 chr8 113422202 113422202 TCGA-KK-A6E0 INV 29 4 * CSMD3 chr8 110042071 110042071 chr8 137833570 137833570 TCGA-KK-A6E0 DUP 13 41 * AC046195.1 chr8 113734393 113734393 chr8 113756888 113756888 TCGA-KK-A6E0 DEL 14 2 * * chr8 114128578 114128578 chr8 139057088 139057088 TCGA-KK-A6E0 DEL 17 32 * * chr8 114129791 114129791 chr8 138177048 138177048 TCGA-KK-A6E0 DUP 10 47 * FAM135B chr8 136376448 136376448 chr8 137833659 137833659 TCGA-KK-A6E0 INV 1 28 LINC02055 AC046195.1 chr8 13725111 13725111 chr8 14006111 14006111 TCGA-KK-A6E0 INV 1 12 * * chr8 137282952 137282952 chr15 39159215 39159215 TCGA-KK-A6E0 BND 28 1 * LINC02694 chr8 13881191 13881191 chr8 32219230 32219230 TCGA-KK-A6E0 INV 6 32 * NRG1 chr8 142937465 142937465 chr12 2720779 2720796 TCGA-KK-A6E0 BND 14 26 * ITFG2-AS1 chr8 3115866 3115866 chr18 33567819 33567819 TCGA-KK-A6E0 BND 2 30 CSMD1 AC091198.1 chr8 3126792 3126792 chr18 33681209 33681209 TCGA-KK-A6E0 BND 26 20 CSMD1 ASXL3 chr8 5155153 5155153 chr8 14067484 14067484 TCGA-KK-A6E0 DEL 17 12 * * chr8 6273035 6273035 chr8 13605023 13605023 TCGA-KK-A6E0 INV 6 24 * DLC1 chr8 6291654 6291654 chr8 14210754 14210754 TCGA-KK-A6E0 INV 6 43 * SGCZ chr8 67162728 67162728 chr8 68004334 68004334 TCGA-KK-A6E0 DUP 43 26 CSPP1 PREX2 chr8 96427056 96427056 chr8 97510483 97510483 TCGA-KK-A6E0 DEL 15 8 * * chr9 61534668 61534668 chr9 61991964 61991972 TCGA-KK-A6E0 DEL 17 14 * * chr9 79249309 79249309 chr9 79374954 79374954 TCGA-KK-A6E0 DEL 42 10 * * chr9 90631994 90631994 chr9 91216219 91216219 TCGA-KK-A6E0 DUP 18 46 DIRAS2 AUH chr9 97820033 97820033 chr9 99484895 99484895 TCGA-KK-A6E0 DUP 29 38 PTCSC2 * chr9 9794784 9794784 chr9 9827254 9827254 TCGA-KK-A6E0 DEL 16 10 PTPRD PTPRD chrX 27567095 27567098 chrX 28054125 28054125 TCGA-KK-A6E0 DEL 29 1 * * chrX 45086710 45086710 chrX 45102281 45102281 TCGA-KK-A6E0 DEL 17 45 KDM6A KDM6A chr10 107584716 107584716 chr18 77273961 77273961 TCGA-G9-6333 BND 2 17 * GALR1 chr10 107851786 107851786 chr18 77309564 77309564 TCGA-G9-6333 BND 50 44 LINC01435 * chr10 107869929 107869929 chr18 77582262 77582262 TCGA-G9-6333 BND 4 25 LINC01435 * chr10 124749421 124749421 chr10 128273264 128273264 TCGA-G9-6333 INV 34 25 AC068896.1 LINC01163 chr10 124749453 124749454 chr10 125684983 125684990 TCGA-G9-6333 INV 38 1 AC068896.1 AL158835.1 chr10 49117551 49117551 chr10 49151937 49151937 TCGA-G9-6333 DEL 26 20 * * chr10 62291390 62291393 chr5 4689807 4689810 TCGA-G9-6333 BND 30 9 LINC02621 AC106799.2 chr10 66821356 66821356 chr10 67274015 67274015 TCGA-G9-6333 DUP 8 5 CTNNA3 CTNNA3 chr10 87779206 87779206 chr10 88587225 88587225 TCGA-G9-6333 DEL 23 1 ATAD1 LIPJ chr10 87858924 87858924 chr10 128267116 128267116 TCGA-G9-6333 INV 20 31 * LINC01163 chr10 89213704 89213704 chr10 132775125 132775125 TCGA-G9-6333 INV 39 31 LIPA INPP5A chr10 95824702 95824707 chr5 4670666 4670671 TCGA-G9-6333 BND 47 12 ENTPD1 AC106799.2 chr11 47525466 47525466 chr11 47797163 47797163 TCGA-G9-6333 INV 19 3 CELF1 NUP160 chr11 69969261 69969261 chr11 69992565 69992565 TCGA-G9-6333 DEL 8 40 * AP003555.2 chr11 76097864 76097864 chr11 108253014 108253014 TCGA-G9-6333 INV 9 44 UVRAG ATM chr12 11068767 11068767 chr12 11098150 11098166 TCGA-G9-6333 DEL 48 14 PRH1 PRH1 chr12 111077402 111077402 chr12 111077524 111077524 TCGA-G9-6333 INV 49 23 CUX2 CUX2 chr12 118691918 118691918 chr12 118692133 118692133 TCGA-G9-6333 INV 10 25 * * chr12 12985435 12985435 chr12 20616062 20616062 TCGA-G9-6333 INS 45 47 HEBP1 PDE3A chr12 40185998 40185998 chr12 40340822 40340822 TCGA-G9-6333 DEL 43 47 LINC02471 LRRK2 chr12 40333740 40333740 chr12 60283637 60283637 TCGA-G9-6333 DEL 29 34 LRRK2 * chr12 58455508 58455508 chr12 58497776 58497776 TCGA-G9-6333 DEL 39 44 * * chr12 59445537 59445537 chr12 59524041 59524041 TCGA-G9-6333 DEL 26 48 * LINC02448 chr12 60284138 60284138 chr12 60285011 60285011 TCGA-G9-6333 DEL 37 36 * * chr12 60862 60862 chr20 64332664 64332664 TCGA-G9-6333 BND 48 45 * * chr13 110052322 110052322 chr18 10057595 10057595 TCGA-G9-6333 BND 12 18 AL390755.1 * chr13 46541959 46541959 chr13 46714831 46714837 TCGA-G9-6333 INS 9 29 * LRCH1 chr13 47026682 47026682 chr13 47077165 47077165 TCGA-G9-6333 INS 36 8 * * chr13 47027501 47027501 chr13 66869653 66869653 TCGA-G9-6333 DEL 3 12 * PCDH9 chr13 47513365 47513365 chr13 47675069 47675069 TCGA-G9-6333 DEL 30 46 * * chr13 47676394 47676394 chr13 64036448 64036448 TCGA-G9-6333 DEL 27 29 * LINC00355 chr13 47807801 47807801 chr13 67353265 67353265 TCGA-G9-6333 INS 49 30 SUCLA2 * chr13 48122805 48122805 chr13 57330536 57330536 TCGA-G9-6333 DEL 41 7 * * chr13 48238458 48238458 chr13 68098375 68098375 TCGA-G9-6333 DEL 42 32 ITM2B * chr13 57348445 57348445 chr13 57608012 57608012 TCGA-G9-6333 INS 13 44 * * chr13 58017383 58017383 chr13 59133438 59133438 TCGA-G9-6333 INS 25 33 * * chr13 58280538 58280538 chr13 64037792 64037792 TCGA-G9-6333 INS 10 21 * LINC00355 chr13 60213131 60213131 chr13 63887664 63887664 TCGA-G9-6333 DEL 40 24 * LINC00355 chr13 63982588 63982588 chr13 64339531 64339531 TCGA-G9-6333 DEL 5 9 LINC00355 * chr13 64347471 64347471 chr13 65732670 65732670 TCGA-G9-6333 DEL 22 36 * * chr13 67687752 67687752 chr21 9298734 9298734 TCGA-G9-6333 BND 6 25 * * chr13 85585438 85585438 chr13 85607844 85607844 TCGA-G9-6333 DEL 10 39 * * chr14 105568728 105568728 chr14 105688826 105688826 TCGA-G9-6333 INV 14 5 * * chr14 105568937 105568981 chr14 105690698 105690698 TCGA-G9-6333 DUP 45 35 * * chr14 105569118 105569144 chr14 105691281 105691281 TCGA-G9-6333 DUP 41 39 * * chr14 105569217 105569223 chr14 105689312 105689312 TCGA-G9-6333 DUP 31 41 * * chr14 105569445 105569445 chr14 105689739 105689739 TCGA-G9-6333 INV 39 42 * * chr14 105569607 105569622 chr14 105689443 105689443 TCGA-G9-6333 DEL 19 1 * * chr14 105569655 105569663 chr14 105690327 105690327 TCGA-G9-6333 DEL 2 41 * * chr14 36620164 36620164 chr14 45445983 45445983 TCGA-G9-6333 DUP 35 30 AL132857.1 * chr14 41138399 41138399 chr14 41228238 41228238 TCGA-G9-6333 INV 23 21 * * chr14 92948545 92948545 chr14 93908209 93908209 TCGA-G9-6333 INV 13 38 ITPK1 FAM181A-AS1 chr14 92952868 92952868 chr14 93908293 93908293 TCGA-G9-6333 INV 16 30 ITPK1 FAM181A-AS1 chr15 26359960 26359960 chr15 26360189 26360189 TCGA-G9-6333 DEL 27 29 * * chr15 50588449 50588449 chr17 17212794 17212794 TCGA-G9-6333 BND 12 36 TRPM7 MPRIP chr17 16051561 16051561 chr17 16580233 16580233 TCGA-G9-6333 DEL 42 6 NCOR1 * chr17 16109431 16109431 chr21 34748855 34748855 TCGA-G9-6333 BND 29 5 NCOR1 LINC01426 chr17 21412184 21412184 chr17 21661751 21661751 TCGA-G9-6333 INV 35 25 KCNJ12 * chr17 21626938 21626938 chr17 21655166 21655166 TCGA-G9-6333 INV 36 4 AC233702.1 * chr17 42117635 42117635 chr17 42481859 42481859 TCGA-G9-6333 DEL 20 48 KAT2A ATP6V0A1 chr17 42559717 42559717 chr17 44884261 44884261 TCGA-G9-6333 INV 35 8 AC067852.1 EFTUD2 chr17 42564092 42564092 chr17 44885916 44885916 TCGA-G9-6333 INV 15 41 COASY EFTUD2 chr17 7673510 7673510 chr16 4696879 4696879 TCGA-G9-6333 BND 3 45 TP53 ANKS3 chr17 7679632 7679647 chr17 8126884 8126884 TCGA-G9-6333 DEL 17 2 TP53 * chr18 64351185 64351185 chr18 64495068 64495068 TCGA-G9-6333 DEL 3 44 LINC01924 * chr18 71428347 71428347 chr18 77903767 77903767 TCGA-G9-6333 DEL 5 47 * * chr18 71457861 71457861 chr18 77579858 77579858 TCGA-G9-6333 INS 17 4 * * chr18 77882568 77882568 chr10 107614580 107614580 TCGA-G9-6333 BND 23 29 * * chr19 11465044 11465044 chr22 47810085 47810098 TCGA-G9-6333 BND 46 38 ELAVL3 AL117329.1 chr19 42241509 42241509 chr19 42347146 42347146 TCGA-G9-6333 DEL 11 20 GSK3A MEGF8 chr1 121364324 121364324 chr1 145023098 145023098 TCGA-G9-6333 DUP 41 32 SRGAP2C SRGAP2B chr1 143497378 143497378 chr1 143539523 143539523 TCGA-G9-6333 INV 37 6 AC239859.4 * chr1 147837629 147837629 chr18 14980823 14980823 TCGA-G9-6333 BND 5 26 * * chr1 149894413 149894413 chr13 108874445 108874445 TCGA-G9-6333 BND 39 22 BOLA1 MYO16 chr1 149917635 149917635 chr13 109243518 109243518 TCGA-G9-6333 BND 36 34 SV2A * chr1 159438751 159438751 chr1 159442727 159442727 TCGA-G9-6333 DEL 43 36 AL513323.1 AL513323.1 chr1 193011520 193011520 chr1 209146225 209146225 TCGA-G9-6333 DUP 33 30 * * chr1 193013534 193013534 chr1 209275231 209275231 TCGA-G9-6333 DUP 23 13 UCHL5 * chr1 193189635 193189635 chr18 10059293 10059293 TCGA-G9-6333 BND 2 29 CDC73 * chr1 193190166 193190166 chr18 10059373 10059373 TCGA-G9-6333 BND 30 31 CDC73 * chr1 193858923 193858923 chr1 214788694 214788694 TCGA-G9-6333 DEL 46 16 * * chr1 194929026 194929026 chr1 214944884 214944884 TCGA-G9-6333 INS 31 17 AL353072.2 * chr1 196651520 196651520 chr1 214510529 214510529 TCGA-G9-6333 DEL 49 6 CFH PTPN14 chr1 209154497 209154497 chr1 209265537 209265537 TCGA-G9-6333 INV 31 49 AC092810.2 * chr1 209265158 209265158 chr1 209275651 209275651 TCGA-G9-6333 DEL 22 41 * * chr1 209265730 209265730 chr18 10059576 10059576 TCGA-G9-6333 BND 50 23 * * chr1 215106835 215106835 chr1 216206177 216206177 TCGA-G9-6333 DEL 37 34 KCNK2 USH2A chr1 243797511 243797511 chr1 243798254 243798254 TCGA-G9-6333 DEL 39 19 AKT3 AKT3 chr1 32788366 32788366 chr17 16110642 16110642 TCGA-G9-6333 BND 19 29 YARS1 NCOR1 chr1 32792376 32792376 chr17 5065518 5065518 TCGA-G9-6333 BND 48 6 YARS1 * chr1 95052208 95052208 chr1 97397563 97397563 TCGA-G9-6333 DUP 18 4 ALG14 DPYD chr1 95741520 95741520 chr1 97336784 97336784 TCGA-G9-6333 DEL 5 10 LINC02607 DPYD chr1 96055098 96055098 chr13 101797417 101797417 TCGA-G9-6333 BND 23 44 * FGF14 chr1 96057405 96057405 chr1 97397480 97397480 TCGA-G9-6333 DUP 49 16 * DPYD chr1 96093285 96093285 chr13 107795291 107795291 TCGA-G9-6333 BND 48 46 * FAM155A chr1 97397633 97397633 chr13 101798094 101798094 TCGA-G9-6333 BND 49 47 DPYD FGF14 chr1 98599530 98599530 chr13 107804949 107804950 TCGA-G9-6333 BND 44 22 * FAM155A chr20 25783302 25783302 chr20 25845168 25845168 TCGA-G9-6333 DEL 38 26 FAM182B FAM182B chr20 7721016 7721019 chr20 9234448 9234448 TCGA-G9-6333 INS 32 23 * PLCB4 chr21 23316023 23316023 chr21 23339874 23339874 TCGA-G9-6333 DEL 21 26 * * chr21 33269576 33269576 chr21 38500665 38500665 TCGA-G9-6333 DEL 13 42 AP000295.1 ERG chr21 38493244 38493244 chr21 41498561 41498561 TCGA-G9-6333 DEL 4 36 ERG TMPRSS2 chr21 38547774 38547774 chr21 41494705 41494705 TCGA-G9-6333 DEL 29 36 ERG TMPRSS2 chr21 41495389 41495389 chr7 13979394 13979394 TCGA-G9-6333 BND 45 50 TMPRSS2 ETV1 chr22 18429829 18429829 chr22 20346918 20346918 TCGA-G9-6333 DEL 28 7 FAM230A FAM230G chr22 23385724 23385724 chr22 45266169 45266169 TCGA-G9-6333 INV 4 14 CES5AP1 * chr22 29932762 29932762 chr22 48664156 48664156 TCGA-G9-6333 INV 25 32 MTMR3 TAFA5 chr22 31791268 31791268 chrX 2562229 2562229 TCGA-G9-6333 BND 17 36 DEPDC5 * chr22 38409097 38409097 chr22 47418840 47418841 TCGA-G9-6333 DEL 9 50 * * chr22 45265012 45265012 chr22 47418941 47418941 TCGA-G9-6333 DEL 47 16 AL008718.2 * chr2 10399709 10399709 chr17 66799001 66799010 TCGA-G9-6333 BND 31 33 HPCAL1 PRKCA chr2 139380547 139380547 chr2 139410662 139410662 TCGA-G9-6333 DEL 46 12 * * chr2 140386777 140386777 chr2 156742097 156742097 TCGA-G9-6333 DEL 22 5 LRP1B * chr2 186963641 186963641 chr2 186996538 186996538 TCGA-G9-6333 DEL 10 10 * * chr2 22415383 22415383 chr2 56533176 56533176 TCGA-G9-6333 DEL 17 22 AC096570.1 * chr2 231005146 231005146 chr8 141713683 141713683 TCGA-G9-6333 BND 50 15 SPATA3 * chr2 23826458 23826458 chr2 23827991 23827991 TCGA-G9-6333 DEL 29 6 ATAD2B ATAD2B chr2 241990547 241990562 chr9 134685216 134685216 TCGA-G9-6333 BND 11 4 LINC01237 COL5A1 chr2 33442674 33442674 chr2 81442567 81442567 TCGA-G9-6333 DEL 3 25 RASGRP3 * chr2 34107079 34107079 chr2 81635314 81635314 TCGA-G9-6333 DEL 1 34 LINC01320 * chr2 36051644 36051644 chr2 36214548 36214548 TCGA-G9-6333 DEL 4 45 * * chr2 36061102 36061102 chr6 87258831 87258831 TCGA-G9-6333 BND 47 31 * ZNF292 chr2 37321641 37321641 chr2 37990416 37990416 TCGA-G9-6333 DEL 5 8 PRKD3 RMDN2 chr2 37326371 37326371 chr2 37332301 37332301 TCGA-G9-6333 DEL 38 16 AC007391.1 RNU6-939P chr2 56304726 56304726 chr2 82017317 82017317 TCGA-G9-6333 DEL 49 48 AC007744.1 * chr2 56404556 56404556 chr2 56414169 56414169 TCGA-G9-6333 DEL 22 23 * * chr2 75677822 75677825 chr4 159418029 159418030 TCGA-G9-6333 BND 35 38 MRPL19 * chr2 80377431 80377431 chr2 80388052 80388052 TCGA-G9-6333 DEL 9 38 CTNNA2 CTNNA2 chr2 80926276 80926276 chr2 80933216 80933217 TCGA-G9-6333 DEL 45 27 * * chr2 81617396 81617396 chr2 84720939 84720939 TCGA-G9-6333 DEL 8 16 * DNAH6 chr3 101333868 101333869 chr3 112806097 112806098 TCGA-G9-6333 INV 32 19 SENP7 CD200R1L-AS1 chr3 108332272 108332272 chr3 118055048 118055048 TCGA-G9-6333 INS 19 18 HHLA2 AC068633.1 chr3 108594460 108594460 chr16 6743805 6743805 TCGA-G9-6333 BND 28 18 DZIP3 RBFOX1 chr3 167191804 167191804 chr3 167192994 167192994 TCGA-G9-6333 DEL 10 45 * * chr3 189211913 189211918 chr5 108382962 108382966 TCGA-G9-6333 BND 13 17 TPRG1 FBXL17 chr3 191325509 191325509 chr5 109271916 109271916 TCGA-G9-6333 BND 47 44 UTS2B AC008467.1 chr3 191327240 191327242 chr5 108328888 108328890 TCGA-G9-6333 BND 2 26 UTS2B FBXL17 chr3 191548995 191548997 chr5 43398498 43398500 TCGA-G9-6333 BND 43 9 AC073365.1 CCL28 chr3 191966929 191966929 chr5 103573888 103573888 TCGA-G9-6333 BND 45 36 * * chr3 192455392 192455393 chr5 109283984 109283985 TCGA-G9-6333 BND 46 43 FGF12 AC008467.1 chr3 1927469 1927469 chr3 1937569 1937569 TCGA-G9-6333 DEL 6 17 * * chr3 69256065 69256065 chr3 73495770 73495770 TCGA-G9-6333 INV 16 49 FRMD4B PDZRN3 chr3 77091095 77091095 chr3 79489505 79489505 TCGA-G9-6333 DEL 14 24 ROBO2 ROBO1 chr3 77152919 77152919 chr3 79627358 79627358 TCGA-G9-6333 INS 44 20 ROBO2 ROBO1 chr3 77738301 77738301 chr3 77817318 77817318 TCGA-G9-6333 DEL 50 46 * * chr3 78607467 78607467 chr3 79717830 79717830 TCGA-G9-6333 DEL 33 25 ROBO1 ROBO1 chr3 86119662 86119662 chr7 87999206 87999206 TCGA-G9-6333 BND 12 28 * ADAM22 chr3 88065665 88065665 chr14 44016663 44016663 TCGA-G9-6333 BND 20 38 CGGBP1 LINC02307 chr3 98449024 98449027 chr5 105497239 105497242 TCGA-G9-6333 BND 8 14 AC117473.1 * chr3 98488814 98488814 chr3 191831806 191831806 TCGA-G9-6333 DEL 29 39 * * chr3 98814342 98814342 chr5 28913744 28913744 TCGA-G9-6333 BND 5 32 ST3GAL6 * chr3 99170786 99170789 chr5 100039964 100039967 TCGA-G9-6333 BND 12 46 * * chr4 101190720 101190720 chr4 101328368 101328368 TCGA-G9-6333 DEL 34 46 PPP3CA PPP3CA chr4 101328309 101328322 chr4 112737026 112737026 TCGA-G9-6333 INV 47 37 PPP3CA * chr4 104073182 104073182 chr4 105166546 105166546 TCGA-G9-6333 DEL 29 14 * TET2 chr4 110393357 110393357 chr4 131273103 131273103 TCGA-G9-6333 DEL 31 31 ENPEP RNU6-224P chr4 110417494 110417494 chr4 114593522 114593522 TCGA-G9-6333 INS 45 42 ENPEP * chr4 111251575 111251575 chr4 129087715 129087715 TCGA-G9-6333 INS 15 3 * SCLT1 chr4 113230003 113230003 chr4 113231039 113231039 TCGA-G9-6333 DEL 6 7 ANK2 ANK2 chr4 114083440 114083440 chr4 114083662 114083662 TCGA-G9-6333 DEL 4 36 * * chr4 114619104 114619104 chr4 116061487 116061487 TCGA-G9-6333 DEL 11 1 UGT8 AC027613.1 chr4 134112565 134112565 chr4 134113629 134113629 TCGA-G9-6333 DEL 37 21 * * chr4 134319492 134319492 chr4 135574202 135574202 TCGA-G9-6333 DEL 24 40 AC015631.1 * chr4 143833313 143833313 chr4 143837030 143837030 TCGA-G9-6333 DEL 3 7 AC107223.1 AC107223.1 chr4 14816453 14816453 chr4 17478245 17478245 TCGA-G9-6333 DEL 7 39 LINC00504 QDPR chr4 15568829 15568829 chr4 18783014 18783014 TCGA-G9-6333 INS 1 18 CC2D2A * chr4 16068652 16068652 chr4 25967238 25967238 TCGA-G9-6333 DEL 33 3 PROM1 * chr4 16742861 16742861 chr4 17176573 17176573 TCGA-G9-6333 DEL 39 20 LDB2 LINC02493 chr4 18134126 18134126 chr4 104812186 104812186 TCGA-G9-6333 INS 19 25 * AC004053.1 chr4 189108774 189108774 chr4 189388915 189388915 TCGA-G9-6333 DEL 20 37 * * chr4 189691960 189691960 chr4 189734895 189734895 TCGA-G9-6333 INV 13 39 * * chr4 22834494 22834494 chr4 112302668 112302668 TCGA-G9-6333 DEL 34 3 * ALPK1 chr4 4107300 4107300 chr4 4157521 4157521 TCGA-G9-6333 DEL 30 43 AC116562.3 OR7E99P chr4 44390503 44390503 chr4 189695672 189695672 TCGA-G9-6333 INS 50 38 KCTD8 * chr4 45690628 45690628 chr4 47413050 47413050 TCGA-G9-6333 DEL 1 20 * GABRB1 chr4 45712297 45712297 chr4 105112249 105112249 TCGA-G9-6333 INS 5 47 * AC096577.1 chr4 46277843 46277843 chr4 47884123 47884123 TCGA-G9-6333 DEL 47 22 GABRA2 AC107068.2 chr4 47358740 47358740 chr4 104107204 104107204 TCGA-G9-6333 DEL 48 27 GABRB1 * chr4 49486987 49486987 chr4 49568656 49568656 TCGA-G9-6333 INV 34 39 AC119751.3 * chr4 60389932 60389932 chr4 60390092 60390092 TCGA-G9-6333 DEL 36 18 * * chr4 60405489 60405489 chr4 129122090 129122090 TCGA-G9-6333 DEL 3 26 * * chr4 60509124 60509124 chr4 63196910 63196910 TCGA-G9-6333 DEL 18 4 * * chr4 60602105 60602105 chr4 112737138 112737138 TCGA-G9-6333 INV 42 49 * * chr4 63750342 63750342 chr4 63751168 63751168 TCGA-G9-6333 DEL 29 32 * * chr4 7695516 7695535 chr20 20337513 20337513 TCGA-G9-6333 BND 8 24 SORCS2 CFAP61 chr4 90020203 90020203 chr4 90227584 90227584 TCGA-G9-6333 DEL 19 50 * CCSER1 chr5 100656357 100656358 chr3 98618354 98618355 TCGA-G9-6333 BND 29 36 AC027315.1 * chr5 103834707 103834707 chr3 98844071 98844071 TCGA-G9-6333 BND 25 32 * DCBLD2 chr5 105497239 105497242 chr3 98449024 98449027 TCGA-G9-6333 BND 18 9 * AC117473.1 chr5 106050360 106050360 chr5 106436281 106436281 TCGA-G9-6333 INS 21 45 * * chr5 108328888 108328890 chr3 191327240 191327242 TCGA-G9-6333 BND 17 1 FBXL17 UTS2B chr5 109283984 109283985 chr3 192455392 192455393 TCGA-G9-6333 BND 5 16 AC008467.1 FGF12 chr5 131505438 131505438 chr5 131902249 131902249 TCGA-G9-6333 INS 35 38 RAPGEF6 MEIKIN chr5 139434300 139434300 chr5 139522838 139522838 TCGA-G9-6333 DUP 14 22 DNAJC18 * chr5 159862211 159862211 chr5 159879013 159879013 TCGA-G9-6333 DEL 21 49 LINC01847 ADRA1B chr5 163335140 163335140 chr5 167371092 167371092 TCGA-G9-6333 DEL 23 24 AC113414.1 TENM2 chr5 1998793 1998793 chr5 4913968 4913968 TCGA-G9-6333 DEL 10 16 * * chr5 2012818 2012818 chr10 62752784 62752784 TCGA-G9-6333 BND 38 18 * AC067751.1 chr5 26006596 26006596 chr5 44537754 44537754 TCGA-G9-6333 INS 33 50 * * chr5 26847466 26847466 chr5 28274477 28274477 TCGA-G9-6333 INS 4 32 * * chr5 3194056 3194059 chr10 95827370 95827373 TCGA-G9-6333 BND 21 47 * ENTPD1 chr5 41283539 41283539 chr5 41541479 41541479 TCGA-G9-6333 DEL 47 41 * * chr5 41691203 41691204 chr5 42875573 42875573 TCGA-G9-6333 DEL 20 13 * SELENOP chr5 43398498 43398500 chr3 191548995 191548997 TCGA-G9-6333 BND 46 11 CCL28 AC073365.1 chr5 44334176 44334176 chr5 45093139 45093139 TCGA-G9-6333 INS 21 12 FGF10 AC114954.1 chr5 45806119 45806119 chr3 98777384 98777384 TCGA-G9-6333 BND 19 48 * ST3GAL6 chr5 4625852 4625852 chr5 4864175 4864175 TCGA-G9-6333 DEL 23 40 AC106799.2 AC106799.2 chr5 4689807 4689810 chr10 62291390 62291393 TCGA-G9-6333 BND 47 7 AC106799.2 LINC02621 chr5 4791853 4791853 chr10 95438301 95438301 TCGA-G9-6333 BND 22 22 AC106799.2 SORBS1 chr5 50948702 50948702 chr16 7151758 7151758 TCGA-G9-6333 BND 28 11 * RBFOX1 chr5 55123412 55123412 chr5 65609405 65609405 TCGA-G9-6333 INV 39 4 CDC20B TRIM23 chr5 58017354 58017354 chr5 58027652 58027652 TCGA-G9-6333 DUP 46 36 * * chr5 59192698 59192698 chr5 60033283 60033283 TCGA-G9-6333 INV 50 4 PDE4D PDE4D chr5 83505443 83505443 chr5 85182979 85182979 TCGA-G9-6333 DEL 39 5 VCAN * chr5 8362256 8362256 chr5 8424160 8424160 TCGA-G9-6333 DEL 35 25 LINC02226 LINC02226 chr5 85167058 85167058 chr5 87291755 87291755 TCGA-G9-6333 DEL 33 25 * RASA1 chr5 86224461 86224461 chr5 86527857 86527857 TCGA-G9-6333 DEL 15 47 * * chr5 97626436 97626436 chr5 104962775 104962775 TCGA-G9-6333 DEL 8 7 LINC01340 AC099520.1 chr5 97862972 97862972 chr5 98141259 98141259 TCGA-G9-6333 DEL 36 16 * LINC01846 chr5 98524650 98524650 chr5 101542519 101542519 TCGA-G9-6333 DEL 25 23 * * chr5 98722870 98722870 chr5 102296743 102296743 TCGA-G9-6333 DEL 19 37 * SLCO4C1 chr5 98922475 98922475 chr3 191496091 191496091 TCGA-G9-6333 BND 48 13 CHD1 AC073365.1 chr5 99533851 99533851 chr5 131514174 131514174 TCGA-G9-6333 INS 25 20 GUSBP8 RAPGEF6 chr6 115988108 115988108 chr6 116124196 116124196 TCGA-G9-6333 DEL 27 1 FRK NT5DC1 chr6 382463 382464 chr16 33626065 33626065 TCGA-G9-6333 BND 17 50 * * chr6 76236242 76236242 chr6 77412667 77412667 TCGA-G9-6333 DEL 5 8 * * chr6 76240337 76240337 chr6 78627339 78627339 TCGA-G9-6333 DUP 7 37 * * chr6 76245100 76245100 chr13 65568773 65568773 TCGA-G9-6333 BND 31 44 * * chr6 77517076 77517076 chr6 78422149 78422149 TCGA-G9-6333 INV 13 1 * * chr6 78403785 78403785 chr6 81390555 81390555 TCGA-G9-6333 INS 40 37 * * chr6 78463452 78463452 chr6 126808166 126808166 TCGA-G9-6333 DEL 23 22 * * chr6 78626028 78626028 chr13 65570267 65570267 TCGA-G9-6333 BND 11 1 * * chr6 80708342 80708342 chr6 85604644 85604644 TCGA-G9-6333 INS 2 26 * AL589666.1 chr6 84138763 84138763 chr6 85406550 85406550 TCGA-G9-6333 DEL 20 1 CEP162 * chr6 85065786 85065786 chr6 85467616 85467616 TCGA-G9-6333 DEL 49 50 * NT5E chr6 86747315 86747315 chr14 104267634 104267634 TCGA-G9-6333 BND 36 32 * LINC02691 chr6 87229372 87229372 chr2 34339420 34339420 TCGA-G9-6333 BND 29 7 ZNF292 LINC01320 chr6 92958204 92958204 chr18 8456352 8456352 TCGA-G9-6333 BND 11 48 * * chr6 9371641 9371641 chr14 92782266 92782266 TCGA-G9-6333 BND 25 18 * * chr6 9571261 9571262 chr6 127742034 127742035 TCGA-G9-6333 INV 41 29 * THEMIS chr6 97755138 97755138 chr6 97979706 97979706 TCGA-G9-6333 DEL 20 23 AL589740.1 AL589740.1 chr6 99209262 99209262 chr6 126804048 126804048 TCGA-G9-6333 INS 11 26 * * chr7 127124345 127124345 chr15 22875507 22875507 TCGA-G9-6333 BND 5 28 GRM8 CYFIP1 chr7 129518697 129518697 chr7 129518932 129518932 TCGA-G9-6333 INV 16 48 * * chr7 146790635 146790635 chr7 146823804 146823804 TCGA-G9-6333 DEL 36 31 CNTNAP2 CNTNAP2 chr7 150909719 150909719 chr7 157482716 157482716 TCGA-G9-6333 DUP 6 7 * AC006372.3 chr7 16135309 16135309 chr7 16267917 16267917 TCGA-G9-6333 DEL 4 27 CRPPA CRPPA chr7 16177190 16177190 chr8 79730733 79730733 TCGA-G9-6333 BND 4 39 CRPPA * chr7 16285181 16285181 chr8 105862270 105862270 TCGA-G9-6333 BND 6 10 CRPPA ZFPM2-AS1 chr7 17632868 17632868 chr7 17652857 17652857 TCGA-G9-6333 DEL 32 18 * * chr7 17684103 17684103 chr8 76204605 76204605 TCGA-G9-6333 BND 26 37 * * chr7 39015205 39015205 chr7 39227125 39227125 TCGA-G9-6333 DEL 35 27 POU6F2 POU6F2 chr7 48030495 48030495 chr8 14042201 14042201 TCGA-G9-6333 BND 42 13 SUN3 * chr7 52747655 52747655 chr7 87708007 87708007 TCGA-G9-6333 DEL 9 5 * ABCB1 chr7 52751610 52751610 chr10 43908214 43908214 TCGA-G9-6333 BND 46 15 * LINC02659 chr7 55178059 55178060 chr8 135618527 135618528 TCGA-G9-6333 BND 21 34 EGFR KHDRBS3 chr7 56291615 56291615 chr7 56307746 56307746 TCGA-G9-6333 DEL 9 45 * * chr7 62671781 62671781 chr8 42274274 42274274 TCGA-G9-6333 BND 27 8 * IKBKB chr7 62921065 62921065 chr7 62941439 62941439 TCGA-G9-6333 DEL 20 28 * * chr7 64978721 64978721 chr7 64987612 64987612 TCGA-G9-6333 INV 42 27 ZNF117 ZNF117 chr7 64981428 64981428 chr7 77721989 77721989 TCGA-G9-6333 INV 26 44 ZNF117 RSBN1L chr7 66081906 66081906 chr7 149627082 149627083 TCGA-G9-6333 INV 30 45 ASL * chr7 66438220 66438220 chr7 149627082 149627083 TCGA-G9-6333 DUP 32 6 LINC00174 * chr7 68365841 68365841 chr7 82133954 82133954 TCGA-G9-6333 DEL 11 2 * CACNA2D1 chr7 68371240 68371240 chr7 68917637 68917637 TCGA-G9-6333 DUP 32 50 * * chr7 68879623 68879623 chr7 90935828 90935828 TCGA-G9-6333 INV 5 24 * CDK14 chr7 68917547 68917547 chr7 82148065 82148065 TCGA-G9-6333 INV 41 44 * CACNA2D1 chr7 71262997 71262997 chr7 82133954 82133954 TCGA-G9-6333 INV 29 1 GALNT17 CACNA2D1 chr7 71738733 71738733 chr7 107928291 107928291 TCGA-G9-6333 INV 32 19 * DLD chr7 72630790 72630790 chr12 132613359 132613359 TCGA-G9-6333 BND 26 12 TYW1B * chr7 80758924 80758924 chr7 90265546 90265546 TCGA-G9-6333 DEL 34 28 SEMA3C CFAP69 chr7 82883162 82883162 chr10 45107880 45107880 TCGA-G9-6333 BND 13 9 PCLO AL358394.3 chr7 82883412 82883412 chr12 128960656 128960656 TCGA-G9-6333 BND 20 33 PCLO GLT1D1 chr7 83835637 83835637 chr7 83840879 83840879 TCGA-G9-6333 DEL 29 33 * * chr7 87076088 87076088 chr7 87079558 87079558 TCGA-G9-6333 DEL 11 30 * * chr7 87657270 87657270 chr14 45455607 45455607 TCGA-G9-6333 BND 26 13 ABCB1 * chr7 88766115 88766115 chr12 119603151 119603151 TCGA-G9-6333 BND 10 9 ZNF804B TMEM233 chr7 89183770 89183770 chr9 94736546 94736546 TCGA-G9-6333 BND 10 14 ZNF804B AOPEP chr7 89734215 89734215 chr10 43933906 43933906 TCGA-G9-6333 BND 26 47 * * chr7 90443827 90443827 chr7 91379378 91379378 TCGA-G9-6333 DEL 12 40 CLDN12 AC079760.2 chr7 90748386 90748386 chr12 132649979 132649979 TCGA-G9-6333 BND 41 19 CDK14 POLE chr7 91598788 91598788 chr7 91598878 91598878 TCGA-G9-6333 INV 40 36 * * chr8 111475475 111475475 chr8 115893045 115893045 TCGA-G9-6333 DEL 15 7 LINC02237 * chr8 116123620 116123620 chr8 138067002 138067002 TCGA-G9-6333 DEL 11 4 LINC00536 AC046195.1 chr8 133242282 133242282 chr8 133266373 133266373 TCGA-G9-6333 DEL 17 38 NDRG1 NDRG1 chr8 135618527 135618528 chr7 55178059 55178060 TCGA-G9-6333 BND 36 34 KHDRBS3 EGFR chr8 136187413 136187413 chr8 137713898 137713898 TCGA-G9-6333 DEL 33 33 LINC02055 * chr8 136604111 136604113 chr8 137061547 137061547 TCGA-G9-6333 INS 28 16 LINC02055 LINC02055 chr8 14089447 14089447 chr8 14091932 14091932 TCGA-G9-6333 DEL 50 38 * SGCZ chr8 14379283 14379283 chr8 35709518 35709518 TCGA-G9-6333 DEL 15 26 SGCZ UNC5D chr8 14480937 14480937 chr8 14533402 14533402 TCGA-G9-6333 DEL 29 25 SGCZ SGCZ chr8 19706360 19706360 chr8 21231923 21231923 TCGA-G9-6333 DUP 11 27 CSGALNACT1 * chr8 21219526 21219526 chr8 24239239 24239239 TCGA-G9-6333 DEL 42 8 * * chr8 22158556 22158556 chr8 23680132 23680132 TCGA-G9-6333 INV 11 5 LGI3 NKX3-1 chr8 24237498 24237498 chr8 67030519 67030519 TCGA-G9-6333 INV 8 4 * PPP1R42 chr8 24253475 24253475 chr8 66638439 66638439 TCGA-G9-6333 INV 1 13 * VCPIP1 chr8 24320899 24320899 chr8 28045746 28045746 TCGA-G9-6333 INV 44 31 ADAM28 NUGGC chr8 24337914 24337914 chr8 67230633 67230633 TCGA-G9-6333 INV 21 31 ADAM28 ARFGEF1 chr8 24412298 24412298 chr8 67230375 67230375 TCGA-G9-6333 DEL 33 31 AC120193.1 ARFGEF1 chr8 31672150 31672150 chr8 35742167 35742167 TCGA-G9-6333 INS 40 33 NRG1 UNC5D chr8 34476144 34476144 chr8 34488635 34488635 TCGA-G9-6333 DEL 27 21 * * chr8 35690876 35690876 chr8 35741761 35741761 TCGA-G9-6333 DEL 5 24 UNC5D UNC5D chr8 40063585 40063585 chr16 35977149 35977149 TCGA-G9-6333 BND 46 39 * * chr8 40161807 40161807 chr8 41469797 41469797 TCGA-G9-6333 DEL 18 30 AC022733.1 * chr8 60401912 60401914 chrX 146684771 146684773 TCGA-G9-6333 BND 38 31 LINC01301 * chr8 60403144 60403146 chrX 145685523 145685525 TCGA-G9-6333 BND 27 19 LINC01301 * chr8 60469509 60469509 chrX 145644003 145644003 TCGA-G9-6333 BND 13 47 LINC01301 * chr8 60525031 60525033 chrX 148023013 148023015 TCGA-G9-6333 BND 20 37 RAB2A FMR1NB chr8 60881190 60881190 chrX 146757455 146757455 TCGA-G9-6333 BND 15 24 * * chr8 63010166 63010166 chr12 45797376 45797376 TCGA-G9-6333 BND 47 36 * ARID2 chr8 63640695 63640695 chr8 63642559 63642559 TCGA-G9-6333 DEL 39 40 * * chr8 78840192 78840193 chr7 16159538 16159539 TCGA-G9-6333 BND 50 50 AC083837.1 CRPPA chr8 79574239 79574239 chr8 80370307 80370307 TCGA-G9-6333 DEL 22 8 * AC034114.2 chr8 79619296 79619296 chr8 136588439 136588439 TCGA-G9-6333 INS 40 41 STMN2 LINC02055 chr8 79674857 79674857 chr7 17420087 17420087 TCGA-G9-6333 BND 5 34 * AC019117.3 chr8 79708079 79708079 chr8 79770207 79770207 TCGA-G9-6333 DEL 28 45 * LINC01607 chr8 80231594 80231594 chr7 17824056 17824056 TCGA-G9-6333 BND 18 35 TPD52 SNX13 chr8 93020162 93020162 chr18 67277934 67277934 TCGA-G9-6333 BND 36 45 * * chr9 117364214 117364214 chr9 117999653 117999653 TCGA-G9-6333 INS 43 17 ASTN2 * chr9 126343396 126343396 chrX 64822231 64822231 TCGA-G9-6333 BND 11 5 MVB12B * chr9 126464259 126464259 chrX 64229969 64229969 TCGA-G9-6333 BND 28 34 MVB12B ASB12 chr9 27771270 27771270 chr9 31314703 31314703 TCGA-G9-6333 INV 32 15 * * chr9 27771291 27771291 chr9 29561792 29561792 TCGA-G9-6333 INV 28 41 * * chr9 28037961 28037961 chr9 32405743 32405743 TCGA-G9-6333 DEL 6 13 LINGO2 ACO1 chr9 28038152 28038153 chr9 31688945 31688945 TCGA-G9-6333 DEL 5 6 LINGO2 * chr9 29561368 29561377 chr9 31317861 31317861 TCGA-G9-6333 DUP 14 13 * * chr9 30345791 30345791 chr9 30346097 30346097 TCGA-G9-6333 DEL 11 48 * * chr9 31053405 31053405 chr9 31053941 31053941 TCGA-G9-6333 INV 27 49 * * chr9 31053405 31053405 chr9 31055897 31055897 TCGA-G9-6333 INV 22 44 * * chr9 31436599 31436600 chr9 37782706 37782707 TCGA-G9-6333 INV 40 15 * AL138752.2 chr9 31690528 31690528 chr9 32405608 32405608 TCGA-G9-6333 DEL 40 27 * ACO1 chr9 32315410 32315410 chrX 55061520 55061520 TCGA-G9-6333 BND 18 36 * * chr9 34197967 34197967 chr9 34198067 34198067 TCGA-G9-6333 INV 22 43 UBAP1 UBAP1 chr9 39077812 39077812 chr9 67289597 67289597 TCGA-G9-6333 DUP 19 12 CNTNAP3 CNTNAP3P2 chr9 41747101 41747101 chr9 41754823 41754823 TCGA-G9-6333 DEL 24 34 * * chr9 73246562 73246562 chr9 76757993 76757993 TCGA-G9-6333 INV 14 47 * PRUNE2 chrX 120875857 120875857 chrX 120986759 120986759 TCGA-G9-6333 DEL 42 36 CT47B1 CT47A1 chrX 122159139 122159139 chrX 140553934 140553934 TCGA-G9-6333 DEL 19 41 * * chrX 131299151 131299151 chrX 136422795 136422795 TCGA-G9-6333 DUP 46 20 IGSF1 * chrX 135335315 135335315 chrX 140399412 140399412 TCGA-G9-6333 DEL 26 50 ZNF75D * chrX 135538948 135538948 chrX 140574124 140574124 TCGA-G9-6333 INV 29 45 INTS6L * chrX 140403111 140403111 chrX 154712210 154712210 TCGA-G9-6333 INV 11 16 * GAB3 chrX 145179736 145179736 chrX 145259343 145259343 TCGA-G9-6333 INV 24 4 * * chrX 145188509 145188509 chrX 145440400 145440400 TCGA-G9-6333 INV 47 17 * * chrX 145525070 145525070 chrX 152089215 152089215 TCGA-G9-6333 DEL 50 4 * * chrX 145644003 145644003 chr8 60469509 60469509 TCGA-G9-6333 BND 40 1 * LINC01301 chrX 145685523 145685525 chr8 60403144 60403146 TCGA-G9-6333 BND 5 6 * LINC01301 chrX 146684771 146684773 chr8 60401912 60401914 TCGA-G9-6333 BND 33 37 * LINC01301 chrX 147955102 147955104 chr8 61045191 61045193 TCGA-G9-6333 BND 47 30 * * chrX 148023013 148023015 chr8 60525031 60525033 TCGA-G9-6333 BND 25 23 FMR1NB RAB2A chrX 151195422 151195422 chrX 151196970 151196970 TCGA-G9-6333 INV 7 39 * * chrX 153169201 153169201 chrX 153169323 153169323 TCGA-G9-6333 INV 28 48 * * chrX 33186258 33186258 chrX 33189544 33189544 TCGA-G9-6333 DEL 47 43 DMD DMD chrX 62847892 62847892 chrX 67810472 67810472 TCGA-G9-6333 DUP 42 24 * * chrX 62891636 62891636 chrX 65936845 65936845 TCGA-G9-6333 DEL 28 48 * * chrX 63314457 63314457 chrX 63314663 63314663 TCGA-G9-6333 INV 41 25 * * chrX 63563024 63563034 chrX 63563024 63563034 TCGA-G9-6333 INV 45 49 * * chrX 63785997 63785997 chrX 63790971 63790971 TCGA-G9-6333 INV 18 45 ARHGEF9 ARHGEF9 chrX 65940336 65940336 chrX 67810246 67810246 TCGA-G9-6333 DUP 32 4 * * chrX 66703129 66703129 chrX 66703330 66703330 TCGA-G9-6333 INV 5 31 * * chrX 67739199 67739199 chrX 67740563 67740563 TCGA-G9-6333 INV 15 45 * * chrX 99245716 99245716 chrX 99251200 99251200 TCGA-G9-6333 DEL 36 6 * * chr10 28179989 28179989 chr2 82461356 82461356 TCGA-VN-A88R BND 8 25 MPP7 * chr11 104790772 104790772 chr11 110019368 110019368 TCGA-VN-A88R INS 32 31 * RDX chr11 104794286 104794286 chr11 107901517 107901517 TCGA-VN-A88R DEL 26 8 * SLC35F2 chr11 104813041 104813041 chr11 106348861 106348861 TCGA-VN-A88R INS 34 19 * * chr11 106388089 106388089 chr11 106762085 106762085 TCGA-VN-A88R INS 23 8 * GUCY1A2 chr11 106487929 106487929 chr11 110071315 110071315 TCGA-VN-A88R DEL 8 26 * RDX chr11 106898475 106898475 chr11 112127468 112127468 TCGA-VN-A88R INS 37 21 GUCY1A2 AP002884.2 chr11 108310942 108310942 chr11 112144459 112144459 TCGA-VN-A88R DEL 9 2 ATM IL18 chr11 33690428 33690428 chr11 33699153 33699153 TCGA-VN-A88R DEL 3 24 AL049629.1 C11orf91 chr12 12331168 12331168 chr16 66335268 66335268 TCGA-VN-A88R BND 40 39 MANSC1 * chr12 61170329 61170330 chr16 64537862 64537863 TCGA-VN-A88R BND 5 36 * AC092131.1 chr12 61233317 61233317 chr16 58263073 58263073 TCGA-VN-A88R BND 10 32 AC090017.1 CCDC113 chr12 93412257 93412260 chr7 158732693 158732696 TCGA-VN-A88R BND 9 26 UBE2N ESYT2 chr12 93412572 93412572 chr7 159275202 159275202 TCGA-VN-A88R BND 35 13 UBE2N * chr14 24875532 24875532 chr14 24914167 24914167 TCGA-VN-A88R DEL 42 6 STXBP6 STXBP6 chr14 27570913 27570913 chr14 27580914 27580914 TCGA-VN-A88R DEL 29 38 AL390334.1 AL390334.1 chr15 69856699 69856699 chr15 70867188 70867188 TCGA-VN-A88R INS 11 45 * LRRC49 chr16 57881754 57881754 chr16 66333968 66333968 TCGA-VN-A88R DEL 36 44 * * chr16 60110246 60110247 chr12 61491378 61491379 TCGA-VN-A88R BND 16 22 * * chr16 62825989 62825989 chr16 62852794 62852794 TCGA-VN-A88R DEL 46 17 * * chr16 64537862 64537863 chr12 61170329 61170330 TCGA-VN-A88R BND 34 34 AC092131.1 * chr16 7200213 7200213 chr16 7201318 7201318 TCGA-VN-A88R DEL 46 32 RBFOX1 RBFOX1 chr17 733955 733955 chr17 771741 771741 TCGA-VN-A88R INS 6 2 TLCD3A GLOD4 chr18 69821713 69821713 chr18 69827474 69827474 TCGA-VN-A88R DEL 42 17 DOK6 DOK6 chr1 103040383 103040383 chr1 158124396 158124396 TCGA-VN-A88R INS 41 39 COL11A1 * chr1 103843552 103843552 chr1 103873020 103873020 TCGA-VN-A88R DEL 7 19 * * chr1 103958298 103958298 chr1 106865386 106865386 TCGA-VN-A88R INS 46 35 * * chr1 106181952 106181952 chr1 106222420 106222420 TCGA-VN-A88R DEL 9 12 * * chr1 157990420 157990420 chr1 159799894 159799894 TCGA-VN-A88R INS 33 39 * FCRL6 chr1 158752518 158752518 chr1 159367271 159367271 TCGA-VN-A88R DEL 16 6 OR6N1 AL513323.1 chr1 158753322 158753322 chr1 159828807 159828807 TCGA-VN-A88R DEL 7 9 OR6N1 SLAMF8 chr1 192217240 192217240 chr2 212695641 212695641 TCGA-VN-A88R BND 10 4 AL390957.1 AC093865.1 chr1 193371500 193371500 chr1 193380117 193380117 TCGA-VN-A88R DEL 25 18 * * chr1 194472275 194472275 chr1 196435738 196435738 TCGA-VN-A88R DEL 9 2 * KCNT2 chr1 85596535 85596535 chr1 87517712 87517712 TCGA-VN-A88R INS 21 39 * * chr1 86509535 86509535 chr1 159610646 159610646 TCGA-VN-A88R DEL 8 13 * * chr1 86558729 86558729 chr1 87991936 87991936 TCGA-VN-A88R INS 31 22 CLCA4 PKN2-AS1 chr1 87119623 87119623 chr1 105650372 105650372 TCGA-VN-A88R DEL 1 13 AC093155.3 * chr1 87554915 87554915 chr1 89316073 89316073 TCGA-VN-A88R INS 34 20 * * chr1 87971171 87971171 chr1 104111493 104111493 TCGA-VN-A88R DEL 39 13 PKN2-AS1 AC092506.1 chr1 88173883 88173883 chr1 88175252 88175252 TCGA-VN-A88R DEL 7 39 PKN2-AS1 PKN2-AS1 chr1 89311005 89311005 chr1 105609350 105609350 TCGA-VN-A88R INS 20 33 * LINC01676 chr1 95797048 95797048 chr1 95797581 95797581 TCGA-VN-A88R DEL 8 12 * * chr20 32560394 32560394 chr20 35964761 35964761 TCGA-VN-A88R DEL 14 37 NOL4L CNBD2 chr20 37185436 37185436 chr6 29578979 29578979 TCGA-VN-A88R BND 7 45 RPN2 GABBR1 chr20 46992485 46992488 chr2 123137240 123137243 TCGA-VN-A88R BND 32 27 EYA2 * chr22 46084380 46084380 chr22 46087584 46087584 TCGA-VN-A88R DEL 36 49 MIRLET7BHG MIRLET7BHG chr2 110763279 110763279 chr2 126174914 126174914 TCGA-VN-A88R INS 47 39 ACOXL * chr2 123137240 123137243 chr20 46992485 46992488 TCGA-VN-A88R BND 40 10 * EYA2 chr2 162289624 162289624 chr2 163177289 163177289 TCGA-VN-A88R DEL 29 49 IFIH1 * chr2 77857553 77857553 chr2 84414845 84414845 TCGA-VN-A88R DEL 23 42 * * chr2 77859578 77859578 chr2 163158722 163158722 TCGA-VN-A88R INS 14 49 * * chr2 78764842 78764842 chr2 80182306 80182306 TCGA-VN-A88R DEL 40 14 * CTNNA2 chr2 80589718 80589718 chr10 28146394 28146394 TCGA-VN-A88R BND 7 4 CTNNA2 MPP7 chr2 82672630 82672630 chr2 82676325 82676325 TCGA-VN-A88R DEL 16 4 * * chr2 83932437 83932437 chr2 162319162 162319162 TCGA-VN-A88R DEL 10 10 * IFIH1 chr2 85739164 85739164 chr2 85773485 85773485 TCGA-VN-A88R DEL 17 23 * ATOH8 chr3 2759087 2759087 chr3 5322942 5322942 TCGA-VN-A88R DEL 50 6 CNTN4 * chr4 122473275 122473275 chr4 122973339 122973339 TCGA-VN-A88R DEL 25 15 * SPATA5 chr4 145512851 145512851 chr4 145534236 145534236 TCGA-VN-A88R DEL 41 50 SMAD1 SMAD1 chr4 165239479 165239479 chr5 102855854 102855854 TCGA-VN-A88R BND 21 1 KLHL2 PAM chr4 165319534 165319534 chr4 165326895 165326895 TCGA-VN-A88R DEL 5 25 KLHL2 MSMO1 chr4 167368310 167368310 chr5 100774933 100774933 TCGA-VN-A88R BND 18 15 * * chr4 170689091 170689091 chr4 170689288 170689288 TCGA-VN-A88R DEL 31 37 * * chr4 173946011 173946011 chr4 173992122 173992122 TCGA-VN-A88R DEL 43 16 AC106895.2 AC106895.2 chr4 58554209 58554209 chr4 58555958 58555958 TCGA-VN-A88R DEL 43 27 * * chr5 100484902 100484903 chr5 101538042 101538042 TCGA-VN-A88R INS 27 19 AC021086.1 * chr5 101098356 101098356 chr5 101118835 101118835 TCGA-VN-A88R DEL 29 38 * * chr5 101494036 101494036 chr5 102816400 102816400 TCGA-VN-A88R INS 7 19 * PAM chr5 143393441 143393441 chr5 143395776 143395776 TCGA-VN-A88R DEL 36 22 NR3C1 NR3C1 chr5 14471835 14471835 chr5 16057518 16057518 TCGA-VN-A88R INS 50 1 TRIO * chr5 164190917 164190917 chr5 164193498 164193498 TCGA-VN-A88R DEL 36 15 AC008662.1 AC008662.1 chr5 98620536 98620536 chr5 101549108 101549108 TCGA-VN-A88R DEL 7 50 * * chr6 112125340 112125340 chr6 154888484 154888484 TCGA-VN-A88R DEL 39 40 LAMA4 TIAM2 chr6 112659922 112659922 chr6 151156880 151156880 TCGA-VN-A88R INS 12 29 * AL138733.1 chr6 115407350 115407350 chr6 115462676 115462676 TCGA-VN-A88R DEL 15 47 * * chr6 144358350 144358350 chr6 144358667 144358667 TCGA-VN-A88R DEL 49 50 UTRN UTRN chr6 151231200 151231200 chr6 151288755 151288755 TCGA-VN-A88R DEL 29 9 * AKAP12 chr6 152592576 152592576 chr6 153565775 153565775 TCGA-VN-A88R INS 40 29 SYNE1 * chr6 30123895 30123895 chr6 30358043 30358043 TCGA-VN-A88R DEL 38 20 * * chr6 4052802 4052806 chr5 15461874 15461878 TCGA-VN-A88R BND 9 9 PRPF4B * chr6 53882767 53882767 chr6 58330532 58330532 TCGA-VN-A88R INS 48 19 LRRC1 AL445250.1 chr6 54105581 54105581 chr6 115629769 115629769 TCGA-VN-A88R DEL 7 22 MLIP * chr6 54871391 54871391 chr6 55661111 55661111 TCGA-VN-A88R DEL 11 16 FAM83B * chr6 55639536 55639536 chr6 151230480 151230480 TCGA-VN-A88R DEL 19 29 * * chr6 55826168 55826168 chr6 152717682 152717682 TCGA-VN-A88R INS 4 40 BMP5 MYCT1 chr6 58450612 58450612 chr6 151530688 151530688 TCGA-VN-A88R DEL 13 7 * CCDC170 chr6 70347502 70347502 chr6 132384616 132384616 TCGA-VN-A88R DEL 26 17 * MOXD1 chr7 117229754 117229754 chr7 117232310 117232310 TCGA-VN-A88R DEL 33 6 ST7 * chr7 158732693 158732696 chr12 93412257 93412260 TCGA-VN-A88R BND 7 24 ESYT2 UBE2N chr7 64103271 64103271 chr7 64115822 64115822 TCGA-VN-A88R DEL 38 48 AC115220.1 GUSBP6 chr7 64119186 64119186 chr7 64126398 64126398 TCGA-VN-A88R DEL 40 34 GUSBP6 GUSBP6 chr8 134734185 134734185 chr8 134734964 134734964 TCGA-VN-A88R DEL 47 20 * * chrX 45079876 45079876 chrX 45080209 45080209 TCGA-VN-A88R DEL 44 46 KDM6A KDM6A chrX 62666338 62666338 chrX 63043317 63043317 TCGA-VN-A88R DEL 35 24 * * chrX 63004640 63004640 chrX 64729336 64729336 TCGA-VN-A88R DEL 48 50 * * chr10 106779551 106779551 chr10 106861225 106861225 TCGA-EJ-A7NM DEL 26 4 SORCS1 SORCS1 chr10 56519511 56519511 chr10 56519653 56519653 TCGA-EJ-A7NM DEL 24 37 * * chr10 87929801 87929801 chr10 88075442 88075442 TCGA-EJ-A7NM DEL 5 31 PTEN * chr11 109377954 109377954 chr11 123030772 123030772 TCGA-EJ-A7NM INS 31 12 AP003049.2 * chr11 110397370 110397370 chr11 121514905 121514905 TCGA-EJ-A7NM INS 14 43 LINC02732 SORL1 chr11 120754621 120754621 chr11 123383071 123383071 TCGA-EJ-A7NM INS 32 30 GRIK4 GRAMD1B chr12 11068619 11068622 chr12 11098150 11098166 TCGA-EJ-A7NM DEL 35 47 PRH1 PRH1 chr12 20346957 20346959 chr5 109944257 109944260 TCGA-EJ-A7NM BND 17 47 * * chr12 21794080 21794080 chr12 37535529 37535529 TCGA-EJ-A7NM INS 15 34 * * chr12 72845792 72845792 chr15 94343061 94343061 TCGA-EJ-A7NM BND 45 22 * MCTP2 chr13 37321591 37321591 chr13 81220501 81220501 TCGA-EJ-A7NM DEL 15 20 * * chr13 48396844 48396844 chr12 46144110 46144110 TCGA-EJ-A7NM BND 1 34 RB1 * chr13 81399224 81399224 chr13 83573377 83573377 TCGA-EJ-A7NM DEL 13 24 * * chr14 24419932 24419932 chr1 23899811 23899811 TCGA-EJ-A7NM BND 40 37 * CNR2 chr14 40693311 40693311 chr14 46621520 46621520 TCGA-EJ-A7NM INS 22 37 * * chr14 40700116 40700116 chr14 46771027 46771027 TCGA-EJ-A7NM DEL 8 21 * * chr14 85807171 85807171 chr14 86363058 86363058 TCGA-EJ-A7NM DEL 5 3 * LINC02309 chr15 20243808 20243808 chr5 145774747 145774747 TCGA-EJ-A7NM BND 30 2 RHPN2P1 PRELID2 chr15 20250478 20250478 chr5 89277262 89277262 TCGA-EJ-A7NM BND 12 18 RHPN2P1 MEF2C-AS1 chr15 37089285 37089285 chr2 150144329 150144329 TCGA-EJ-A7NM BND 40 8 MEIS2 * chr16 24847122 24847122 chr16 24861595 24861595 TCGA-EJ-A7NM INV 37 33 SLC5A11 SLC5A11 chr16 33339602 33339602 chr16 33491248 33491248 TCGA-EJ-A7NM DEL 34 41 * * chr16 48095490 48095492 chr8 33544650 33544652 TCGA-EJ-A7NM BND 13 40 ABCC12 * chr16 7213091 7213091 chr16 7215605 7215605 TCGA-EJ-A7NM DEL 22 41 RBFOX1 RBFOX1 chr17 37936730 37936730 chr17 38244000 38244000 TCGA-EJ-A7NM INV 4 4 * NPEPPSP1 chr17 45624364 45624364 chr17 46221515 46221515 TCGA-EJ-A7NM INV 14 11 LINC02210 KANSL1 chr17 7676026 7676027 chr17 7676026 7676027 TCGA-EJ-A7NM DEL 24 19 TP53 TP53 chr18 1948323 1948323 chr18 4144003 4144003 TCGA-EJ-A7NM INS 13 44 AP005230.1 DLGAP1 chr18 30015882 30015882 chr18 30511163 30511163 TCGA-EJ-A7NM DEL 32 23 * * chr18 30496601 30496601 chr18 64921829 64921829 TCGA-EJ-A7NM DEL 4 48 * * chr18 30825916 30825916 chr18 52134612 52134612 TCGA-EJ-A7NM DEL 38 50 * * chr18 31132043 31132044 chr4 156234193 156234194 TCGA-EJ-A7NM BND 46 14 DSCAS * chr18 37241787 37241787 chr18 37280572 37280572 TCGA-EJ-A7NM DEL 30 10 * CELF4 chr18 37477178 37477178 chr18 41046137 41046137 TCGA-EJ-A7NM DEL 28 18 CELF4 * chr18 4433731 4433731 chr3 160989792 160989792 TCGA-EJ-A7NM BND 20 41 DLGAP1 PPM1L chr18 45223249 45223249 chr18 45406442 45406442 TCGA-EJ-A7NM DEL 1 48 SLC14A2 SLC14A2 chr18 45587875 45587875 chr4 156823798 156823798 TCGA-EJ-A7NM BND 21 4 SLC14A2 PDGFC chr18 4654059 4654059 chr18 5226112 5226112 TCGA-EJ-A7NM DEL 12 49 * * chr18 4848252 4848252 chr18 5910866 5910866 TCGA-EJ-A7NM DEL 6 16 AP005203.1 * chr18 51951580 51951580 chr4 154536998 154536998 TCGA-EJ-A7NM BND 35 4 * PLRG1 chr18 52018429 52018429 chr4 156816218 156816218 TCGA-EJ-A7NM BND 10 13 * PDGFC chr18 77925046 77925046 chr18 78043540 78043540 TCGA-EJ-A7NM DUP 14 40 * * chr18 79541976 79541976 chr20 51456093 51456093 TCGA-EJ-A7NM BND 46 3 * NFATC2 chr1 147230624 147230624 chr1 147346504 147346504 TCGA-EJ-A7NM INV 17 27 FMO5 LINC00624 chr1 160771675 160771675 chr7 11935569 11935569 TCGA-EJ-A7NM BND 7 28 * * chr1 214329045 214329045 chr1 237774640 237774640 TCGA-EJ-A7NM DEL 7 20 SMYD2 RYR2 chr1 226133300 226133300 chr2 189103683 189103683 TCGA-EJ-A7NM BND 4 14 * COL5A2 chr1 41527413 41527413 chr1 41545248 41545248 TCGA-EJ-A7NM DUP 38 22 HIVEP3 HIVEP3 chr1 83805109 83805109 chr1 96309198 96309198 TCGA-EJ-A7NM DEL 35 31 LINC01725 LINC01787 chr20 1580324 1580328 chr20 1613498 1613516 TCGA-EJ-A7NM DEL 17 10 SIRPB1 SIRPB1 chr20 30274391 30274391 chr20 30319979 30319979 TCGA-EJ-A7NM DEL 2 12 * * chr21 38455682 38455682 chr21 41506937 41506937 TCGA-EJ-A7NM DEL 9 24 ERG TMPRSS2 chr21 38470538 38470538 chr21 41497771 41497771 TCGA-EJ-A7NM DEL 47 31 ERG TMPRSS2 chr2 107485508 107485508 chr2 107486293 107486293 TCGA-EJ-A7NM DEL 20 20 LINC01885 LINC01885 chr2 127197917 127197917 chr13 26973472 26973472 TCGA-EJ-A7NM BND 46 33 CYP27C1 AL160035.1 chr2 128340254 128340254 chr17 66798870 66798909 TCGA-EJ-A7NM BND 2 12 * PRKCA chr2 132883442 132883442 chr6 48616927 48616927 TCGA-EJ-A7NM BND 40 10 NCKAP5 * chr2 139682708 139682708 chr2 139685966 139685966 TCGA-EJ-A7NM DEL 22 46 * * chr2 150143844 150143844 chr2 185932668 185932668 TCGA-EJ-A7NM DEL 18 37 * * chr2 152491092 152491092 chr2 152492348 152492348 TCGA-EJ-A7NM DEL 16 29 FMNL2 FMNL2 chr2 152506651 152506651 chr2 153225692 153225692 TCGA-EJ-A7NM DEL 45 32 FMNL2 * chr2 152620835 152620835 chr2 154485481 154485481 TCGA-EJ-A7NM DEL 15 39 FMNL2 * chr2 222880066 222880066 chr7 13933965 13933965 TCGA-EJ-A7NM BND 1 38 ACSL3 ETV1 chr2 229733000 229733000 chr10 5371103 5371103 TCGA-EJ-A7NM BND 21 16 * UCN3 chr2 229733227 229733227 chr10 5370536 5370536 TCGA-EJ-A7NM BND 15 26 * UCN3 chr2 45614149 45614149 chrX 47785226 47785226 TCGA-EJ-A7NM BND 32 13 * * chr2 49777402 49777402 chr2 53357583 53357583 TCGA-EJ-A7NM INS 39 41 * * chr2 50680992 50680992 chr2 53367807 53367807 TCGA-EJ-A7NM DEL 39 27 NRXN1 * chr2 54816367 54816367 chr2 239196706 239196706 TCGA-EJ-A7NM INV 28 9 EML6 HDAC4 chr2 95532730 95532730 chr2 95595312 95595312 TCGA-EJ-A7NM DUP 21 1 * TRIM43 chr3 100121581 100121581 chr3 111704734 111704734 TCGA-EJ-A7NM INS 7 15 CMSS1 PLCXD2 chr3 100987635 100987635 chr3 101195250 101195250 TCGA-EJ-A7NM DEL 32 26 ABI3BP * chr3 102432398 102432398 chr3 149394293 149394293 TCGA-EJ-A7NM DEL 30 41 ZPLD1 * chr3 108524323 108524323 chr3 108624330 108624330 TCGA-EJ-A7NM DEL 38 45 MYH15 DZIP3 chr3 117614832 117614832 chr3 118520864 118520864 TCGA-EJ-A7NM INS 28 36 * AC068633.1 chr3 117956895 117956895 chr3 118006781 118006781 TCGA-EJ-A7NM DEL 29 31 AC092691.1 AC068633.1 chr3 118111456 118111456 chr3 148584185 148584185 TCGA-EJ-A7NM DEL 33 7 AC068633.1 AC069410.1 chr3 118526127 118526127 chr3 148404685 148404685 TCGA-EJ-A7NM INS 2 12 AC068633.1 AC069410.1 chr3 146768841 146768841 chr3 146984317 146984317 TCGA-EJ-A7NM DEL 16 39 * AC092957.1 chr3 147078962 147078962 chr3 147083255 147083255 TCGA-EJ-A7NM DEL 24 19 AC092957.1 AC092957.1 chr3 147644567 147644567 chr3 147668790 147668790 TCGA-EJ-A7NM DEL 48 32 * * chr3 148380035 148380035 chr3 149527476 149527476 TCGA-EJ-A7NM DEL 42 2 LINC02046 WWTR1 chr3 148920621 148920621 chr3 161380979 161380979 TCGA-EJ-A7NM INS 11 29 AC092979.1 * chr3 150331420 150331420 chr3 151881118 151881118 TCGA-EJ-A7NM DEL 39 21 * AADACL2-AS1 chr3 150332600 150332600 chr3 165570417 165570417 TCGA-EJ-A7NM INS 38 32 * LINC01322 chr3 151483260 151483260 chr3 161109454 161109454 TCGA-EJ-A7NM INS 37 34 * NMD3 chr3 152201562 152201562 chr3 163775706 163775706 TCGA-EJ-A7NM DEL 23 39 * * chr3 152208975 152208975 chr3 163758042 163758042 TCGA-EJ-A7NM INS 45 19 * * chr3 160989792 160989792 chr18 4433731 4433731 TCGA-EJ-A7NM BND 39 49 PPM1L DLGAP1 chr3 161086028 161086028 chr3 163927657 163927657 TCGA-EJ-A7NM INS 19 47 B3GALNT1 * chr3 163100550 163100550 chr3 163102777 163102777 TCGA-EJ-A7NM DEL 15 17 AC128685.1 AC128685.1 chr3 164549021 164549021 chr3 164556437 164556437 TCGA-EJ-A7NM DEL 17 5 * * chr3 94313753 94313753 chr3 95908176 95908176 TCGA-EJ-A7NM INS 22 21 * * chr3 95590308 95590310 chr3 95593758 95593758 TCGA-EJ-A7NM DEL 2 19 * * chr3 95889997 95889997 chr3 96607423 96607423 TCGA-EJ-A7NM DEL 2 21 * * chr3 97282477 97282477 chr3 148835715 148835715 TCGA-EJ-A7NM INS 24 20 EPHA6 CPB1 chr3 98032626 98032626 chr3 112383035 112383035 TCGA-EJ-A7NM INS 24 19 GABRR3 * chr3 98986958 98986958 chr3 107706843 107706843 TCGA-EJ-A7NM DEL 32 18 AC091212.1 BBX chr3 99000406 99000406 chr3 107710292 107710293 TCGA-EJ-A7NM INS 9 21 AC091212.1 BBX chr3 99018356 99018356 chr3 105030447 105030447 TCGA-EJ-A7NM DEL 36 47 AC091212.1 * chr3 99225556 99225556 chr3 109116087 109116087 TCGA-EJ-A7NM INS 7 8 * MORC1 chr4 103896186 103896186 chr4 103897043 103897043 TCGA-EJ-A7NM DEL 38 40 * * chr4 106887315 106887315 chr4 106988793 106988793 TCGA-EJ-A7NM DEL 41 45 * DKK2 chr4 112006114 112006114 chr4 157954364 157954366 TCGA-EJ-A7NM INS 1 31 AC004704.1 * chr4 116018152 116018152 chr4 126670713 126670713 TCGA-EJ-A7NM DEL 43 5 AC027613.1 * chr4 135501046 135501046 chr4 135509927 135509927 TCGA-EJ-A7NM DEL 18 27 * * chr4 137357354 137357354 chr4 137381204 137381204 TCGA-EJ-A7NM DEL 39 40 * * chr4 156083594 156083594 chr4 156459561 156459561 TCGA-EJ-A7NM DEL 19 38 * * chr4 156441305 156441305 chr4 156683642 156683642 TCGA-EJ-A7NM DEL 32 26 * * chr4 156505715 156505715 chr18 46196612 46196612 TCGA-EJ-A7NM BND 38 23 * C18orf25 chr4 156711904 156711904 chr18 52829569 52829569 TCGA-EJ-A7NM BND 8 39 * DCC chr4 156816218 156816218 chr18 52018429 52018429 TCGA-EJ-A7NM BND 26 6 PDGFC * chr4 172097324 172097324 chr4 177875490 177875490 TCGA-EJ-A7NM DEL 5 27 GALNTL6 LINC01098 chr4 172109850 172109850 chr4 177854910 177854910 TCGA-EJ-A7NM INS 20 8 GALNTL6 LINC01098 chr4 175499284 175499284 chr4 175736663 175736663 TCGA-EJ-A7NM DEL 12 12 * GPM6A chr4 59197039 59197039 chr4 59197378 59197378 TCGA-EJ-A7NM DEL 17 5 * * chr4 62795058 62795058 chr4 62796157 62796157 TCGA-EJ-A7NM INV 10 1 * * chr4 64873946 64873946 chr4 130666991 130666991 TCGA-EJ-A7NM DEL 5 15 * * chr4 67148661 67148661 chr4 130093677 130093677 TCGA-EJ-A7NM DEL 5 27 * * chr4 67166419 67166419 chr4 130733276 130733276 TCGA-EJ-A7NM INS 17 17 * * chr4 67324776 67324776 chr4 130724028 130724028 TCGA-EJ-A7NM INS 7 13 * * chr5 100009431 100009431 chr5 100048992 100048992 TCGA-EJ-A7NM DEL 30 27 * MTND5P10 chr5 101139224 101139224 chr1 248514645 248514645 TCGA-EJ-A7NM BND 25 8 * OR2G6 chr5 106613565 106613565 chr5 106613758 106613758 TCGA-EJ-A7NM DEL 18 32 * * chr5 109944257 109944260 chr12 20346957 20346959 TCGA-EJ-A7NM BND 6 30 * * chr5 112190622 112190622 chr5 123375061 123375061 TCGA-EJ-A7NM DEL 35 32 EPB41L4A CEP120 chr5 113450494 113450494 chr5 113451012 113451012 TCGA-EJ-A7NM DEL 50 39 MCC MCC chr5 123371529 123371529 chr12 21121700 21121700 TCGA-EJ-A7NM BND 2 41 CEP120 AC022335.1 chr5 20703630 20703630 chr5 96810924 96810924 TCGA-EJ-A7NM INS 21 42 LINC02241 * chr5 22591305 22591305 chr5 121469862 121469862 TCGA-EJ-A7NM DEL 3 42 CDH12 * chr5 25333938 25333938 chr5 31400192 31400192 TCGA-EJ-A7NM DEL 24 7 * * chr5 98699056 98699056 chr5 120707528 120707528 TCGA-EJ-A7NM DEL 50 23 * * chr6 46177490 46177490 chr6 58452848 58452848 TCGA-EJ-A7NM DEL 12 50 * * chr6 48616927 48616927 chr2 132883442 132883442 TCGA-EJ-A7NM BND 42 5 * NCKAP5 chr6 58451218 58451218 chr2 131961271 131961271 TCGA-EJ-A7NM BND 46 18 * AJ239322.2 chr6 65149564 65149564 chr6 65251504 65251504 TCGA-EJ-A7NM DEL 2 41 EYS EYS chr6 65405987 65405987 chr6 65533405 65533405 TCGA-EJ-A7NM DEL 17 46 EYS EYS chr6 84196976 84196976 chr6 84199907 84199907 TCGA-EJ-A7NM DEL 18 8 CEP162 CEP162 chr7 10216429 10216429 chr7 10219365 10219365 TCGA-EJ-A7NM DEL 17 30 * * chr7 10344231 10344231 chr7 13892506 13892506 TCGA-EJ-A7NM DEL 35 29 * ETV1 chr7 117153670 117153670 chr7 117161896 117161896 TCGA-EJ-A7NM DEL 11 7 ST7 ST7 chr7 117161392 117161392 chr7 127409571 127409571 TCGA-EJ-A7NM DEL 49 20 ST7 ZNF800 chr7 11921920 11921920 chr7 15368169 15368169 TCGA-EJ-A7NM DEL 38 24 * AGMO chr7 127371211 127371211 chr7 128598271 128598271 TCGA-EJ-A7NM DEL 10 42 ZNF800 AC090114.3 chr7 128095810 128095810 chr7 128129494 128129494 TCGA-EJ-A7NM INV 40 13 * * chr7 13566063 13566063 chr7 13599310 13599310 TCGA-EJ-A7NM DEL 12 16 AC011287.1 AC011287.1 chr7 16047196 16047196 chr1 160302939 160302939 TCGA-EJ-A7NM BND 5 44 * COPA chr7 33468881 33468881 chr7 33470715 33470715 TCGA-EJ-A7NM DEL 1 31 BBS9 BBS9 chr7 54230744 54230744 chr7 54321029 54321029 TCGA-EJ-A7NM INV 36 32 * * chr7 8334795 8334795 chr7 15251264 15251264 TCGA-EJ-A7NM INS 6 42 AC007128.1 AGMO chr7 84895537 84895537 chr7 128479099 128479099 TCGA-EJ-A7NM INS 36 1 * AC010655.4 chr7 86742477 86742477 chr7 127199742 127199742 TCGA-EJ-A7NM INS 38 33 GRM3 GRM8 chr7 87387730 87387730 chr7 124902461 124902461 TCGA-EJ-A7NM DEL 48 37 CROT POT1 chr7 87406447 87406447 chr7 129626762 129626762 TCGA-EJ-A7NM INS 25 36 ABCB4 NRF1 chr7 8943012 8943012 chr7 12380849 12380849 TCGA-EJ-A7NM INS 22 33 * VWDE chr7 8960802 8960802 chr7 13322396 13322396 TCGA-EJ-A7NM DEL 24 25 * AC011287.1 chr8 119920643 119920643 chr8 120562254 120562254 TCGA-EJ-A7NM DEL 18 45 DEPTOR SNTB1 chr8 119921575 119921588 chr8 120134055 120134055 TCGA-EJ-A7NM INS 35 25 DEPTOR COL14A1 chr8 119921575 119921588 chr8 121155987 121155987 TCGA-EJ-A7NM INS 36 46 DEPTOR * chr8 119922491 119922491 chr8 120135233 120135233 TCGA-EJ-A7NM DEL 41 40 DEPTOR COL14A1 chr8 120570311 120570311 chr8 122223241 122223241 TCGA-EJ-A7NM DEL 23 15 SNTB1 * chr8 121294503 121294503 chr8 122651447 122651447 TCGA-EJ-A7NM DEL 29 21 * * chr8 122223721 122223721 chr8 122654218 122654218 TCGA-EJ-A7NM DEL 39 48 * * chr8 32822486 32822486 chr8 32833743 32833743 TCGA-EJ-A7NM DEL 37 17 * * chr8 33544650 33544652 chr16 48095490 48095492 TCGA-EJ-A7NM BND 27 42 * ABCC12 chr8 46606203 46606203 chr8 47344913 47344913 TCGA-EJ-A7NM DUP 7 32 ASNSP1 SPIDR chr8 83306040 83306040 chr8 83310076 83310076 TCGA-EJ-A7NM DEL 38 21 * * chrX 1459745 1459745 chrX 1474242 1474242 TCGA-EJ-A7NM INV 8 24 * P2RY8 chr10 42574726 42574726 chr10 43455539 43455539 TCGA-XJ-A83G INV 44 29 ZNF33B ZNF487 chr10 58671589 58671589 chr10 65669972 65669972 TCGA-XJ-A83G DUP 50 22 BICC1 LINC01515 chr10 74216455 74216455 chr10 80494526 80494526 TCGA-XJ-A83G INV 12 30 ADK TSPAN14 chr10 76138387 76138387 chr10 82728690 82728690 TCGA-XJ-A83G DUP 28 2 LRMDA NRG3 chr10 77403917 77403917 chr20 58336344 58336344 TCGA-XJ-A83G BND 46 26 KCNMA1 RAB22A chr10 96140912 96140912 chr10 98889635 98889635 TCGA-XJ-A83G INV 2 14 ZNF518A HPSE2 chr11 105364520 105364520 chr11 105818191 105818191 TCGA-XJ-A83G DEL 19 44 CARD18 GRIA4 chr11 123888445 123888445 chr11 124108988 124108988 TCGA-XJ-A83G DEL 50 43 * OR10N1P chr11 70658205 70658205 chr20 58196730 58196730 TCGA-XJ-A83G BND 13 10 SHANK2 * chr11 91096123 91096123 chr11 91096432 91096432 TCGA-XJ-A83G DEL 31 11 * * chr12 104123981 104123981 chr13 24937863 24937863 TCGA-XJ-A83G BND 4 6 NFYB TPTE2P1 chr12 110880894 110880894 chr12 131540123 131540123 TCGA-XJ-A83G DEL 47 4 CCDC63 * chr12 81139121 81139121 chrX 66816524 66816524 TCGA-XJ-A83G BND 41 6 ACSS3 * chr12 81221694 81221694 chrX 66801700 66801700 TCGA-XJ-A83G BND 27 5 ACSS3 * chr12 81348103 81348103 chrX 67140837 67140837 TCGA-XJ-A83G BND 18 19 PPFIA2 * chr12 81777941 81777941 chrX 64833885 64833885 TCGA-XJ-A83G BND 46 8 * * chr12 82399143 82399143 chrX 66693320 66693320 TCGA-XJ-A83G BND 50 43 METTL25 * chr13 107494532 107494532 chr14 76276575 76276575 TCGA-XJ-A83G BND 14 42 FAM155A * chr13 108825765 108825765 chr13 109127521 109127521 TCGA-XJ-A83G INV 36 10 MYO16 MYO16 chr13 109347492 109347492 chr13 109348041 109348041 TCGA-XJ-A83G INV 17 15 * * chr13 110372251 110372251 chr13 110374652 110374652 TCGA-XJ-A83G INV 37 11 COL4A2 COL4A2 chr13 112593170 112593170 chr13 112727688 112727688 TCGA-XJ-A83G DEL 45 11 * ATP11A chr13 21658269 21658269 chr13 30431110 30431110 TCGA-XJ-A83G INV 29 16 * * chr13 23229499 23229499 chr13 30320101 30320101 TCGA-XJ-A83G DEL 33 28 SGCG LINC00427 chr13 85825814 85825814 chr13 106857994 106857994 TCGA-XJ-A83G DEL 21 34 * * chr13 85897782 85897782 chr13 107366756 107366756 TCGA-XJ-A83G INS 35 4 * FAM155A chr14 60271535 60271535 chr14 69370169 69370169 TCGA-XJ-A83G DEL 27 16 PPM1A * chr14 67974311 67974311 chr14 68156965 68156965 TCGA-XJ-A83G DEL 50 10 RAD51B RAD51B chr15 20535053 20535053 chr15 28561001 28561001 TCGA-XJ-A83G INV 20 13 GOLGA6L6 AC138749.1 chr15 20535694 20535694 chr15 22466238 22466238 TCGA-XJ-A83G INV 5 22 GOLGA6L6 GOLGA6L22 chr15 22770761 22770761 chr15 28842630 28842630 TCGA-XJ-A83G INV 34 39 AC138649.1 PDCD6IPP2 chr16 31959840 31959840 chr16 33951568 33951568 TCGA-XJ-A83G INV 49 20 * IGHV3OR16-16 chr16 46915454 46915454 chr16 46917586 46917586 TCGA-XJ-A83G INV 40 11 GPT2 GPT2 chr17 19174375 19174375 chr17 19203984 19203984 TCGA-XJ-A83G DEL 12 35 AC007952.8 AC106017.1 chr17 31395642 31395642 chr17 48756444 48756444 TCGA-XJ-A83G INV 45 49 RAB11FIP4 * chr17 53586131 53586131 chr17 64020430 64020430 TCGA-XJ-A83G INV 18 27 AC034268.2 ICAM2 chr17 53682940 53682940 chr17 53687439 53687439 TCGA-XJ-A83G INV 19 29 AC034268.2 AC034268.2 chr17 61649660 61649660 chr17 61653088 61653088 TCGA-XJ-A83G INV 11 50 * * chr17 61670215 61670215 chr17 61670430 61670430 TCGA-XJ-A83G INV 34 13 * * chr17 61776102 61776102 chr17 62397774 62397774 TCGA-XJ-A83G DEL 31 48 BRIP1 EFCAB3 chr17 62494103 62494103 chr19 7084212 7084212 TCGA-XJ-A83G BND 34 24 TLK2 ZNF557 chr17 63336242 63336242 chr20 35307141 35307141 TCGA-XJ-A83G BND 5 26 TANC2 UQCC1 chr17 63359511 63359511 chrX 2723738 2723738 TCGA-XJ-A83G BND 14 3 TANC2 CD99 chr17 64012746 64012746 chrX 2737304 2737304 TCGA-XJ-A83G BND 28 24 ICAM2 CD99 chr17 64877129 64877129 chrX 1651837 1651837 TCGA-XJ-A83G BND 11 22 LRRC37A3 * chr17 74515590 74515590 chr17 75183873 75183873 TCGA-XJ-A83G INS 19 39 * SUMO2 chr18 40087828 40087828 chr18 40088115 40088115 TCGA-XJ-A83G INS 47 12 LINC01477 LINC01477 chr19 10656312 10656312 chr20 37652402 37652402 TCGA-XJ-A83G BND 41 31 ILF3 * chr19 16893919 16893919 chr19 17551680 17551680 TCGA-XJ-A83G INV 32 34 CPAMD8 NIBAN3 chr19 28784224 28784224 chr19 30482307 30482307 TCGA-XJ-A83G DUP 6 49 * ZNF536 chr19 29863818 29863818 chr19 30235943 30235943 TCGA-XJ-A83G INV 11 42 * ZNF536 chr19 29917803 29917803 chr19 29918182 29918182 TCGA-XJ-A83G INV 17 32 AC008507.3 * chr19 54738697 54738697 chr19 54833844 54833844 TCGA-XJ-A83G DUP 17 2 KIR2DL3 KIR2DS4 chr19 57639245 57639245 chrX 52003109 52003109 TCGA-XJ-A83G BND 25 43 ZNF211 * chr19 7557177 7557177 chr19 7557305 7557305 TCGA-XJ-A83G INV 6 23 PNPLA6 PNPLA6 chr19 9051575 9051575 chr20 34321905 34321905 TCGA-XJ-A83G BND 18 27 * * chr19 9535324 9535324 chr19 9535468 9535468 TCGA-XJ-A83G INV 6 22 ZNF426 ZNF426 chr20 36319615 36319615 chr20 36320116 36320116 TCGA-XJ-A83G INV 3 22 DLGAP4 DLGAP4 chr21 28749476 28749476 chr21 28752493 28752493 TCGA-XJ-A83G INV 37 38 * * chr21 46106420 46106420 chr21 46170307 46170307 TCGA-XJ-A83G INV 30 25 COL6A2 SPATC1L chr22 18351275 18351275 chr22 18768342 18768342 TCGA-XJ-A83G DUP 10 15 * * chr2 103623967 103623967 chr2 140874362 140874362 TCGA-XJ-A83G DEL 38 30 * LRP1B chr2 11114125 11114125 chr2 26655104 26655118 TCGA-XJ-A83G DEL 49 48 AC062028.1 * chr2 142569737 142569737 chr2 213130283 213130283 TCGA-XJ-A83G DEL 45 43 * IKZF2 chr2 52868077 52868077 chr8 115242946 115242946 TCGA-XJ-A83G BND 37 49 AC010967.1 * chr3 120397420 120397420 chr3 120588607 120588607 TCGA-XJ-A83G DUP 13 18 AC063952.1 * chr3 120568733 120568733 chr3 160666981 160666981 TCGA-XJ-A83G DUP 12 8 * * chr3 120606953 120606953 chr3 160603623 160603623 TCGA-XJ-A83G INV 49 25 * * chr3 198139964 198139964 chr7 77155 77155 TCGA-XJ-A83G BND 48 42 * AC093627.1 chr3 89246701 89246701 chr3 134537003 134537003 TCGA-XJ-A83G DUP 4 27 EPHA3 CEP63 chr3 89249076 89249076 chr3 164862346 164862346 TCGA-XJ-A83G INV 48 19 EPHA3 * chr3 89274573 89274573 chr8 72997696 72997696 TCGA-XJ-A83G BND 36 11 EPHA3 * chr4 105244874 105244874 chr4 105664512 105664512 TCGA-XJ-A83G DUP 13 6 TET2 ARHGEF38 chr4 149257597 149257597 chr4 149257883 149257883 TCGA-XJ-A83G DEL 46 2 LINC02355 LINC02355 chr4 162014099 162014099 chr4 171315895 171315895 TCGA-XJ-A83G DUP 50 23 FSTL5 * chr4 177043681 177043681 chr4 183826864 183826864 TCGA-XJ-A83G INS 32 14 * STOX2 chr4 179454481 179454481 chr4 183834872 183834872 TCGA-XJ-A83G DEL 43 34 AC020551.1 STOX2 chr4 17947290 17947290 chrX 23197339 23197339 TCGA-XJ-A83G BND 23 12 LCORL PTCHD1-AS chr4 184499002 184499002 chr4 185889074 185889074 TCGA-XJ-A83G DEL 17 47 * SORBS2 chr4 185675254 185675254 chr8 113989314 113989314 TCGA-XJ-A83G BND 36 6 SORBS2 * chr4 188450740 188450740 chr4 188814258 188814258 TCGA-XJ-A83G DEL 3 27 LINC01060 * chr4 34422145 34422145 chr4 34429184 34429184 TCGA-XJ-A83G DEL 22 37 * * chr4 52815288 52815288 chr10 93809654 93809654 TCGA-XJ-A83G BND 7 21 LINC01618 * chr5 100550083 100550083 chr5 169827311 169827311 TCGA-XJ-A83G DEL 15 9 FAM174A DOCK2 chr5 162957417 162957417 chr5 166755752 166755752 TCGA-XJ-A83G INS 30 22 AC113414.1 * chr5 55616592 55616592 chr5 60930176 60930176 TCGA-XJ-A83G DUP 22 19 * ERCC8 chr5 59014166 59014166 chr5 59137689 59137689 TCGA-XJ-A83G DEL 46 49 PDE4D PDE4D chr5 692045 692045 chr5 783334 783334 TCGA-XJ-A83G INV 11 11 TPPP * chr5 79102435 79102435 chr5 88304289 88304289 TCGA-XJ-A83G INV 49 14 DMGDH TMEM161B-AS1 chr5 87416379 87416379 chr20 47220438 47220438 TCGA-XJ-A83G BND 19 4 AC018754.1 ZMYND8 chr5 98181844 98181844 chr5 103493896 103493896 TCGA-XJ-A83G DEL 6 30 * PDZPH1P chr5 99832840 99832840 chr5 160883663 160883663 TCGA-XJ-A83G DEL 29 46 * * chr5 99890335 99890335 chr5 101438507 101438507 TCGA-XJ-A83G INS 22 7 * * chr5 99962490 99962490 chr5 170806690 170806690 TCGA-XJ-A83G DEL 42 45 * GABRP chr5 99972665 99972665 chr5 103847161 103847161 TCGA-XJ-A83G INS 45 20 * * chr6 165127883 165127883 chr20 38194563 38194563 TCGA-XJ-A83G BND 12 41 * * chr6 61180561 61180561 chr6 61299972 61299972 TCGA-XJ-A83G DEL 43 29 * * chr6 64275414 64275414 chr6 68108541 68108541 TCGA-XJ-A83G DEL 17 16 EYS * chr6 66232953 66232953 chr6 69044328 69044328 TCGA-XJ-A83G INS 30 3 * ADGRB3 chr6 69552805 69552805 chr6 70231309 70231309 TCGA-XJ-A83G DEL 29 2 * COL9A1 chr6 69553536 69553536 chr6 70047562 70047562 TCGA-XJ-A83G INS 18 26 * COL19A1 chr7 114986582 114986582 chr7 115164375 115164375 TCGA-XJ-A83G DEL 18 8 MDFIC LINC01392 chr7 124536381 124536381 chr7 124539218 124539218 TCGA-XJ-A83G INV 14 43 * * chr8 101647880 101647880 chr19 19668553 19668553 TCGA-XJ-A83G BND 1 2 GRHL2 ZNF101 chr8 106818921 106818921 chr8 106819109 106819109 TCGA-XJ-A83G INV 36 34 * * chr8 124062712 124062712 chr8 124062870 124062870 TCGA-XJ-A83G INV 32 42 FER1L6 FER1L6 chr8 46076949 46076949 chr8 46468273 46468273 TCGA-XJ-A83G DEL 5 3 * * chr8 81328032 81328032 chr8 113336834 113336834 TCGA-XJ-A83G INV 35 24 * CSMD3 chr8 81777080 81777080 chr10 76138439 76138439 TCGA-XJ-A83G BND 49 9 * LRMDA chr9 36869536 36869536 chr19 8720161 8720173 TCGA-XJ-A83G BND 46 12 PAX5 OR2Z1 chr9 61533703 61533705 chr9 61992749 61992749 TCGA-XJ-A83G INV 37 41 * * chrX 48281390 48281390 chrX 52613049 52613049 TCGA-XJ-A83G DUP 2 23 AC245047.4 SSXP1 chrX 48692063 48692063 chrX 49169709 49169709 TCGA-XJ-A83G INV 2 40 * * chrX 64809897 64809897 chrX 67157448 67157448 TCGA-XJ-A83G INV 22 36 * * chrX 64823679 64823679 chrX 67138061 67138061 TCGA-XJ-A83G INV 25 2 * * chrX 65729345 65729345 chrX 67142418 67142418 TCGA-XJ-A83G INV 46 25 MSN * chrX 65731683 65731683 chrX 67826296 67826296 TCGA-XJ-A83G INV 44 20 MSN * chrX 67136112 67136112 chrX 67137552 67137552 TCGA-XJ-A83G INV 50 46 * * chrX 68215196 68215196 chrX 68215323 68215323 TCGA-XJ-A83G INV 15 5 OPHN1 OPHN1 chrX 68489121 68489121 chrX 68489336 68489336 TCGA-XJ-A83G INV 44 10 * * chrX 68847860 68847860 chrX 68847907 68847907 TCGA-XJ-A83G INV 12 43 * * chrX 69087812 69087812 chrX 69088118 69088118 TCGA-XJ-A83G INV 40 27 * * chrX 69139591 69139591 chrX 69139660 69139660 TCGA-XJ-A83G INV 46 17 * * chrX 69323428 69323428 chrX 69323735 69323735 TCGA-XJ-A83G INV 9 35 * * chrX 69814034 69814034 chrX 69840799 69840799 TCGA-XJ-A83G INV 26 21 EDA EDA chrX 69820511 69820511 chrX 69820748 69820748 TCGA-XJ-A83G INV 46 39 EDA EDA chr10 111595680 111595680 chr10 111632889 111632889 TCGA-G9-7510 DUP 34 42 * * chr10 115467824 115467824 chr10 115509777 115509777 TCGA-G9-7510 DUP 31 30 ATRNL1 ATRNL1 chr10 119567037 119567037 chr10 119602825 119602825 TCGA-G9-7510 DUP 15 14 * * chr10 123790917 123790917 chr10 123826199 123826199 TCGA-G9-7510 DUP 2 30 CPXM2 CPXM2 chr10 62692305 62692305 chr10 62754124 62754124 TCGA-G9-7510 DUP 46 28 AC067751.1 AC067751.1 chr10 74140899 74140899 chr22 44476482 44476482 TCGA-G9-7510 BND 25 45 AP3M1 * chr10 87818807 87818807 chr10 88393289 88393289 TCGA-G9-7510 DEL 46 49 ATAD1 RNLS chr10 98608115 98608115 chr10 98650990 98650990 TCGA-G9-7510 DUP 48 38 HPSE2 HPSE2 chr10 98954406 98954406 chr19 50862733 50862733 TCGA-G9-7510 BND 31 31 HPSE2 KLK2 chr11 106116652 106116652 chr11 106151799 106151799 TCGA-G9-7510 DUP 28 14 LINC02719 * chr11 129883446 129883446 chr11 134986714 134986714 TCGA-G9-7510 INS 3 10 NFRKB AP003062.1 chr11 16780000 16780000 chr11 16820589 16820589 TCGA-G9-7510 DUP 6 17 PLEKHA7 PLEKHA7 chr11 1861676 1861690 chr11 1894040 1894040 TCGA-G9-7510 DUP 13 4 LSP1 * chr11 38585317 38585317 chr11 38981846 38981846 TCGA-G9-7510 DEL 42 8 * * chr11 38884578 38884578 chr11 38894256 38894256 TCGA-G9-7510 DEL 31 5 * * chr11 40082804 40082804 chr11 50414596 50414596 TCGA-G9-7510 DEL 6 46 * AC024405.1 chr11 41839816 41839816 chr11 42676899 42676899 TCGA-G9-7510 DEL 9 47 LINC01499 * chr11 43897740 43897740 chr11 43925301 43925301 TCGA-G9-7510 DEL 28 49 ALKBH3 AC087521.3 chr11 48363393 48363393 chr11 50310835 50310835 TCGA-G9-7510 INS 49 44 * AC024405.2 chr11 49685487 49685487 chr11 132026802 132026802 TCGA-G9-7510 DEL 42 19 AC136759.1 NTM chr11 62942439 62942439 chr11 62974168 62974168 TCGA-G9-7510 DUP 48 28 SLC22A6 SLC22A6 chr11 85975710 85975710 chr11 86031688 86031688 TCGA-G9-7510 DEL 12 3 PICALM PICALM chr11 8618696 8618696 chr11 8677399 8677399 TCGA-G9-7510 DUP 1 14 TRIM66 TRIM66 chr11 86518523 86518523 chr11 90844664 90844664 TCGA-G9-7510 DEL 16 19 AP001831.1 DISC1FP1 chr11 87311870 87311870 chr11 88977780 88977780 TCGA-G9-7510 DEL 6 9 TMEM135 GRM5 chr11 88170049 88170049 chr11 88924388 88924388 TCGA-G9-7510 DEL 13 25 RAB38 GRM5 chr12 109634485 109634485 chr12 118707542 118707542 TCGA-G9-7510 INV 9 46 * * chr12 11032951 11032951 chr12 11065089 11065089 TCGA-G9-7510 DUP 21 38 PRH1 PRH1 chr12 11066005 11066005 chr12 11098150 11098166 TCGA-G9-7510 DEL 1 22 PRH1 PRH1 chr12 111192554 111192554 chr12 111239586 111239586 TCGA-G9-7510 DUP 18 11 CUX2 CUX2 chr12 11353557 11353557 chr12 11393102 11393102 TCGA-G9-7510 DUP 39 44 PRB1 PRB1 chr12 118693034 118693034 chr12 118732856 118732856 TCGA-G9-7510 DUP 43 23 * * chr12 12718174 12718179 chr12 12718174 12718179 TCGA-G9-7510 DEL 36 3 CDKN1B CDKN1B chr12 1300959 1300959 chr12 1342846 1342846 TCGA-G9-7510 DUP 42 40 ERC1 ERC1 chr12 29934400 29934400 chr12 124178152 124178152 TCGA-G9-7510 INV 41 46 * RFLNA chr12 45721 45721 chr12 46109 46109 TCGA-G9-7510 INV 25 16 * * chr12 51302435 51302435 chr12 51342507 51342507 TCGA-G9-7510 DUP 1 15 BIN2 CELA1 chr12 56221281 56221281 chr12 56263064 56263064 TCGA-G9-7510 DUP 22 33 RNF41 * chr12 58559268 58559268 chr12 109687825 109687825 TCGA-G9-7510 DUP 40 15 AC020637.1 * chr13 100491542 100491542 chr13 100524823 100524823 TCGA-G9-7510 DUP 15 34 PCCA PCCA chr13 32467790 32467790 chr13 32499224 32499224 TCGA-G9-7510 DUP 30 39 N4BP2L2 N4BP2L2 chr13 32938917 32938917 chr13 43796040 43796040 TCGA-G9-7510 INV 21 38 * * chr13 42114148 42114154 chr13 46479644 46479644 TCGA-G9-7510 DEL 27 21 DGKH LINC01198 chr13 42114148 42114154 chr13 46478377 46478377 TCGA-G9-7510 DUP 32 43 DGKH LINC01198 chr13 63883218 63883218 chr13 63927396 63927396 TCGA-G9-7510 DUP 40 7 LINC00355 LINC00355 chr13 78065637 78065637 chr13 78110279 78110279 TCGA-G9-7510 DUP 38 13 OBI1-AS1 OBI1-AS1 chr13 83745654 83745654 chr13 83787112 83787112 TCGA-G9-7510 DUP 11 48 * * chr13 98328963 98328963 chr13 98386814 98386814 TCGA-G9-7510 DUP 34 5 FARP1 FARP1 chr14 105568756 105568757 chr14 105688710 105688710 TCGA-G9-7510 INV 26 41 * * chr14 105568898 105568911 chr14 105690059 105690059 TCGA-G9-7510 DUP 44 25 * * chr14 105568937 105568981 chr14 105688275 105688275 TCGA-G9-7510 INV 14 19 * * chr14 105569118 105569144 chr14 105691140 105691140 TCGA-G9-7510 DUP 45 49 * * chr14 105569185 105569185 chr14 105683320 105683320 TCGA-G9-7510 INV 37 34 * * chr14 105569274 105569274 chr14 105689335 105689335 TCGA-G9-7510 DUP 28 29 * * chr14 105569308 105569308 chr14 105687684 105687684 TCGA-G9-7510 INV 20 31 * * chr14 105569529 105569547 chr14 105688776 105688776 TCGA-G9-7510 DEL 19 11 * * chr14 105569933 105569933 chr14 105689632 105689637 TCGA-G9-7510 DEL 5 41 * * chr14 20130044 20130044 chr22 41940806 41940806 TCGA-G9-7510 BND 39 8 * CENPM chr14 20131402 20131402 chr22 41443049 41443049 TCGA-G9-7510 BND 42 27 * TOB2 chr14 37629447 37629447 chr14 37666356 37666356 TCGA-G9-7510 DUP 8 32 TTC6 TTC6 chr14 37935897 37935897 chr7 13937780 13937780 TCGA-G9-7510 BND 9 10 TTC6 ETV1 chr14 41138662 41138662 chr14 41200894 41200894 TCGA-G9-7510 DEL 18 46 * * chr14 63363561 63363561 chr14 63396381 63396381 TCGA-G9-7510 DUP 37 10 * PPP2R5E chr14 64117947 64117947 chr14 64158181 64158181 TCGA-G9-7510 DUP 33 12 SYNE2 SYNE2 chr14 70715777 70715777 chr7 16116673 16116673 TCGA-G9-7510 BND 1 44 * CRPPA chr14 90204959 90204959 chr14 90248472 90248472 TCGA-G9-7510 DUP 47 18 * * chr15 38401940 38401940 chr15 38437335 38437335 TCGA-G9-7510 DUP 41 15 * * chr15 66257110 66257110 chr15 66312806 66312806 TCGA-G9-7510 DUP 9 38 * DIS3L chr15 69437813 69437813 chr15 69475961 69475961 TCGA-G9-7510 DUP 18 36 KIF23 DRAIC chr15 73674182 73674182 chr15 73706962 73706962 TCGA-G9-7510 DUP 3 3 * CD276 chr15 93629458 93629458 chr15 93677212 93677212 TCGA-G9-7510 DUP 33 12 AC110023.1 AC110023.1 chr16 29766893 29766893 chr16 29805459 29805459 TCGA-G9-7510 DUP 36 27 * MAZ chr16 29840675 29840675 chr16 29876721 29876721 TCGA-G9-7510 DUP 5 32 MVP SEZ6L2 chr16 31363996 31363996 chr16 31410894 31410894 TCGA-G9-7510 DUP 28 48 ITGAX ITGAD chr16 3588460 3588460 chr16 3624864 3624864 TCGA-G9-7510 DUP 47 8 SLX4 DNASE1 chr16 4584243 4584243 chr16 4618955 4618955 TCGA-G9-7510 DUP 25 16 C16orf96 MGRN1 chr16 57774107 57774107 chr16 59789817 59789817 TCGA-G9-7510 DEL 32 15 KIFC3 * chr16 57775546 57775546 chr16 59793646 59793646 TCGA-G9-7510 INS 1 24 KIFC3 * chr16 57917544 57917544 chr16 62359595 62359595 TCGA-G9-7510 INS 28 41 CNGB1 * chr16 59803425 59803425 chr16 62459989 62459989 TCGA-G9-7510 INS 45 38 * * chr16 62365464 62365464 chr16 62674817 62674817 TCGA-G9-7510 INS 21 33 * * chr16 72583007 72583007 chr16 72681214 72681214 TCGA-G9-7510 DEL 3 36 LINC01572 AC004943.2 chr16 9349398 9349398 chr5 99065299 99065299 TCGA-G9-7510 BND 41 36 * * chr17 1705352 1705352 chr17 1736686 1736686 TCGA-G9-7510 DUP 34 47 TLCD2 WDR81 chr17 28669780 28669780 chr17 28703156 28703156 TCGA-G9-7510 DUP 47 43 SUPT6H * chr17 30181376 30181376 chr17 30237426 30237426 TCGA-G9-7510 DUP 25 28 NSRP1 SLC6A4 chr17 4322056 4322056 chr17 4365605 4365605 TCGA-G9-7510 DUP 10 10 UBE2G1 UBE2G1 chr17 45614474 45614474 chr17 46231658 46231658 TCGA-G9-7510 DEL 7 27 * * chr17 46178993 46178993 chr17 48177273 48177273 TCGA-G9-7510 DUP 8 43 KANSL1 SKAP1 chr17 56792396 56792401 chr17 66799001 66799010 TCGA-G9-7510 DUP 47 3 C17orf67 PRKCA chr17 56792730 56792746 chr17 66798870 66798909 TCGA-G9-7510 DUP 42 36 C17orf67 PRKCA chr17 56793166 56793166 chr17 66798935 66798935 TCGA-G9-7510 INV 39 43 C17orf67 PRKCA chr17 61507105 61507105 chr17 61563632 61563632 TCGA-G9-7510 DUP 34 48 * * chr17 61689465 61689465 chr17 61726681 61726681 TCGA-G9-7510 DUP 35 17 BRIP1 BRIP1 chr17 65752994 65752994 chr17 65797498 65797498 TCGA-G9-7510 DUP 34 1 CEP112 CEP112 chr17 7678559 7678559 chr16 68831088 68831088 TCGA-G9-7510 BND 14 8 TP53 CDH1 chr18 41610122 41610122 chr18 41647933 41647933 TCGA-G9-7510 DUP 1 19 KC6 * chr18 55265349 55265349 chr18 55305907 55305907 TCGA-G9-7510 DUP 22 2 TCF4 TCF4 chr18 57869677 57869677 chr18 57914786 57914786 TCGA-G9-7510 DUP 21 42 * * chr19 19026612 19026612 chr19 19058151 19058151 TCGA-G9-7510 DUP 31 41 SUGP2 ARMC6 chr19 31080891 31080891 chr19 31115507 31115507 TCGA-G9-7510 DUP 41 12 * AC020912.1 chr19 31241961 31241961 chr19 31280099 31280099 TCGA-G9-7510 DUP 26 38 * TSHZ3 chr19 33100992 33100992 chr19 33134729 33134729 TCGA-G9-7510 DUP 24 20 GPATCH1 WDR88 chr19 33772984 33772984 chr19 33835272 33835272 TCGA-G9-7510 DUP 20 25 CHST8 * chr19 38281453 38281453 chr19 38315333 38315333 TCGA-G9-7510 DUP 23 48 SPINT2 YIF1B chr19 42620535 42620535 chr19 42654582 42654582 TCGA-G9-7510 DUP 43 47 LIPE-AS1 CEACAMP5 chr1 112766997 112766997 chr5 37782170 37782170 TCGA-G9-7510 BND 1 3 * * chr1 151494382 151494382 chr1 151530878 151530878 TCGA-G9-7510 DUP 26 10 * CGN chr1 151576043 151576043 chr1 151622925 151622925 TCGA-G9-7510 DUP 20 16 TUFT1 SNX27 chr1 152223788 152223788 chr1 152258452 152258452 TCGA-G9-7510 DUP 27 28 FLG-AS1 FLG-AS1 chr1 155333699 155333699 chr1 155383686 155383686 TCGA-G9-7510 DUP 44 14 * ASH1L chr1 156112704 156112704 chr1 166430276 166430276 TCGA-G9-7510 DEL 14 37 LMNA AL583804.1 chr1 164573510 164573510 chr1 191747077 191747077 TCGA-G9-7510 INS 39 26 PBX1 * chr1 165077639 165077639 chr5 116022912 116022912 TCGA-G9-7510 BND 25 30 * LVRN chr1 194438896 194438896 chr1 194440004 194440004 TCGA-G9-7510 DEL 42 39 * * chr1 197482915 197482915 chr1 197528743 197528743 TCGA-G9-7510 DUP 26 16 * DENND1B chr1 197933215 197933215 chr1 197998253 197998253 TCGA-G9-7510 DUP 2 44 LHX9 * chr1 19854942 19854942 chr1 19913348 19913348 TCGA-G9-7510 DUP 13 3 * * chr1 204737369 204737369 chr9 120237154 120237154 TCGA-G9-7510 BND 36 13 * * chr1 205613170 205613170 chr6 33761683 33761683 TCGA-G9-7510 BND 49 19 ELK4 * chr1 205613195 205613195 chr9 112847555 112847555 TCGA-G9-7510 BND 2 42 ELK4 SNX30 chr1 228124133 228124133 chr5 93646454 93646454 TCGA-G9-7510 BND 46 2 * FAM172A chr1 23426248 23426248 chr1 23476449 23476449 TCGA-G9-7510 DUP 27 9 * ASAP3 chr1 247490426 247490437 chr9 99190833 99190835 TCGA-G9-7510 BND 10 49 OR2W5 * chr1 29728767 29728767 chr1 29763038 29763038 TCGA-G9-7510 DUP 9 27 * AL645944.2 chr1 35064376 35064376 chr1 35096609 35096609 TCGA-G9-7510 DUP 20 18 ZMYM1 ZMYM1 chr1 46789273 46789273 chr1 46823401 46823401 TCGA-G9-7510 DUP 1 48 CYP4B1 * chr1 56601568 56601568 chr1 56636518 56636518 TCGA-G9-7510 DUP 26 19 PLPP3 PLPP3 chr1 59216804 59216804 chr1 59219621 59219621 TCGA-G9-7510 INV 1 49 LINC01358 LINC01358 chr1 59517828 59517828 chr1 59554944 59554944 TCGA-G9-7510 DUP 47 21 FGGY FGGY chr1 62794660 62794660 chr1 62830641 62830641 TCGA-G9-7510 DUP 32 35 ATG4C ATG4C chr1 64509023 64509023 chr1 64541180 64541180 TCGA-G9-7510 DUP 47 42 CACHD1 CACHD1 chr1 90249174 90249174 chr1 90319331 90319331 TCGA-G9-7510 DUP 25 13 * * chr1 99878499 99878499 chr1 99924207 99924207 TCGA-G9-7510 DUP 31 28 AGL * chr20 13607386 13607386 chr20 13619259 13619259 TCGA-G9-7510 DEL 16 32 TASP1 TASP1 chr20 15923566 15923566 chr20 15957735 15957735 TCGA-G9-7510 DUP 33 26 MACROD2 MACROD2 chr20 17486390 17486390 chr20 17490327 17490327 TCGA-G9-7510 DEL 31 29 * * chr20 22378331 22378331 chr20 22431540 22431540 TCGA-G9-7510 DUP 18 22 AL133464.1 AL133464.1 chr20 35990365 35990365 chr20 36024971 36024971 TCGA-G9-7510 DUP 6 39 CNBD2 CNBD2 chr20 36088227 36088227 chr20 36121648 36121648 TCGA-G9-7510 DUP 49 18 AL035420.2 EPB41L1 chr20 41659015 41659015 chr20 41694858 41694858 TCGA-G9-7510 DUP 21 40 * * chr21 38453669 38453669 chr21 41500864 41500864 TCGA-G9-7510 DEL 14 6 ERG TMPRSS2 chr21 38462013 38462013 chr21 41505035 41505035 TCGA-G9-7510 DEL 22 44 ERG TMPRSS2 chr21 38470744 38470744 chr21 41498683 41498690 TCGA-G9-7510 DEL 17 6 ERG TMPRSS2 chr21 41805988 41805997 chr21 43337430 43337430 TCGA-G9-7510 DUP 12 10 PRDM15 * chr22 28882635 28882635 chr22 28885750 28885750 TCGA-G9-7510 DEL 48 47 ZNRF3 ZNRF3 chr22 40941616 40941616 chr22 40975490 40975490 TCGA-G9-7510 DUP 41 32 * * chr2 140131008 140131008 chr2 140177966 140177966 TCGA-G9-7510 DUP 34 17 LINC01853 * chr2 141280619 141280619 chr2 141316325 141316325 TCGA-G9-7510 DUP 16 38 LRP1B LRP1B chr2 147004536 147004536 chr2 147036664 147036664 TCGA-G9-7510 DUP 11 2 * * chr2 147839127 147839127 chr2 147855590 147855590 TCGA-G9-7510 DEL 17 16 * ACVR2A chr2 151996870 151996870 chr2 183172264 183172264 TCGA-G9-7510 DEL 19 38 CACNB4 * chr2 159867818 159867818 chr2 159924807 159924807 TCGA-G9-7510 DUP 37 6 LY75 * chr2 160684687 160684687 chr11 118799403 118799403 TCGA-G9-7510 BND 22 22 * * chr2 161307011 161307011 chr3 70151652 70151668 TCGA-G9-7510 BND 6 43 AC009299.2 SAMMSON chr2 163485637 163485637 chr2 163527349 163527349 TCGA-G9-7510 DUP 34 12 * * chr2 167617705 167617705 chr2 167649295 167649295 TCGA-G9-7510 DUP 21 36 * * chr2 178598117 178598117 chr2 178642083 178642083 TCGA-G9-7510 DUP 12 6 TTN TTN chr2 183150333 183150333 chr2 211477532 211477532 TCGA-G9-7510 DEL 40 2 NUP35 ERBB4 chr2 184951981 184951981 chr2 184986517 184986517 TCGA-G9-7510 DUP 43 7 * * chr2 186608195 186608195 chr2 212282080 212282080 TCGA-G9-7510 DEL 6 33 ITGAV ERBB4 chr2 186708184 186708184 chr2 212440056 212440056 TCGA-G9-7510 INS 31 24 FAM171B ERBB4 chr2 187361922 187361922 chr2 187396682 187396682 TCGA-G9-7510 DUP 34 36 AC007319.1 AC007319.1 chr2 198492178 198492178 chr2 198552228 198552228 TCGA-G9-7510 DUP 9 38 PLCL1 PLCL1 chr2 199440515 199440515 chr2 211165746 211165746 TCGA-G9-7510 DEL 24 50 SATB2 * chr2 208166286 208166286 chr2 208218587 208218587 TCGA-G9-7510 DUP 13 18 C2orf80 TPT1P2 chr2 210595321 210595321 chr3 183070861 183070861 TCGA-G9-7510 BND 28 35 CPS1 MCCC1 chr2 210639444 210639444 chr2 211686112 211686112 TCGA-G9-7510 DEL 46 47 CPS1 ERBB4 chr2 210924054 210924054 chr2 212406426 212406426 TCGA-G9-7510 INV 4 3 * ERBB4 chr2 210925795 210925795 chr2 216504002 216504002 TCGA-G9-7510 DUP 10 28 * RPL37A chr2 210990551 210990551 chr2 211178199 211178199 TCGA-G9-7510 DUP 24 28 * * chr2 210990825 210990825 chr2 216504513 216504513 TCGA-G9-7510 DEL 5 33 * RPL37A chr2 211314780 211314780 chr2 212387176 212387176 TCGA-G9-7510 INV 47 35 * ERBB4 chr2 218617517 218617517 chr2 218663870 218663870 TCGA-G9-7510 DUP 20 44 PLCD4 RNF25 chr2 218854958 218854958 chr2 218895109 218895109 TCGA-G9-7510 DUP 8 5 * WNT10A chr2 238871117 238871117 chr9 89371869 89371869 TCGA-G9-7510 BND 24 29 TWIST2 SEMA4D chr2 25721585 25721585 chr10 98957081 98957081 TCGA-G9-7510 BND 14 35 * HPSE2 chr2 42586203 42586203 chr2 42631540 42631540 TCGA-G9-7510 DUP 24 16 MTA3 MTA3 chr2 47997410 47997410 chr2 48037426 48037426 TCGA-G9-7510 DUP 1 44 AC092650.1 AC092650.1 chr2 48354924 48354924 chr2 48388341 48388341 TCGA-G9-7510 DUP 33 32 FOXN2 * chr2 49357176 49357176 chr2 53130879 53130879 TCGA-G9-7510 DEL 12 13 AC009975.1 * chr2 58103176 58103176 chr3 183070526 183070526 TCGA-G9-7510 BND 43 29 VRK2 MCCC1 chr2 58203560 58203560 chr2 212536150 212536150 TCGA-G9-7510 DUP 29 11 FANCL ERBB4 chr2 60156649 60156649 chr2 210959815 210959815 TCGA-G9-7510 DEL 33 42 * * chr2 60157688 60157688 chr2 135852236 135852236 TCGA-G9-7510 INV 16 11 * MCM6 chr2 65784768 65784768 chr2 65822297 65822297 TCGA-G9-7510 DUP 34 4 AC007389.1 AC007389.1 chr2 73413323 73413323 chr2 210594245 210594245 TCGA-G9-7510 DUP 39 6 ALMS1 CPS1 chr2 73680052 73680052 chr2 135852562 135852562 TCGA-G9-7510 INV 47 1 ALMS1P1 MCM6 chr2 88369089 88369089 chr2 88383881 88383881 TCGA-G9-7510 DEL 19 1 U6 RNU6-1168P chr3 100061574 100061574 chr3 165717088 165717088 TCGA-G9-7510 INS 19 50 CMSS1 * chr3 100203308 100203308 chr3 100246892 100246892 TCGA-G9-7510 DUP 6 50 TMEM30CP * chr3 100246957 100246957 chr3 100286912 100286912 TCGA-G9-7510 DUP 26 19 * TBC1D23 chr3 100372502 100372502 chr3 100408011 100408011 TCGA-G9-7510 DUP 11 1 TOMM70 LNP1 chr3 100987137 100987137 chr3 101774236 101774236 TCGA-G9-7510 DEL 25 20 ABI3BP * chr3 100998760 100998760 chr3 165133859 165133859 TCGA-G9-7510 INS 26 29 * * chr3 101163205 101163205 chr3 165715075 165715075 TCGA-G9-7510 INS 36 28 ACTR3P3 * chr3 102118639 102118639 chr3 167321529 167321529 TCGA-G9-7510 INS 3 42 ZPLD1 ZBBX chr3 102385740 102385740 chr3 164575149 164575149 TCGA-G9-7510 DEL 41 10 ZPLD1 * chr3 109450541 109450541 chr3 109508131 109508131 TCGA-G9-7510 DUP 44 49 LINC01205 * chr3 116946910 116946910 chr3 117035219 117035219 TCGA-G9-7510 DEL 22 32 LSAMP LSAMP chr3 118104922 118104922 chr3 118140875 118140875 TCGA-G9-7510 DUP 13 21 AC068633.1 AC068633.1 chr3 118515798 118515798 chr3 118578296 118578296 TCGA-G9-7510 DUP 44 47 AC068633.1 * chr3 13118534 13118534 chr3 13150600 13150600 TCGA-G9-7510 DUP 47 3 IQSEC1 IQSEC1 chr3 132333078 132333078 chr3 132333131 132333131 TCGA-G9-7510 INV 22 34 ACP3 ACP3 chr3 159433665 159433665 chr3 159475788 159475788 TCGA-G9-7510 DUP 38 4 IQCJ-SCHIP1 IQCJ-SCHIP1 chr3 165695433 165695433 chr3 165978463 165978463 TCGA-G9-7510 DEL 17 44 * * chr3 166129101 166129101 chr3 168991269 168991269 TCGA-G9-7510 DEL 39 50 * * chr3 30063686 30063686 chr3 30098626 30098626 TCGA-G9-7510 DUP 21 25 * * chr3 36006443 36006444 chr3 78826183 78826183 TCGA-G9-7510 DEL 16 32 * ROBO1 chr3 36054640 36054640 chr3 58448182 58448182 TCGA-G9-7510 INS 44 40 * * chr3 51735797 51735797 chr3 51767836 51767836 TCGA-G9-7510 DUP 9 3 * * chr3 70151652 70151668 chr3 72827018 72827018 TCGA-G9-7510 DEL 33 31 SAMMSON SHQ1 chr3 78987230 78987230 chr3 78987498 78987498 TCGA-G9-7510 DEL 45 35 ROBO1 ROBO1 chr3 81008837 81008837 chr3 82886966 82886966 TCGA-G9-7510 INS 11 19 LINC02027 * chr3 82412498 82412498 chr3 83018256 83018256 TCGA-G9-7510 DEL 43 39 LINC02008 * chr3 82642495 82642495 chr3 84706941 84706941 TCGA-G9-7510 INS 4 45 * LINC00971 chr3 82854168 82854168 chr3 83611181 83611181 TCGA-G9-7510 DEL 3 14 * * chr3 84856174 84856174 chr3 89825134 89825134 TCGA-G9-7510 DEL 3 5 LINC00971 * chr3 85997876 85997876 chr3 86077377 86077377 TCGA-G9-7510 DEL 2 27 CADM2 * chr3 86012512 86012512 chr3 86047847 86047847 TCGA-G9-7510 DUP 19 31 CADM2 CADM2 chr3 87982441 87982441 chr3 88020541 88020541 TCGA-G9-7510 DUP 17 25 * * chr3 98624978 98624978 chr3 99100866 99100866 TCGA-G9-7510 DEL 41 7 * * chr3 99671528 99671528 chr3 101154840 101154840 TCGA-G9-7510 INS 39 24 COL8A1 * chr3 99911192 99911192 chr3 165699783 165699783 TCGA-G9-7510 DEL 49 41 CMSS1 * chr3 99927908 99927908 chr3 101100493 101100493 TCGA-G9-7510 DEL 32 8 CMSS1 * chr3 99956109 99956109 chr3 168894734 168894734 TCGA-G9-7510 INS 2 36 CMSS1 * chr4 101816289 101816289 chr4 101848143 101848143 TCGA-G9-7510 DUP 11 19 BANK1 BANK1 chr4 124926102 124926102 chr4 124926154 124926154 TCGA-G9-7510 DEL 41 39 * * chr4 140397400 140397400 chr4 140439693 140439693 TCGA-G9-7510 DUP 49 21 CLGN * chr4 146303347 146303347 chr4 146349140 146349140 TCGA-G9-7510 DUP 21 27 SLC10A7 SLC10A7 chr4 159395135 159395135 chr4 159427681 159427681 TCGA-G9-7510 DUP 28 10 * * chr4 159892921 159892921 chr4 159933011 159933011 TCGA-G9-7510 DUP 8 38 * * chr4 162357224 162357224 chr4 162360361 162360361 TCGA-G9-7510 DEL 8 10 * * chr4 168162783 168162783 chr4 168194600 168194600 TCGA-G9-7510 DUP 35 35 ANXA10 * chr4 23119128 23119128 chr4 23126620 23126620 TCGA-G9-7510 DEL 34 22 * * chr4 55412599 55412599 chr4 55452585 55452585 TCGA-G9-7510 DUP 28 7 TMEM165 TMEM165 chr4 65742654 65742654 chr4 65780969 65780969 TCGA-G9-7510 DUP 36 24 * * chr4 67661580 67661580 chr4 67698043 67698043 TCGA-G9-7510 DUP 37 31 UBA6 UBA6 chr4 69256266 69256266 chr4 69369343 69369343 TCGA-G9-7510 DEL 25 20 * * chr4 80913899 80913899 chr4 80954207 80954207 TCGA-G9-7510 DUP 31 22 CFAP299 CFAP299 chr5 129675282 129675282 chr5 129717332 129717332 TCGA-G9-7510 DUP 5 1 ADAMTS19 ADAMTS19 chr5 142976925 142976925 chr5 143000957 143000957 TCGA-G9-7510 DEL 47 20 ARHGAP26 ARHGAP26 chr5 148212429 148212429 chr5 148250889 148250889 TCGA-G9-7510 DUP 19 9 SPINK6 * chr5 159356846 159356849 chr9 70597144 70597154 TCGA-G9-7510 BND 37 9 AC008691.1 TRPM3 chr5 23063128 23063128 chr5 23127048 23127048 TCGA-G9-7510 DUP 18 38 * * chr5 36739063 36739063 chr5 36779667 36779667 TCGA-G9-7510 DUP 47 10 * * chr5 37608439 37608439 chr5 37637755 37637755 TCGA-G9-7510 DEL 35 22 WDR70 WDR70 chr5 40492532 40492532 chr5 40530518 40530518 TCGA-G9-7510 DUP 3 36 AC114977.1 TTC33 chr5 79225407 79225407 chr5 79276145 79276145 TCGA-G9-7510 DUP 39 46 DMGDH JMY chr5 88537881 88537881 chr5 90032339 90032339 TCGA-G9-7510 DEL 8 7 LINC00461 * chr5 90456105 90456105 chr5 116746378 116746378 TCGA-G9-7510 DEL 6 11 * LINC02214 chr5 93609866 93609866 chr5 93645973 93645973 TCGA-G9-7510 DUP 37 19 * FAM172A chr5 94096533 94096533 chr5 94906708 94906708 TCGA-G9-7510 INV 21 23 FAM172A MCTP1 chr5 94428670 94428670 chr5 95555301 95555301 TCGA-G9-7510 INV 34 49 KIAA0825 TTC37 chr5 99612560 99612560 chr5 99615274 99615274 TCGA-G9-7510 DEL 41 17 * * chr6 106816884 106816884 chr6 107364303 107364303 TCGA-G9-7510 DEL 25 8 * PDSS2 chr6 117183421 117183421 chr6 117248164 117248164 TCGA-G9-7510 DUP 20 48 * * chr6 139507010 139507010 chr6 145867324 145867324 TCGA-G9-7510 INV 48 18 AL592429.2 SHPRH chr6 146953972 146953972 chr6 146988262 146988262 TCGA-G9-7510 DUP 6 38 STXBP5-AS1 STXBP5-AS1 chr6 150432280 150432280 chr6 150469122 150469122 TCGA-G9-7510 DUP 31 33 * * chr6 150532922 150532922 chr6 150568697 150568697 TCGA-G9-7510 DUP 41 33 * * chr6 15904222 15904222 chr6 15936996 15936996 TCGA-G9-7510 DUP 44 45 * * chr6 159381282 159381282 chrX 45727136 45727136 TCGA-G9-7510 BND 4 9 AL357832.1 * chr6 16280903 16280903 chr6 16316145 16316145 TCGA-G9-7510 DUP 4 41 GMPR ATXN1 chr6 26386726 26386726 chr6 26426114 26426114 TCGA-G9-7510 DUP 44 5 BTN2A2 BTN2A3P chr6 32445813 32445813 chr6 32489240 32489240 TCGA-G9-7510 DUP 1 3 * * chr6 32528852 32528852 chr6 32588455 32588455 TCGA-G9-7510 DUP 37 7 HLA-DRB5 HLA-DRB1 chr6 36191767 36191767 chr6 36230713 36230713 TCGA-G9-7510 DUP 10 20 Z84485.1 BRPF3 chr6 39899637 39899637 chr9 90875748 90875768 TCGA-G9-7510 BND 27 18 DAAM2 SYK chr6 40226586 40226586 chr6 40261570 40261570 TCGA-G9-7510 DUP 39 13 * * chr6 76501802 76501802 chr6 76536799 76536799 TCGA-G9-7510 DUP 12 8 * LINC02540 chr6 7813064 7813064 chr6 7858054 7858054 TCGA-G9-7510 DUP 29 46 BMP6 BMP6 chr6 79289720 79289720 chr6 79333848 79333848 TCGA-G9-7510 DUP 18 41 * * chr7 117369043 117369043 chr7 117403590 117403590 TCGA-G9-7510 DUP 4 24 ASZ1 ASZ1 chr7 122854031 122854031 chr7 122890575 122890575 TCGA-G9-7510 DUP 34 29 CADPS2 * chr7 139767915 139767915 chr7 139809702 139809702 TCGA-G9-7510 DUP 34 45 HIPK2 TBXAS1 chr7 140736608 140736608 chr7 140770202 140770202 TCGA-G9-7510 DUP 12 29 BRAF BRAF chr7 157545933 157545933 chr7 157753565 157753565 TCGA-G9-7510 DEL 43 11 PTPRN2 PTPRN2 chr7 159069615 159069615 chr7 159117912 159117912 TCGA-G9-7510 DUP 50 12 VIPR2 VIPR2 chr7 37524196 37524196 chr7 37571386 37571386 TCGA-G9-7510 DUP 13 28 * * chr7 3977920 3977920 chr7 4014209 4014209 TCGA-G9-7510 DUP 14 39 SDK1 SDK1 chr7 65930983 65930983 chr7 65971855 65971855 TCGA-G9-7510 DUP 34 34 VKORC1L1 GUSB chr7 69730787 69730787 chr7 69767710 69767710 TCGA-G9-7510 DUP 10 25 AUTS2 AUTS2 chr8 103475564 103475564 chr8 103524357 103524357 TCGA-G9-7510 DUP 21 6 AC012213.5 RIMS2 chr8 111785281 111785281 chr8 111818457 111818457 TCGA-G9-7510 DUP 29 33 * * chr8 36738247 36738247 chr8 36774458 36774458 TCGA-G9-7510 DUP 16 13 AC090809.1 AC090809.1 chr8 37997485 37997485 chr8 38047805 38047805 TCGA-G9-7510 DUP 38 10 * EIF4EBP1 chr8 39496193 39496193 chr8 39527036 39527036 TCGA-G9-7510 DUP 37 17 ADAM3A AC123767.1 chr8 47835656 47835656 chr18 13383478 13383478 TCGA-G9-7510 BND 23 22 PRKDC LDLRAD4 chr8 57542229 57542229 chr8 57582834 57582834 TCGA-G9-7510 DUP 15 26 AC090796.1 AC090796.1 chr8 59189078 59189078 chr8 84216126 84216126 TCGA-G9-7510 DUP 23 46 * RALYL chr8 76554164 76554164 chr8 76612984 76612984 TCGA-G9-7510 DUP 15 23 ZFHX4-AS1 ZFHX4-AS1 chr8 79150894 79150894 chr8 79178291 79178291 TCGA-G9-7510 DEL 23 25 * * chr8 86867989 86867989 chr12 85072494 85072494 TCGA-G9-7510 BND 50 23 CNBD1 LRRIQ1 chr8 92249613 92249613 chr8 92286360 92286360 TCGA-G9-7510 DUP 12 22 * * chr9 101787815 101787815 chr9 104044105 104044105 TCGA-G9-7510 DEL 45 22 * * chr9 124505886 124505886 chr9 124544803 124544803 TCGA-G9-7510 DUP 24 25 NR5A1 NR6A1 chr9 16690272 16690272 chr9 16738017 16738017 TCGA-G9-7510 DUP 45 29 BNC2 BNC2 chr9 16938220 16938220 chr9 16971516 16971516 TCGA-G9-7510 DUP 23 49 AL162725.2 AL162725.2 chr9 25370583 25370583 chr9 25401461 25401461 TCGA-G9-7510 DUP 4 30 * * chr9 25693347 25693347 chr9 25743760 25743760 TCGA-G9-7510 DUP 33 18 * * chr9 35119323 35119323 chr9 35150360 35150360 TCGA-G9-7510 DUP 49 19 * AL353795.1 chr9 7595895 7595895 chr9 7597231 7597231 TCGA-G9-7510 DEL 22 28 * PPIAP33 chr9 90875748 90875768 chr9 112847521 112847521 TCGA-G9-7510 DEL 33 20 SYK SNX30 chrX 18528098 18528098 chrX 18538590 18538590 TCGA-G9-7510 INV 42 11 CDKL5 CDKL5 chrX 66799448 66799448 chrX 66816585 66816586 TCGA-G9-7510 INV 43 12 * * chrX 66816585 66816586 chrX 67075360 67075360 TCGA-G9-7510 INV 29 3 * * chrX 86683311 86683311 chrX 86713561 86713561 TCGA-G9-7510 DUP 45 20 DACH2 DACH2 chr10 109297627 109297627 chr10 109839849 109839849 TCGA-QU-A6IL DEL 14 10 * * chr10 82505551 82505551 chr10 82507207 82507207 TCGA-QU-A6IL DEL 35 21 NRG3 NRG3 chr11 28428566 28428566 chr13 60980332 60980332 TCGA-QU-A6IL BND 15 15 METTL15 * chr12 72206250 72206250 chr12 74234974 74234974 TCGA-QU-A6IL DEL 47 38 TRHDE LINC02882 chr13 55337297 55337297 chr13 55347788 55347788 TCGA-QU-A6IL DEL 11 33 * * chr13 59655136 59655136 chr13 59667170 59667170 TCGA-QU-A6IL DEL 29 19 * DIAPH3 chr14 26646914 26646914 chr14 26654163 26654163 TCGA-QU-A6IL DEL 32 6 LINC02588 LINC02588 chr15 98905913 98905913 chr15 99092743 99092743 TCGA-QU-A6IL INS 30 40 IGF1R AC036108.1 chr17 82631267 82631267 chr17 82631600 82631600 TCGA-QU-A6IL INS 39 30 FOXK2 FOXK2 chr1 107262772 107262772 chr1 107268277 107268277 TCGA-QU-A6IL DEL 14 30 NTNG1 NTNG1 chr1 1227325 1227325 chr1 1227500 1227500 TCGA-QU-A6IL DEL 25 28 SDF4 SDF4 chr1 197589626 197589626 chr2 216129053 216129053 TCGA-QU-A6IL BND 50 27 DENND1B XRCC5 chr1 97817503 97817503 chr1 98549738 98549738 TCGA-QU-A6IL DEL 17 38 DPYD * chr20 22505486 22505486 chr20 22505591 22505599 TCGA-QU-A6IL DEL 16 36 * * chr2 114006815 114006815 chr2 114081319 114081319 TCGA-QU-A6IL DEL 41 1 LINC01191 * chr2 115246205 115246205 chr2 115798817 115798817 TCGA-QU-A6IL DEL 38 16 DPP10 DPP10 chr2 125542648 125542648 chr2 132809291 132809291 TCGA-QU-A6IL DEL 1 2 * NCKAP5 chr2 166596184 166596184 chr2 185117452 185117452 TCGA-QU-A6IL DEL 7 6 * * chr2 214764529 214764529 chr2 216913334 216913334 TCGA-QU-A6IL DEL 31 27 BARD1 AC007563.2 chr2 216712148 216712148 chr2 217077973 217077973 TCGA-QU-A6IL INS 21 12 AC007563.2 * chr2 216907533 216907533 chr2 217403393 217403393 TCGA-QU-A6IL DEL 4 24 AC007563.2 DIRC3 chr2 52101050 52101050 chr2 53047215 53047215 TCGA-QU-A6IL DEL 46 3 AC007402.1 * chr3 146685426 146685426 chr3 147221731 147221731 TCGA-QU-A6IL DEL 44 14 * AC092957.1 chr3 147230973 147230973 chr3 168689801 168689801 TCGA-QU-A6IL DEL 9 6 AC092957.1 EGFEM1P chr3 147747470 147747470 chr3 147756630 147756630 TCGA-QU-A6IL DEL 3 44 * * chr3 1892771 1892771 chr3 1928778 1928778 TCGA-QU-A6IL DEL 25 26 * * chr3 3335738 3335738 chr3 3340669 3340669 TCGA-QU-A6IL DEL 18 15 AC034195.1 AC034195.1 chr3 85469588 85469588 chr3 89060917 89060917 TCGA-QU-A6IL INS 25 31 CADM2 * chr3 90117833 90117833 chr3 90122805 90122805 TCGA-QU-A6IL DEL 45 12 * * chr4 111269098 111269098 chr4 117522539 117522539 TCGA-QU-A6IL DEL 10 33 * LINC01378 chr4 115227909 115227909 chr4 115252880 115252880 TCGA-QU-A6IL DEL 26 2 * * chr4 125392865 125392865 chr4 125392980 125392980 TCGA-QU-A6IL DEL 29 3 FAT4 FAT4 chr4 147415520 147415520 chr4 180514841 180514841 TCGA-QU-A6IL DEL 4 1 * * chr4 147864472 147864472 chr4 156572654 156572654 TCGA-QU-A6IL DEL 8 1 ARHGAP10 * chr4 147866240 147866240 chr4 178966015 178966015 TCGA-QU-A6IL INS 39 7 ARHGAP10 * chr4 156840031 156840031 chr4 180511900 180511900 TCGA-QU-A6IL INS 49 32 PDGFC * chr4 169941235 169941235 chr4 169942485 169942485 TCGA-QU-A6IL DEL 34 1 LINC02275 LINC02275 chr4 171062142 171062142 chr4 171118554 171118554 TCGA-QU-A6IL DEL 43 10 * * chr4 173919910 173919910 chr4 173921740 173921740 TCGA-QU-A6IL DEL 45 34 LINC02269 LINC02269 chr4 178627883 178627883 chr4 178628252 178628252 TCGA-QU-A6IL DEL 25 12 * * chr4 180938892 180938892 chr4 180942367 180942367 TCGA-QU-A6IL DEL 18 43 * * chr4 189117347 189117347 chr4 189117451 189117451 TCGA-QU-A6IL DEL 18 15 * * chr4 23553357 23553357 chr4 24760582 24760582 TCGA-QU-A6IL DEL 31 25 * * chr4 58046882 58046882 chr4 58639713 58639713 TCGA-QU-A6IL DEL 10 10 * * chr4 62782431 62782431 chr4 62790730 62790730 TCGA-QU-A6IL DEL 17 19 * * chr5 152818333 152818333 chr5 152835621 152835621 TCGA-QU-A6IL DEL 31 42 LINC01470 LINC01470 chr5 83591443 83591443 chr5 83657579 83657579 TCGA-QU-A6IL DEL 22 4 * HAPLN1 chr5 98882420 98882420 chr5 99212743 99212743 TCGA-QU-A6IL INS 37 33 CHD1 * chr6 101219032 101219032 chr6 101230175 101230175 TCGA-QU-A6IL DEL 12 15 GRIK2 GRIK2 chr6 62709437 62709437 chr6 64767922 64767922 TCGA-QU-A6IL INS 14 46 * EYS chr6 65148833 65148833 chr6 121316887 121316887 TCGA-QU-A6IL DEL 6 37 EYS TBC1D32 chr6 98892180 98892180 chr6 98896797 98896797 TCGA-QU-A6IL DEL 19 32 FBXL4 FBXL4 chr7 123276794 123276794 chr7 123277429 123277429 TCGA-QU-A6IL DEL 17 50 * * chr7 83887288 83887288 chr7 83918676 83918676 TCGA-QU-A6IL DEL 49 42 * * chr8 104504484 104504484 chr8 106128442 106128442 TCGA-QU-A6IL DEL 36 27 LRP12 * chr8 112510154 112510154 chr8 112510391 112510391 TCGA-QU-A6IL DEL 2 16 CSMD3 CSMD3 chr8 112744876 112744876 chr8 112746709 112746709 TCGA-QU-A6IL DEL 38 3 CSMD3 CSMD3 chr8 13142817 13142817 chr8 34431551 34431551 TCGA-QU-A6IL DEL 41 10 DLC1 * chr8 139278575 139278575 chr8 139286499 139286499 TCGA-QU-A6IL DEL 48 26 * * chr8 34633505 34633505 chr8 34635823 34635823 TCGA-QU-A6IL DEL 6 11 * * chr8 49990796 49990796 chr8 49991736 49991736 TCGA-QU-A6IL DEL 21 18 SNTG1 SNTG1 chr8 62778900 62778900 chr8 71473714 71473714 TCGA-QU-A6IL INS 6 13 NKAIN3 EYA1 chr8 88415360 88415360 chr8 88418564 88418564 TCGA-QU-A6IL DEL 44 45 AC090578.1 AC090578.1 chrX 104210734 104210734 chrX 104466199 104466199 TCGA-QU-A6IL DEL 25 44 * * chrX 104665027 104665027 chrX 104665391 104665391 TCGA-QU-A6IL DEL 2 50 IL1RAPL2 IL1RAPL2 chrX 88393112 88393112 chrX 88393995 88393995 TCGA-QU-A6IL DEL 4 14 * * chr10 17598641 17598641 chr10 18201702 18201702 TCGA-YL-A8HM INS 18 39 HACD1 CACNB2 chr10 75407069 75407069 chr7 30579540 30579540 TCGA-YL-A8HM BND 47 34 ZNF503-AS2 GARS1-DT chr10 83920744 83920744 chr10 99396601 99396601 TCGA-YL-A8HM DEL 22 1 * * chr12 83352203 83352203 chr16 59208867 59208867 TCGA-YL-A8HM BND 25 4 * * chr12 84390204 84390204 chr16 60360356 60360356 TCGA-YL-A8HM BND 45 12 * NPAP1L chr12 84653830 84653830 chr16 58179102 58179102 TCGA-YL-A8HM BND 3 13 * CSNK2A2 chr12 99768734 99768734 chr12 100758214 100758214 TCGA-YL-A8HM INS 33 36 ANKS1B ANO4 chr14 37079699 37079699 chr14 37595144 37595144 TCGA-YL-A8HM INS 32 12 SLC25A21 FOXA1 chr14 37567091 37567091 chr14 37572952 37572952 TCGA-YL-A8HM DEL 11 32 AL121790.2 AL121790.1 chr16 59440748 59440748 chr16 59997303 59997303 TCGA-YL-A8HM INS 49 4 * LINC02141 chr16 60604533 60604536 chr12 83356478 83356481 TCGA-YL-A8HM BND 6 15 * * chr18 58166327 58166327 chr18 58364203 58364203 TCGA-YL-A8HM INS 37 16 NEDD4L NEDD4L chr18 61164859 61164859 chr18 63031244 63031244 TCGA-YL-A8HM INS 8 17 * * chr18 61679672 61679673 chr4 105828960 105828961 TCGA-YL-A8HM BND 49 36 AC105094.2 INTS12 chr18 62220163 62220163 chr4 105075242 105075242 TCGA-YL-A8HM BND 43 36 RELCH AC096577.1 chr18 62263898 62263899 chr4 173335960 173335961 TCGA-YL-A8HM BND 12 10 RELCH HMGB2 chr18 62347398 62347398 chr4 174329220 174329220 TCGA-YL-A8HM BND 3 24 TNFRSF11A CEP44 chr18 63055944 63055944 chr18 64800304 64800304 TCGA-YL-A8HM INS 44 10 * * chr18 64016486 64016486 chr4 174742865 174742865 TCGA-YL-A8HM BND 1 35 SERPINB8 GLRA3 chr18 64169889 64169889 chr4 104340476 104340476 TCGA-YL-A8HM BND 14 21 LINC01924 AC004052.1 chr18 64263303 64263303 chr4 103550832 103550832 TCGA-YL-A8HM BND 30 1 LINC01924 AC105460.2 chr18 64360852 64360856 chr4 104965501 104965505 TCGA-YL-A8HM BND 5 18 LINC01924 AC004053.1 chr18 64415451 64415451 chr4 174330633 174330633 TCGA-YL-A8HM BND 20 9 LINC01924 CEP44 chr18 64454565 64454569 chr4 172641614 172641618 TCGA-YL-A8HM BND 18 40 * GALNTL6 chr18 64464234 64464241 chr4 173885993 173886000 TCGA-YL-A8HM BND 42 27 * AC106895.1 chr18 65381240 65381240 chr4 174734211 174734211 TCGA-YL-A8HM BND 46 50 * GLRA3 chr18 66118513 66118513 chr4 102596547 102596547 TCGA-YL-A8HM BND 3 1 * NFKB1 chr18 66729303 66729303 chr18 70029427 70029427 TCGA-YL-A8HM INS 40 3 * RTTN chr18 67226773 67226773 chr3 82674892 82674892 TCGA-YL-A8HM BND 25 6 * * chr18 68509459 68509459 chr3 21470401 21470401 TCGA-YL-A8HM BND 31 9 * ZNF385D chr18 68715194 68715194 chr18 69498774 69498774 TCGA-YL-A8HM DEL 24 31 TMX3 DOK6 chr18 68782644 68782644 chr18 69605610 69605610 TCGA-YL-A8HM INS 27 40 CCDC102B DOK6 chr18 69834790 69834790 chr18 70033775 70033775 TCGA-YL-A8HM DEL 24 39 DOK6 RTTN chr18 70135242 70135242 chr18 70139556 70139556 TCGA-YL-A8HM DEL 27 39 RTTN RTTN chr18 71285752 71285752 chr18 79388147 79388147 TCGA-YL-A8HM DEL 2 17 * * chr1 103072891 103072893 chr5 46215807 46215809 TCGA-YL-A8HM BND 30 9 COL11A1 * chr1 239358205 239358205 chr1 239360439 239360439 TCGA-YL-A8HM DEL 28 31 * * chr1 45453768 45453768 chr1 45989662 45989662 TCGA-YL-A8HM INS 34 3 TESK2 MAST2 chr20 15082908 15082908 chr20 15166622 15166622 TCGA-YL-A8HM DEL 12 28 MACROD2 MACROD2 chr2 116652483 116652483 chr2 116688489 116688489 TCGA-YL-A8HM DEL 46 48 * AC104408.1 chr2 137873795 137873795 chr2 137875648 137875648 TCGA-YL-A8HM DEL 21 23 * * chr2 140975390 140975390 chr2 141038054 141038054 TCGA-YL-A8HM DEL 28 17 LRP1B LRP1B chr2 143189453 143189453 chr2 143190410 143190410 TCGA-YL-A8HM DEL 21 14 ARHGAP15 ARHGAP15 chr2 82750951 82750951 chr2 83688158 83688158 TCGA-YL-A8HM DEL 25 46 * * chr3 102193577 102193577 chr3 102213966 102213966 TCGA-YL-A8HM DEL 12 27 ZPLD1 ZPLD1 chr3 181846005 181846005 chr3 181846477 181846477 TCGA-YL-A8HM DEL 45 4 * * chr3 19731474 19731474 chr3 23373529 23373529 TCGA-YL-A8HM DEL 11 42 * UBE2E2 chr3 20018335 20018335 chr3 88362479 88362479 TCGA-YL-A8HM INS 13 21 * CSNKA2IP chr3 21426430 21426430 chr4 101358556 101358556 TCGA-YL-A8HM BND 44 5 ZNF385D * chr3 21777848 21777849 chr18 68546049 68546050 TCGA-YL-A8HM BND 7 42 ZNF385D * chr3 27270409 27270409 chr3 28597180 28597180 TCGA-YL-A8HM DEL 22 50 NEK10 AC098650.1 chr3 28033929 28033929 chr3 28627279 28627279 TCGA-YL-A8HM DEL 2 6 LINC01967 AC098650.1 chr3 83325287 83325288 chr12 128342911 128342912 TCGA-YL-A8HM BND 17 50 * TMEM132C chr3 93817806 93817809 chr18 70311049 70311052 TCGA-YL-A8HM BND 37 25 * SOCS6 chr3 94431663 94431663 chr4 63711764 63711764 TCGA-YL-A8HM BND 33 50 * * chr3 96756326 96756326 chr3 96756465 96756465 TCGA-YL-A8HM DEL 13 30 * * chr4 100787539 100787539 chr4 102554461 102554461 TCGA-YL-A8HM DEL 18 47 EMCN NFKB1 chr4 100884010 100884010 chr18 65386918 65386918 TCGA-YL-A8HM BND 40 6 * * chr4 101000192 101000192 chr4 101527308 101527308 TCGA-YL-A8HM DEL 48 37 * BANK1 chr4 101341265 101341265 chr18 70083399 70083399 TCGA-YL-A8HM BND 46 32 PPP3CA RTTN chr4 101419016 101419020 chr18 66129984 66129988 TCGA-YL-A8HM BND 9 5 BANK1 * chr4 102022293 102022293 chr4 172263902 172263902 TCGA-YL-A8HM DEL 13 11 BANK1 GALNTL6 chr4 102039330 102039330 chr4 102565576 102565576 TCGA-YL-A8HM INS 9 18 BANK1 NFKB1 chr4 102052594 102052594 chr4 181776163 181776163 TCGA-YL-A8HM DEL 15 19 BANK1 * chr4 102053117 102053117 chr4 181769326 181769326 TCGA-YL-A8HM INS 29 41 BANK1 * chr4 102279626 102279628 chr18 63399202 63399204 TCGA-YL-A8HM BND 35 21 SLC39A8 VPS4B chr4 102529348 102529348 chr4 181740914 181740914 TCGA-YL-A8HM DEL 18 19 NFKB1 * chr4 102949034 102949034 chr4 172192850 172192850 TCGA-YL-A8HM DEL 25 4 SLC9B1 GALNTL6 chr4 103006026 103006026 chr4 103539008 103539008 TCGA-YL-A8HM INS 28 25 SLC9B1 * chr4 103181000 103181000 chr18 64809192 64809192 TCGA-YL-A8HM BND 47 18 CENPE * chr4 104316606 104316606 chr4 171932593 171932593 TCGA-YL-A8HM DEL 48 29 AC004052.1 GALNTL6 chr4 105075242 105075242 chr18 62220163 62220163 TCGA-YL-A8HM BND 30 28 AC096577.1 RELCH chr4 105150729 105150729 chr4 175874235 175874235 TCGA-YL-A8HM DEL 50 49 TET2 GPM6A chr4 105188935 105188935 chr4 173849050 173849050 TCGA-YL-A8HM INS 27 13 TET2 * chr4 105554294 105554294 chr4 173320506 173320506 TCGA-YL-A8HM INS 39 1 ARHGEF38 GALNT7 chr4 107134209 107134209 chr4 107137432 107137432 TCGA-YL-A8HM DEL 36 16 DKK2 DKK2 chr4 108064544 108064544 chr4 108075787 108075787 TCGA-YL-A8HM DEL 3 7 LEF1 LEF1 chr4 109207837 109207837 chr4 116315528 116315528 TCGA-YL-A8HM DEL 8 21 COL25A1 * chr4 109217127 109217127 chr4 114396179 114396179 TCGA-YL-A8HM INS 21 49 COL25A1 * chr4 109466966 109466966 chr4 165607379 165607379 TCGA-YL-A8HM DEL 46 50 SEC24B * chr4 109515267 109515267 chr4 111585390 111585390 TCGA-YL-A8HM INS 45 47 SEC24B * chr4 109988804 109988804 chr4 113141313 113141313 TCGA-YL-A8HM DEL 39 18 EGF ANK2 chr4 110175003 110175003 chr4 166004533 166004533 TCGA-YL-A8HM DEL 48 21 ELOVL6 TLL1 chr4 110213995 110213995 chr4 164866408 164866408 TCGA-YL-A8HM INS 15 16 * * chr4 111634401 111634401 chr4 111736345 111736345 TCGA-YL-A8HM INS 43 22 * * chr4 111890277 111890277 chr4 166195372 166195372 TCGA-YL-A8HM INS 47 38 AC004704.1 * chr4 112784487 112784487 chr4 116273660 116273660 TCGA-YL-A8HM INS 3 17 * AC027613.1 chr4 125742271 125742271 chr4 149193868 149193868 TCGA-YL-A8HM DEL 2 31 AC104664.1 LINC02355 chr4 126114627 126114627 chr4 177575996 177575996 TCGA-YL-A8HM DEL 14 8 * AC078881.1 chr4 126481806 126481806 chr4 179200939 179200939 TCGA-YL-A8HM INS 9 5 * * chr4 127058993 127058993 chr4 128299892 128299892 TCGA-YL-A8HM DEL 35 6 AC096773.1 LINC02615 chr4 127914461 127914461 chr4 178716149 178716149 TCGA-YL-A8HM INS 32 19 * * chr4 128132145 128132145 chr4 177877402 177877402 TCGA-YL-A8HM INS 46 17 LARP1B LINC01098 chr4 128136248 128136248 chr4 181521644 181521644 TCGA-YL-A8HM INS 43 39 LARP1B AC093840.1 chr4 128245096 128245096 chr4 149230598 149230598 TCGA-YL-A8HM DEL 5 11 * LINC02355 chr4 129010001 129010001 chr4 181929386 181929386 TCGA-YL-A8HM DEL 37 39 SCLT1 TENM3-AS1 chr4 129182157 129182157 chr4 149199950 149199950 TCGA-YL-A8HM INS 34 17 * LINC02355 chr4 129867451 129867451 chr4 131395018 131395018 TCGA-YL-A8HM DEL 44 33 LINC02465 LINC02377 chr4 133478156 133478156 chr4 133480858 133480858 TCGA-YL-A8HM DEL 13 28 * * chr4 136766523 136766523 chr4 137204056 137204056 TCGA-YL-A8HM DEL 27 11 * LINC02511 chr4 136769927 136769927 chr4 179709321 179709321 TCGA-YL-A8HM INS 1 35 * * chr4 136899340 136899340 chr4 177481009 177481009 TCGA-YL-A8HM INS 5 28 LINC02511 AC078881.1 chr4 149231159 149231159 chr4 177254911 177254911 TCGA-YL-A8HM INS 16 34 LINC02355 * chr4 149890127 149890127 chr4 178020883 178020883 TCGA-YL-A8HM INS 47 19 IQCM * chr4 166173786 166173786 chr4 168434993 168434993 TCGA-YL-A8HM INS 37 9 * DDX60L chr4 166601522 166601522 chr4 168439429 168439429 TCGA-YL-A8HM DEL 41 30 * DDX60L chr4 172040862 172040862 chr4 175865844 175865844 TCGA-YL-A8HM INS 40 11 GALNTL6 GPM6A chr4 172147004 172147004 chr4 178715505 178715505 TCGA-YL-A8HM DEL 41 35 GALNTL6 * chr4 172220336 172220336 chr4 174547675 174547675 TCGA-YL-A8HM DEL 45 8 GALNTL6 * chr4 172641614 172641618 chr18 64454565 64454569 TCGA-YL-A8HM BND 34 18 GALNTL6 * chr4 172661885 172661885 chr4 173224169 173224169 TCGA-YL-A8HM INS 33 13 GALNTL6 GALNT7 chr4 173048755 173048755 chr4 173277286 173277286 TCGA-YL-A8HM DEL 5 11 * GALNT7 chr4 173222424 173222424 chr18 64418014 64418014 TCGA-YL-A8HM BND 13 22 GALNT7 LINC01924 chr4 173335960 173335961 chr18 62263898 62263899 TCGA-YL-A8HM BND 49 12 HMGB2 RELCH chr4 173885993 173886000 chr18 64464234 64464241 TCGA-YL-A8HM BND 13 3 AC106895.1 * chr4 174329220 174329220 chr18 62347398 62347398 TCGA-YL-A8HM BND 5 35 CEP44 TNFRSF11A chr4 174419615 174419615 chr3 22020969 22020969 TCGA-YL-A8HM BND 25 23 * ZNF385D chr4 174742865 174742865 chr18 64016486 64016486 TCGA-YL-A8HM BND 12 47 GLRA3 SERPINB8 chr4 177100007 177100007 chr4 181575474 181575474 TCGA-YL-A8HM DEL 6 5 * * chr4 177339554 177339554 chr4 178034941 178034941 TCGA-YL-A8HM DEL 36 10 NEIL3 * chr4 177885471 177885471 chr4 178680065 178680065 TCGA-YL-A8HM INS 26 26 LINC01098 * chr4 178034792 178034792 chr4 179729851 179729851 TCGA-YL-A8HM DEL 44 9 * * chr4 179229689 179229689 chr4 180157435 180157435 TCGA-YL-A8HM INS 45 26 * * chr5 101949594 101949594 chr5 107127544 107127544 TCGA-YL-A8HM DEL 48 22 * * chr5 102016580 102016593 chr8 65522400 65522414 TCGA-YL-A8HM BND 2 16 * * chr5 46188627 46188627 chr5 88359958 88359958 TCGA-YL-A8HM DEL 41 12 * TMEM161B-AS1 chr5 46215807 46215809 chr1 103072891 103072893 TCGA-YL-A8HM BND 38 19 * COL11A1 chr5 50747996 50747996 chr5 50761518 50761518 TCGA-YL-A8HM DEL 9 4 PARP8 PARP8 chr5 51231276 51231276 chr5 51908826 51908826 TCGA-YL-A8HM INS 31 7 * * chr5 51776338 51776338 chr5 53596301 53596301 TCGA-YL-A8HM DEL 37 11 * NDUFS4 chr5 52292506 52292506 chr5 99845574 99845574 TCGA-YL-A8HM INS 2 45 * * chr5 84990921 84990921 chr5 85006655 85006655 TCGA-YL-A8HM DEL 34 7 * * chr5 85141749 85141749 chr5 88244332 88244332 TCGA-YL-A8HM DEL 12 18 * TMEM161B chr5 85863429 85863429 chr5 87191287 87191287 TCGA-YL-A8HM INS 9 43 * * chr5 85968066 85968066 chr5 99862967 99862967 TCGA-YL-A8HM DEL 16 8 * * chr5 86061319 86061319 chr5 88235971 88235971 TCGA-YL-A8HM INS 49 9 * TMEM161B chr5 86071035 86071035 chr5 87252430 87252430 TCGA-YL-A8HM DEL 49 19 * * chr5 86603447 86603447 chr5 87010113 87010113 TCGA-YL-A8HM DEL 44 41 * AC109492.1 chr5 88235971 88235971 chrX 94535909 94535909 TCGA-YL-A8HM BND 34 40 TMEM161B * chr5 96433434 96433434 chr5 97721968 97721968 TCGA-YL-A8HM DEL 32 15 AC104123.1 * chr5 97730771 97730771 chr8 86293539 86293539 TCGA-YL-A8HM BND 48 41 * SLC7A13 chr5 99187662 99187673 chr8 110547235 110547245 TCGA-YL-A8HM BND 50 32 * * chr6 92827584 92827584 chr6 114668870 114668870 TCGA-YL-A8HM DEL 25 11 * * chr6 93123798 93123798 chr6 93128621 93128621 TCGA-YL-A8HM DEL 5 21 * * chr6 96889919 96889919 chr6 96890518 96890518 TCGA-YL-A8HM DEL 44 31 NDUFAF4 NDUFAF4 chr7 30579270 30579270 chr10 75406734 75406734 TCGA-YL-A8HM BND 25 12 GARS1-DT ZNF503-AS2 chr7 56171170 56171170 chr7 56172252 56172252 TCGA-YL-A8HM DEL 8 29 * * chr7 81172383 81172383 chr7 81172710 81172710 TCGA-YL-A8HM DEL 10 47 * * chr7 8909332 8909332 chrX 117704457 117704457 TCGA-YL-A8HM BND 16 17 * * chr8 110547235 110547245 chr5 99187662 99187673 TCGA-YL-A8HM BND 11 43 * * chr8 124437477 124437477 chr8 124628155 124628158 TCGA-YL-A8HM INS 33 12 * MTSS1 chr8 124552212 124552212 chr8 124628155 124628158 TCGA-YL-A8HM DEL 39 29 NDUFB9 MTSS1 chr8 124627118 124627118 chr8 124769916 124769916 TCGA-YL-A8HM INS 33 2 MTSS1 * chr8 132568641 132568641 chr8 132571571 132571571 TCGA-YL-A8HM DEL 32 46 * * chr8 50685963 50685963 chr8 50725701 50725701 TCGA-YL-A8HM DEL 43 34 SNTG1 SNTG1 chr8 50788054 50788054 chr8 50818627 50818627 TCGA-YL-A8HM DEL 7 13 SNTG1 * chr8 51190617 51190617 chr8 51281609 51281609 TCGA-YL-A8HM DEL 1 32 * AC012413.1 chr8 51324351 51324351 chr8 51345743 51345743 TCGA-YL-A8HM DEL 6 39 PXDNL PXDNL chr8 51462804 51462804 chr8 51536205 51536205 TCGA-YL-A8HM DEL 13 10 PXDNL PXDNL chr8 76180581 76180581 chr8 76226128 76226128 TCGA-YL-A8HM DEL 37 21 * * chr8 78276185 78276185 chr8 78278999 78278999 TCGA-YL-A8HM DEL 41 44 * * chr8 84721885 84721885 chr5 84847660 84847660 TCGA-YL-A8HM BND 31 29 RALYL * chr9 9451545 9451545 chr9 9462803 9462803 TCGA-YL-A8HM DEL 36 2 PTPRD PTPRD chrX 98866536 98866536 chrX 99167561 99167561 TCGA-YL-A8HM DEL 4 32 AL157778.1 * chr10 20189465 20189465 chr10 20794374 20794374 TCGA-KK-A8IF DEL 2 19 PLXDC2 NEBL chr10 26291892 26291892 chr10 26605580 26605580 TCGA-KK-A8IF DEL 15 9 GAD2 AL160287.1 chr10 31287555 31287555 chr4 16981456 16981456 TCGA-KK-A8IF BND 3 40 ZEB1-AS1 AC106894.1 chr10 55741470 55741470 chr10 55741767 55741767 TCGA-KK-A8IF DEL 18 32 * * chr11 37167266 37167266 chr11 37187139 37187139 TCGA-KK-A8IF DEL 6 35 * * chr11 39920100 39920100 chr11 39921826 39921826 TCGA-KK-A8IF DEL 10 3 * * chr11 80804657 80804657 chr11 80991807 80991807 TCGA-KK-A8IF DEL 31 32 * * chr12 10041350 10041350 chr12 21092585 21092585 TCGA-KK-A8IF DEL 11 28 CLEC9A SLCO1B7 chr12 10222869 10222869 chr12 13287087 13287087 TCGA-KK-A8IF DEL 46 32 GABARAPL1 * chr12 12689142 12689142 chr12 24297838 24297838 TCGA-KK-A8IF DEL 9 27 GPR19 SOX5 chr12 12728069 12728069 chr12 18480112 18480112 TCGA-KK-A8IF INS 25 34 APOLD1 PIK3C2G chr12 13347342 13347342 chr12 13723046 13723046 TCGA-KK-A8IF DEL 32 28 * GRIN2B chr12 15561411 15561411 chr12 24318932 24318932 TCGA-KK-A8IF DEL 17 18 PTPRO SOX5 chr12 15832603 15832603 chr12 17892472 17892472 TCGA-KK-A8IF INS 7 10 EPS8 * chr12 15852588 15852588 chr12 16148992 16148992 TCGA-KK-A8IF INS 7 22 EPS8 * chr12 16151184 16151184 chr12 18903829 18903829 TCGA-KK-A8IF INS 12 37 * * chr12 16402327 16402327 chr12 24706134 24706134 TCGA-KK-A8IF INS 15 37 MGST1 AC023796.1 chr12 19158123 19158123 chr12 19268636 19268636 TCGA-KK-A8IF DEL 23 42 PLEKHA5 PLEKHA5 chr12 19222157 19222157 chr12 24361887 24361887 TCGA-KK-A8IF DEL 8 47 PLEKHA5 SOX5 chr12 21045658 21045658 chr12 23507910 23507910 TCGA-KK-A8IF INS 25 22 SLCO1B3-SLCO1B7 * chr12 21712042 21712042 chr12 22296755 22296755 TCGA-KK-A8IF DEL 45 4 LDHB ST8SIA1 chr12 24336399 24336399 chr12 24737461 24737461 TCGA-KK-A8IF DEL 36 18 SOX5 AC023796.1 chr12 29203780 29203780 chr12 30721671 30721671 TCGA-KK-A8IF DEL 12 47 FAR2 CAPRIN2 chr13 67192892 67192892 chr13 67202586 67202586 TCGA-KK-A8IF DEL 18 1 PCDH9 PCDH9 chr13 67303448 67303448 chr13 68457300 68457300 TCGA-KK-A8IF DEL 18 49 * * chr13 78562388 78562388 chr13 79319356 79319356 TCGA-KK-A8IF DEL 19 13 OBI1-AS1 RBM26 chr13 81721350 81721350 chr13 81741192 81741192 TCGA-KK-A8IF DEL 9 22 * * chr13 85703291 85703291 chr13 85704841 85704841 TCGA-KK-A8IF DEL 50 39 AL356413.1 AL356413.1 chr14 42409981 42409981 chr14 42410159 42410159 TCGA-KK-A8IF DEL 12 17 AL442163.1 AL442163.1 chr15 54200867 54200867 chr15 54404559 54404559 TCGA-KK-A8IF DEL 3 30 UNC13C UNC13C chr16 5564271 5564271 chr1 11238915 11238915 TCGA-KK-A8IF BND 50 24 RBFOX1 MTOR chr16 5934350 5934350 chr16 5934581 5934581 TCGA-KK-A8IF DEL 45 50 RBFOX1 RBFOX1 chr16 6241212 6241212 chr16 6249212 6249212 TCGA-KK-A8IF DEL 6 16 RBFOX1 RBFOX1 chr17 37678362 37678362 chr17 37678414 37678414 TCGA-KK-A8IF DEL 46 4 AC243571.2 AC243571.2 chr1 101721245 101721245 chr1 101721797 101721797 TCGA-KK-A8IF DEL 29 4 LINC01709 LINC01709 chr1 157133594 157133594 chr1 157165556 157165556 TCGA-KK-A8IF DEL 13 12 ETV3 * chr1 167091757 167091757 chr1 167409016 167409016 TCGA-KK-A8IF DEL 40 33 GPA33 POU2F1 chr1 184212032 184212033 chr7 72000921 72000922 TCGA-KK-A8IF BND 42 15 * CALN1 chr1 199090104 199090104 chr1 199126040 199126040 TCGA-KK-A8IF DEL 36 24 * * chr1 214953539 214953539 chr1 214971544 214971544 TCGA-KK-A8IF DEL 15 25 * * chr1 6411577 6411577 chr2 59191119 59191119 TCGA-KK-A8IF BND 8 31 * AC007092.1 chr1 66735539 66735539 chr1 66735872 66735872 TCGA-KK-A8IF DEL 2 25 SGIP1 SGIP1 chr1 72191002 72191002 chr1 72191195 72191195 TCGA-KK-A8IF DEL 22 31 NEGR1 NEGR1 chr20 15862315 15862315 chr20 15890040 15890040 TCGA-KK-A8IF INS 32 48 MACROD2 MACROD2 chr22 17678311 17678311 chr22 17680545 17680545 TCGA-KK-A8IF DEL 26 36 BCL2L13 BCL2L13 chr2 103155314 103155314 chr2 104384395 104384395 TCGA-KK-A8IF DEL 40 37 AC073987.1 * chr2 106911246 106911246 chr2 107513780 107513780 TCGA-KK-A8IF DEL 21 13 * LINC01885 chr2 107606585 107606585 chr2 107647876 107647876 TCGA-KK-A8IF DEL 24 26 * * chr2 116257837 116257837 chr2 162862180 162862180 TCGA-KK-A8IF DEL 25 48 * * chr2 137459049 137459049 chr1 100622459 100622459 TCGA-KK-A8IF BND 22 22 THSD7B * chr2 153747502 153747502 chr2 154069768 154069768 TCGA-KK-A8IF DEL 50 11 * GALNT13 chr2 154067047 154067047 chr3 147579245 147579245 TCGA-KK-A8IF BND 24 24 GALNT13 * chr2 164774676 164774679 chr2 165512909 165512911 TCGA-KK-A8IF DEL 39 11 COBLL1 CSRNP3 chr2 166197999 166197999 chr2 166204516 166204516 TCGA-KK-A8IF DEL 38 25 SCN1A-AS1 SCN1A-AS1 chr2 41162630 41162630 chr2 41169705 41169705 TCGA-KK-A8IF DEL 28 46 * * chr2 58009848 58009848 chr2 58058912 58058912 TCGA-KK-A8IF DEL 27 14 VRK2 VRK2 chr2 59120943 59120943 chr1 75594552 75594552 TCGA-KK-A8IF BND 46 31 AC007092.1 SLC44A5 chr2 83943939 83943943 chr2 83944159 83944159 TCGA-KK-A8IF DEL 22 25 * * chr2 88365140 88365140 chr2 88365379 88365379 TCGA-KK-A8IF DEL 3 9 MRPL45P1 MRPL45P1 chr3 116828666 116828666 chr3 117020655 117020655 TCGA-KK-A8IF DEL 38 32 LSAMP LSAMP chr3 143512154 143512154 chr3 143523863 143523863 TCGA-KK-A8IF DEL 43 4 SLC9A9 SLC9A9 chr3 147605848 147605848 chr2 153758639 153758639 TCGA-KK-A8IF BND 35 24 * * chr3 147857958 147857958 chr8 67783704 67783704 TCGA-KK-A8IF BND 17 41 * * chr3 15430374 15430374 chr3 15430550 15430550 TCGA-KK-A8IF DEL 42 21 METTL6 METTL6 chr3 163379724 163379724 chr3 163382736 163382736 TCGA-KK-A8IF DEL 27 1 * * chr3 191236601 191236601 chr3 191265394 191265394 TCGA-KK-A8IF DEL 33 46 OSTN OSTN chr3 74907240 74907240 chr3 74913848 74913848 TCGA-KK-A8IF DEL 8 46 * * chr3 84346119 84346119 chr3 84352199 84352199 TCGA-KK-A8IF DEL 49 22 * * chr3 87751579 87751579 chr3 87753528 87753528 TCGA-KK-A8IF DEL 36 3 AC108749.1 AC108749.1 chr3 94955205 94955205 chr3 94955449 94955449 TCGA-KK-A8IF DEL 35 18 LINC00879 LINC00879 chr3 95602604 95602604 chr3 95607415 95607415 TCGA-KK-A8IF DEL 49 9 * * chr4 105018164 105018164 chr4 105022872 105022872 TCGA-KK-A8IF DEL 14 46 AC096577.1 AC096577.1 chr4 113406582 113406582 chr4 113413501 113413501 TCGA-KK-A8IF DEL 19 15 * * chr4 126581184 126581184 chr4 126600008 126600008 TCGA-KK-A8IF DEL 15 43 * * chr4 128529926 128529926 chr4 128548696 128548696 TCGA-KK-A8IF DEL 21 18 * * chr4 129319174 129319174 chr4 129328612 129328612 TCGA-KK-A8IF DEL 30 10 * * chr4 14426783 14426783 chr4 19345302 19345302 TCGA-KK-A8IF DEL 43 46 * LINC02438 chr4 14777972 14777972 chr4 16409259 16409259 TCGA-KK-A8IF INS 49 50 LINC00504 AC097515.1 chr4 15197288 15197288 chr4 15605350 15605350 TCGA-KK-A8IF INS 15 10 C1QTNF7-AS1 FBXL5 chr4 15589711 15589711 chr4 19283029 19283029 TCGA-KK-A8IF INS 7 16 CC2D2A LINC02438 chr4 16446505 16446505 chr4 17309744 17309744 TCGA-KK-A8IF DEL 1 4 AC097515.1 * chr4 166282642 166282642 chr4 167560669 167560669 TCGA-KK-A8IF DEL 38 13 * * chr4 93186869 93186870 chr4 93187365 93187365 TCGA-KK-A8IF DEL 17 4 GRID2 GRID2 chr5 102234310 102234310 chr5 106368653 106368653 TCGA-KK-A8IF DEL 7 19 SLCO4C1 * chr5 102475315 102475315 chr5 105896472 105896472 TCGA-KK-A8IF INS 22 30 SLCO6A1 * chr5 105873177 105873177 chr5 105882124 105882126 TCGA-KK-A8IF DEL 22 11 * * chr5 107552866 107552866 chr5 107597203 107597203 TCGA-KK-A8IF DEL 3 34 EFNA5 EFNA5 chr5 122141480 122141480 chr5 122163762 122163762 TCGA-KK-A8IF DEL 22 41 ZNF474 AC010255.2 chr5 29740967 29740967 chr5 29742311 29742311 TCGA-KK-A8IF DEL 42 41 * * chr5 82082758 82082758 chr5 102979018 102979018 TCGA-KK-A8IF INS 5 32 ATG10 PAM chr5 82290788 82290788 chr5 103140379 103140379 TCGA-KK-A8IF DEL 26 7 ATP6AP1L PPIP5K2 chr5 82991951 82991951 chr5 83002904 83002904 TCGA-KK-A8IF DEL 34 12 * * chr5 96469920 96469920 chr5 106918699 106918699 TCGA-KK-A8IF INS 10 29 AC104123.1 LINC01950 chr5 97281075 97281075 chr5 99591835 99591835 TCGA-KK-A8IF DEL 22 39 LIX1-AS1 * chr5 99945127 99945127 chr5 106368928 106368928 TCGA-KK-A8IF INS 29 7 * * chr6 141622716 141622716 chr6 141905064 141905064 TCGA-KK-A8IF DEL 3 34 * * chr6 51996430 51996430 chr6 55106464 55106464 TCGA-KK-A8IF DEL 14 42 PKHD1 HCRTR2 chr6 52000379 52000379 chr6 52001260 52001260 TCGA-KK-A8IF DEL 13 3 PKHD1 PKHD1 chr6 83688224 83688224 chr6 129282269 129282269 TCGA-KK-A8IF DEL 7 26 SNAP91 LAMA2 chr7 111109264 111109264 chr7 111113113 111113113 TCGA-KK-A8IF DEL 11 14 IMMP2L IMMP2L chr7 31246086 31246086 chr7 31250118 31250118 TCGA-KK-A8IF DEL 37 20 * * chr7 84138147 84138147 chr4 15609734 15609734 TCGA-KK-A8IF BND 16 8 SEMA3A FBXL5 chr8 12586090 12586090 chr4 168205594 168205594 TCGA-KK-A8IF BND 24 32 AC068587.4 * chr8 16531360 16531360 chr4 167470910 167470910 TCGA-KK-A8IF BND 17 28 MSR1 * chr8 28762113 28762113 chr8 36367096 36367096 TCGA-KK-A8IF DEL 36 9 * * chr8 31366279 31366279 chr8 31451248 31451248 TCGA-KK-A8IF DEL 8 36 AC068672.2 * chr8 34433342 34433342 chr8 35052610 35052610 TCGA-KK-A8IF INS 39 32 * * chr8 46996123 46996123 chr8 47012266 47012266 TCGA-KK-A8IF DEL 8 19 * * chr8 49901303 49901303 chr8 91494611 91494611 TCGA-KK-A8IF INS 3 38 * * chr8 50442529 50442529 chr8 50442793 50442793 TCGA-KK-A8IF DEL 19 30 SNTG1 SNTG1 chr8 61885281 61885281 chr8 61902835 61902835 TCGA-KK-A8IF DEL 7 18 LINC02842 LINC02842 chr8 67781911 67781911 chr3 147860884 147860884 TCGA-KK-A8IF BND 23 1 * * chr8 67973299 67973299 chr14 28486871 28486871 TCGA-KK-A8IF BND 46 32 PREX2 * chr9 100126643 100126643 chr16 46386376 46386376 TCGA-KK-A8IF BND 25 2 INVS * chr9 104285437 104285437 chr9 104310612 104310612 TCGA-KK-A8IF DEL 21 11 TOPORSLP * chr9 111544842 111544842 chr9 111548264 111548264 TCGA-KK-A8IF DEL 6 48 ZNF483 ZNF483 chr9 20846572 20846572 chr2 107990624 107990624 TCGA-KK-A8IF BND 15 45 FOCAD SLC5A7 chr9 20908759 20908759 chr2 53775927 53775927 TCGA-KK-A8IF BND 43 46 FOCAD ASB3 chrX 112974738 112974738 chrX 141264015 141264015 TCGA-KK-A8IF INS 31 31 * RBMX2P2 chrX 114117929 114117929 chrX 114121398 114121398 TCGA-KK-A8IF DEL 27 23 * * chrX 64528716 64528716 chrX 64551073 64551073 TCGA-KK-A8IF DEL 23 24 * * chr17 51199814 51199814 chr17 59918352 59918352 TCGA-V1-A9OF DEL 23 37 MBTD1 RPS6KB1 chr4 117525812 117525812 chr4 179993492 179993492 TCGA-V1-A9OF INS 27 12 LINC01378 * chr4 90555341 90555341 chr4 93984224 93984224 TCGA-V1-A9OF INS 29 46 CCSER1 * chr4 96738020 96738020 chr4 97287063 97287063 TCGA-V1-A9OF INS 47 16 LINC02267 STPG2 chr8 69411502 69411502 chr4 4399524 4399524 TCGA-V1-A9OF BND 9 19 * NSG1 chr10 42257081 42257081 chr10 42550700 42550700 TCGA-XK-AAJ3 DEL 45 9 AL031601.2 ZNF37BP chr10 42904557 42904557 chr16 50315175 50315175 TCGA-XK-AAJ3 BND 19 3 * ADCY7 chr12 46753058 46753058 chr1 162337498 162337498 TCGA-XK-AAJ3 BND 35 41 AC008014.1 NOS1AP chr13 108373145 108373145 chr7 26314995 26314995 TCGA-XK-AAJ3 BND 20 2 AL138694.1 SNX10 chr13 69607748 69607748 chr13 71313345 71313345 TCGA-XK-AAJ3 DEL 27 11 * * chr13 71044717 71044717 chr8 50948846 50948846 TCGA-XK-AAJ3 BND 48 49 LINC00348 * chr13 71240045 71240045 chr8 50883271 50883271 TCGA-XK-AAJ3 BND 4 49 * * chr13 71273526 71273526 chr8 51305899 51305899 TCGA-XK-AAJ3 BND 27 20 * AC012413.1 chr16 49095387 49095387 chr10 42165575 42165575 TCGA-XK-AAJ3 BND 27 43 * * chr16 50329331 50329331 chr16 50692627 50692627 TCGA-XK-AAJ3 DEL 30 39 BRD7 NOD2 chr16 50366633 50366633 chr16 54415263 54415263 TCGA-XK-AAJ3 DEL 35 1 BRD7 * chr16 50711015 50711015 chr10 42965433 42965433 TCGA-XK-AAJ3 BND 44 29 NOD2 * chr16 5158158 5158158 chr16 5171914 5171914 TCGA-XK-AAJ3 DEL 47 22 AC074051.3 AC074051.3 chr16 51797715 51797715 chr16 55134266 55134266 TCGA-XK-AAJ3 INS 44 38 * * chr16 52587165 52587165 chr16 53133555 53133555 TCGA-XK-AAJ3 INS 33 27 CASC16 CHD9 chr1 73035904 73035904 chr1 73042438 73042438 TCGA-XK-AAJ3 DEL 50 2 * * chr22 42842799 42842799 chr22 42842878 42842878 TCGA-XK-AAJ3 DEL 8 37 ARFGAP3 ARFGAP3 chr3 115773813 115773813 chr3 143838565 143838565 TCGA-XK-AAJ3 INS 12 20 * SLC9A9 chr3 117210031 117210031 chr7 124232936 124232936 TCGA-XK-AAJ3 BND 7 5 * AC006148.1 chr3 118568717 118568717 chr3 118905993 118905993 TCGA-XK-AAJ3 INS 11 45 * IGSF11 chr3 118625160 118625160 chr3 118635299 118635299 TCGA-XK-AAJ3 DEL 39 33 * * chr3 118657246 118657246 chr3 119346357 119346357 TCGA-XK-AAJ3 DEL 38 37 * ARHGAP31 chr3 118659483 118659483 chr3 118939051 118939051 TCGA-XK-AAJ3 INS 15 49 * IGSF11 chr3 143991765 143991766 chr7 124113576 124113577 TCGA-XK-AAJ3 BND 40 28 DIPK2A AC006148.1 chr3 144095069 144095074 chr7 124609481 124609486 TCGA-XK-AAJ3 BND 21 48 * * chr3 144566150 144566153 chr7 124563388 124563391 TCGA-XK-AAJ3 BND 25 37 * * chr3 78087816 78087816 chr3 78672400 78672400 TCGA-XK-AAJ3 DEL 43 45 AC117462.1 ROBO1 chr5 18290067 18290067 chr5 18290163 18290163 TCGA-XK-AAJ3 DEL 8 15 * * chr6 100634830 100634830 chr6 121764508 121764508 TCGA-XK-AAJ3 INS 19 34 ASCC3 * chr6 114190280 114190280 chr6 115310104 115310104 TCGA-XK-AAJ3 DEL 4 26 HDAC2-AS2 * chr6 72328474 72328474 chr7 31568702 31568702 TCGA-XK-AAJ3 BND 43 28 RIMS1 ITPRID1 chr6 96366602 96366602 chr6 104026395 104026395 TCGA-XK-AAJ3 INS 18 28 UFL1-AS1 NPM1P10 chr6 96367508 96367508 chr6 114189617 114189617 TCGA-XK-AAJ3 DEL 5 3 UFL1-AS1 HDAC2-AS2 chr6 99507356 99507356 chr6 101887191 101887191 TCGA-XK-AAJ3 DEL 5 25 USP45 GRIK2 chr7 119341008 119341008 chr7 119358595 119358595 TCGA-XK-AAJ3 DEL 47 1 * * chr7 124113576 124113577 chr3 143991765 143991766 TCGA-XK-AAJ3 BND 35 37 AC006148.1 DIPK2A chr7 124609481 124609486 chr3 144095069 144095074 TCGA-XK-AAJ3 BND 10 41 * * chr7 125662093 125662093 chr7 125664756 125664756 TCGA-XK-AAJ3 DEL 15 41 * * chr7 15575886 15575886 chr7 15577994 15577994 TCGA-XK-AAJ3 DEL 23 16 * * chr8 108547777 108547777 chr8 108556008 108556008 TCGA-XK-AAJ3 DEL 17 49 * * chr8 50303240 50303240 chr13 71242007 71242007 TCGA-XK-AAJ3 BND 20 40 SNTG1 * chr8 50696786 50696786 chr8 51119973 51119973 TCGA-XK-AAJ3 DEL 1 33 SNTG1 * chr8 50986057 50986057 chr8 51164875 51164875 TCGA-XK-AAJ3 INS 49 43 * * chr8 75885337 75885337 chr2 115848283 115848283 TCGA-XK-AAJ3 BND 28 18 * * chr18 53882990 53882990 chr18 53893500 53893500 TCGA-V1-A8MM DEL 33 14 * * chr1 153084131 153084131 chr1 248228877 248228877 TCGA-V1-A8MM DEL 9 6 * * chr1 192776268 192776268 chr1 195293167 195293167 TCGA-V1-A8MM INS 28 27 AL390957.1 * chr1 193104457 193104457 chr1 197542289 197542289 TCGA-V1-A8MM DEL 47 12 GLRX2 DENND1B chr1 193424918 193424918 chr1 248836564 248836564 TCGA-V1-A8MM INS 11 23 * * chr1 194124506 194124506 chr1 197247477 197247477 TCGA-V1-A8MM DEL 8 12 * * chr1 194677771 194677771 chr1 195528714 195528714 TCGA-V1-A8MM INS 30 27 * * chr1 195537193 195537193 chr1 195799538 195799538 TCGA-V1-A8MM INS 12 34 * * chr1 195720515 195720515 chr1 248704000 248704000 TCGA-V1-A8MM DEL 24 26 * LYPD9P chr1 195780453 195780453 chr1 195803927 195803927 TCGA-V1-A8MM DEL 7 25 * * chr1 195994834 195994834 chr1 196994973 196994973 TCGA-V1-A8MM INS 28 29 * CFHR5 chr1 196464077 196464077 chr1 197171273 197171273 TCGA-V1-A8MM DEL 36 38 KCNT2 ZBTB41 chr21 9057957 9057957 chr1 28720732 28720732 TCGA-V1-A8MM BND 19 17 CR392039.4 * chr2 187240719 187240719 chr2 187240972 187240972 TCGA-V1-A8MM DEL 47 32 AC007319.1 AC007319.1 chr3 164720868 164720868 chr3 164721399 164721399 TCGA-V1-A8MM DEL 29 49 LINC01324 LINC01324 chr3 71952677 71952677 chr3 73808972 73808972 TCGA-V1-A8MM DEL 13 25 * LINC02005 chr4 129175868 129175868 chr4 136347905 136347905 TCGA-V1-A8MM DEL 1 20 * AC018680.1 chr4 130717792 130717792 chr4 133365704 133365704 TCGA-V1-A8MM DEL 44 20 * * chr4 14041907 14041907 chr4 15466524 15466524 TCGA-V1-A8MM DEL 1 41 * * chr4 14043125 14043125 chrX 108574826 108574826 TCGA-V1-A8MM BND 17 26 * COL4A5 chr5 100820415 100820415 chr5 103173682 103173682 TCGA-V1-A8MM DEL 39 5 ST8SIA4 PPIP5K2 chr7 23056347 23056347 chr7 23056400 23056400 TCGA-V1-A8MM DEL 20 6 * * chr9 18884759 18884759 chr9 18884839 18884839 TCGA-V1-A8MM INS 37 48 ADAMTSL1 ADAMTSL1 chrX 108570457 108570457 chrX 109544028 109544028 TCGA-V1-A8MM DEL 27 49 COL4A5 NXT2 chrX 109543481 109543481 chrX 109790765 109790765 TCGA-V1-A8MM DEL 50 25 NXT2 * chrX 151475344 151475344 chrX 151477414 151477414 TCGA-V1-A8MM DEL 24 18 * * chr10 115763449 115763449 chr10 116058735 116058735 TCGA-KK-A7B0 DUP 48 39 ATRNL1 GFRA1 chr10 122590479 122590479 chr10 123014158 123014159 TCGA-KK-A7B0 DUP 34 42 DMBT1 ACADSB chr10 124809564 124809564 chr10 125088313 125088313 TCGA-KK-A7B0 DUP 49 30 ABRAXAS2 CTBP2 chr10 21900236 21900236 chr10 24332895 24332895 TCGA-KK-A7B0 DUP 24 19 DNAJC1 KIAA1217 chr10 5095258 5095258 chr10 68842114 68842114 TCGA-KK-A7B0 INV 27 30 AKR1C3 STOX1 chr10 59656732 59656732 chr10 63119856 63119856 TCGA-KK-A7B0 DUP 48 44 SLC16A9 * chr10 61154425 61154425 chr10 64864813 64864813 TCGA-KK-A7B0 DUP 7 38 * * chr10 66191647 66191647 chr10 87927788 87927788 TCGA-KK-A7B0 DUP 21 28 CTNNA3 PTEN chr10 69585295 69585295 chr10 69689233 69689234 TCGA-KK-A7B0 INV 34 1 * LINC02651 chr10 7110003 7110004 chr10 7646596 7646596 TCGA-KK-A7B0 DUP 50 7 * ITIH5 chr10 7120906 7120906 chr10 7120936 7120936 TCGA-KK-A7B0 INV 28 28 * * chr10 7142205 7142205 chr10 11191197 11191197 TCGA-KK-A7B0 DUP 25 38 * CELF2 chr10 75025393 75025394 chr10 75854317 75854317 TCGA-KK-A7B0 DUP 13 31 KAT6B LRMDA chr10 8422835 8422836 chr10 69689233 69689234 TCGA-KK-A7B0 INV 19 39 AC025946.1 LINC02651 chr10 8422908 8422908 chr10 69585109 69585110 TCGA-KK-A7B0 DEL 33 24 AC025946.1 * chr10 87871334 87871334 chr10 91530978 91530978 TCGA-KK-A7B0 DEL 50 12 PTEN * chr10 87919712 87919712 chr10 88104074 88104074 TCGA-KK-A7B0 INV 5 15 PTEN * chr10 88915398 88915401 chr10 89141373 89141375 TCGA-KK-A7B0 DUP 7 21 STAMBPL1 * chr10 91480431 91480431 chr10 92051026 92051026 TCGA-KK-A7B0 DUP 26 43 HECTD2 CPEB3 chr11 100729298 100729298 chr11 100739879 100739879 TCGA-KK-A7B0 DUP 4 40 ARHGAP42 ARHGAP42 chr11 108360358 108360358 chr11 111172670 111172670 TCGA-KK-A7B0 DUP 5 25 ATM LINC02550 chr11 109609994 109609994 chr11 109932104 109932104 TCGA-KK-A7B0 DUP 21 38 * RDX chr11 113846538 113846538 chr11 114107819 114107820 TCGA-KK-A7B0 DUP 25 11 USP28 ZBTB16 chr11 123096467 123096467 chr11 126237616 126237616 TCGA-KK-A7B0 DUP 33 26 CLMP FAM118B chr11 128571472 128571472 chr11 129003726 129003726 TCGA-KK-A7B0 DUP 17 4 ETS1 ARHGAP32 chr11 130025782 130025782 chr11 130864395 130864396 TCGA-KK-A7B0 DUP 20 9 * LINC02551 chr11 16424325 16424325 chr12 80521982 80521982 TCGA-KK-A7B0 BND 40 16 SOX6 PTPRQ chr11 19649229 19649230 chr11 22526672 22526672 TCGA-KK-A7B0 DUP 11 13 NAV2 * chr11 2045787 2045787 chr11 4814568 4814568 TCGA-KK-A7B0 DUP 35 24 * MMP26 chr11 20489356 20489357 chr12 76579687 76579687 TCGA-KK-A7B0 BND 17 34 PRMT3 AC107032.2 chr11 43149864 43149864 chr11 43438083 43438083 TCGA-KK-A7B0 DUP 46 10 HNRNPKP3 TTC17 chr11 66769537 66769537 chr11 70108468 70108468 TCGA-KK-A7B0 DUP 11 10 C11orf80 ANO1 chr11 66943813 66943814 chr11 67847803 67847803 TCGA-KK-A7B0 DUP 29 26 PC ENPP7P7 chr11 67201180 67201180 chr11 70258139 70258139 TCGA-KK-A7B0 DUP 25 7 KDM2A * chr11 68863250 68863250 chr2 239227723 239227723 TCGA-KK-A7B0 BND 11 42 * HDAC4 chr11 78241390 78241390 chr11 82156255 82156256 TCGA-KK-A7B0 DUP 37 24 GAB2 MIR4300HG chr11 89511227 89511227 chr11 89656531 89656531 TCGA-KK-A7B0 DUP 48 48 * FOLH1B chr11 91366272 91366272 chr11 91817891 91817891 TCGA-KK-A7B0 DUP 4 23 * * chr11 93050943 93050943 chr11 96884227 96884227 TCGA-KK-A7B0 DUP 39 14 * * chr12 108997295 108997295 chr12 109477461 109477461 TCGA-KK-A7B0 DUP 44 5 SVOP KCTD10 chr12 111787490 111787490 chr12 112040049 112040049 TCGA-KK-A7B0 DUP 50 36 ALDH2 NAA25 chr12 112957891 112957892 chr12 113711085 113711085 TCGA-KK-A7B0 DUP 47 8 OAS3 LINC01234 chr12 116204456 116204456 chr12 119617854 119617855 TCGA-KK-A7B0 DUP 47 37 MED13L TMEM233 chr12 116683701 116683701 chr12 119671564 119671564 TCGA-KK-A7B0 DUP 4 48 AC125603.2 PRKAB1 chr12 117680593 117680593 chr12 118177458 118177458 TCGA-KK-A7B0 DUP 45 35 KSR2 TAOK3 chr12 123168916 123168916 chr12 123327504 123327504 TCGA-KK-A7B0 DUP 20 32 MPHOSPH9 SBNO1 chr12 123484489 123484489 chr12 123754290 123754291 TCGA-KK-A7B0 DUP 19 29 RILPL1 ATP6V0A2 chr12 166757 166757 chr12 4104403 4104403 TCGA-KK-A7B0 DUP 41 25 IQSEC3 * chr12 17229471 17229479 chr21 29003766 29003766 TCGA-KK-A7B0 BND 44 33 * * chr12 17875477 17875477 chr21 32832172 32832172 TCGA-KK-A7B0 BND 20 39 * C21orf62-AS1 chr12 2063035 2063035 chr12 4196566 4196566 TCGA-KK-A7B0 DUP 4 34 CACNA1C * chr12 4816540 4816540 chr12 7754953 7754954 TCGA-KK-A7B0 DUP 6 28 GALNT8 * chr12 50984057 50984058 chr12 53309545 53309545 TCGA-KK-A7B0 DUP 13 2 SLC11A2 AAAS chr12 51112897 51112898 chr12 54045183 54045183 TCGA-KK-A7B0 DUP 15 15 TFCP2 HOXC4 chr12 54133258 54133258 chr12 57001481 57001481 TCGA-KK-A7B0 DUP 8 9 SMUG1 ZBTB39 chr12 64424143 64424150 chr12 65110648 65110648 TCGA-KK-A7B0 DUP 19 29 XPOT WIF1 chr12 65078490 65078490 chr12 68025350 68025350 TCGA-KK-A7B0 INV 12 2 WIF1 IFNG-AS1 chr12 65604909 65604909 chr12 68050064 68050064 TCGA-KK-A7B0 DUP 12 33 AC025419.1 IFNG-AS1 chr12 65627061 65627061 chr12 65938482 65938482 TCGA-KK-A7B0 DUP 33 50 AC025419.1 HMGA2 chr12 68025722 68025722 chr12 68032034 68032034 TCGA-KK-A7B0 INV 31 24 IFNG-AS1 IFNG-AS1 chr12 68762118 68762119 chr12 72605677 72605677 TCGA-KK-A7B0 DUP 42 36 SLC35E3 TRHDE chr12 69899154 69899154 chr12 72751902 72751903 TCGA-KK-A7B0 DUP 26 9 MYRFL * chr12 78478698 78478698 chr19 3680451 3680451 TCGA-KK-A7B0 BND 12 40 AC128707.1 PIP5K1C chr12 88304210 88304210 chr12 88977394 88977394 TCGA-KK-A7B0 DUP 19 44 * * chr12 91299598 91299598 chr12 91520042 91520042 TCGA-KK-A7B0 DUP 45 12 * * chr12 94508430 94508430 chr12 95172979 95172979 TCGA-KK-A7B0 DUP 2 36 * FGD6 chr12 95559271 95559271 chr12 95657736 95657736 TCGA-KK-A7B0 DUP 32 38 PGAM1P5 PGAM1P5 chr12 96395222 96395222 chr12 100668619 100668628 TCGA-KK-A7B0 DUP 21 9 CDK17 * chr13 100085173 100085173 chr13 100565059 100565059 TCGA-KK-A7B0 DUP 45 22 * GGACT chr13 104002727 104002727 chr13 104680435 104680435 TCGA-KK-A7B0 DUP 35 18 * * chr13 104735231 104735232 chr13 107329570 107329574 TCGA-KK-A7B0 DUP 33 4 * FAM155A chr13 108346093 108346093 chr13 108736693 108736694 TCGA-KK-A7B0 DUP 43 6 AL138694.1 MYO16 chr13 108715988 108715988 chr13 109074295 109074295 TCGA-KK-A7B0 DUP 23 41 MYO16 MYO16 chr13 24063600 24063600 chr13 24262952 24262952 TCGA-KK-A7B0 DUP 48 34 SPATA13 SPATA13 chr13 39394468 39394469 chr13 50335276 50335276 TCGA-KK-A7B0 DEL 27 10 LHFPL6 DLEU1 chr13 40725224 40725224 chr16 53709211 53709211 TCGA-KK-A7B0 BND 30 38 * FTO chr13 50791357 50791357 chr13 52021879 52021880 TCGA-KK-A7B0 DUP 6 49 DLEU7 ALG11 chr13 51817164 51817164 chr13 51955100 51955100 TCGA-KK-A7B0 DUP 20 46 AL162377.3 ATP7B chr13 52014002 52014002 chr13 52316170 52316170 TCGA-KK-A7B0 DUP 8 46 ALG11 TPTE2P2 chr13 53713103 53713106 chr13 53930516 53930516 TCGA-KK-A7B0 DUP 34 4 * * chr13 56052312 56052312 chr13 60967812 60967812 TCGA-KK-A7B0 INS 37 20 * * chr13 57350938 57350938 chr13 59562047 59562047 TCGA-KK-A7B0 INS 13 24 * * chr13 58916932 58916933 chr13 62996906 62996906 TCGA-KK-A7B0 INS 27 12 * * chr13 59487056 59487056 chr13 62322350 62322350 TCGA-KK-A7B0 INS 39 23 * LINC01074 chr13 59574921 59574921 chr13 60788941 60788941 TCGA-KK-A7B0 INS 11 31 * RNY3P5 chr13 66684569 66684569 chr13 67057332 67057332 TCGA-KK-A7B0 DUP 10 7 PCDH9 PCDH9 chr13 67685403 67685403 chr7 84630752 84630752 TCGA-KK-A7B0 BND 19 19 * * chr13 71883313 71883314 chr13 72369137 72369138 TCGA-KK-A7B0 DUP 38 1 * * chr13 81016816 81016817 chr13 81232144 81232144 TCGA-KK-A7B0 DUP 4 26 * * chr13 91634231 91634231 chr13 95563377 95563377 TCGA-KK-A7B0 DUP 20 14 GPC5 CLDN10 chr13 92076357 92076357 chr13 93037206 93037207 TCGA-KK-A7B0 DUP 50 27 GPC5 * chr14 20547750 20547750 chr14 24328350 24328350 TCGA-KK-A7B0 DUP 26 12 * ADCY4 chr14 20969710 20969710 chr14 24773111 24773111 TCGA-KK-A7B0 DUP 24 15 * * chr14 22965520 22965520 chr14 25485093 25485093 TCGA-KK-A7B0 DUP 9 15 AL132780.3 * chr14 23018699 23018699 chr14 23018989 23018989 TCGA-KK-A7B0 INV 13 49 PSMB5 PSMB5 chr14 27292746 27292746 chr14 27443829 27443829 TCGA-KK-A7B0 DUP 8 41 AL390334.1 AL390334.1 chr14 37590562 37590562 chr14 37590747 37590747 TCGA-KK-A7B0 DUP 27 47 FOXA1 FOXA1 chr14 42602263 42602263 chr14 42930375 42930375 TCGA-KK-A7B0 DUP 35 26 AL442163.1 * chr14 44169465 44169465 chr14 44408559 44408559 TCGA-KK-A7B0 DUP 15 42 LINC02307 * chr15 23381338 23381338 chr15 23668365 23668365 TCGA-KK-A7B0 DUP 17 25 * * chr15 24373412 24373412 chr15 24432694 24432694 TCGA-KK-A7B0 DEL 20 31 * * chr15 24419528 24419528 chr15 30048214 30048214 TCGA-KK-A7B0 DUP 40 25 * * chr15 33991586 33991586 chr15 34440044 34440045 TCGA-KK-A7B0 DUP 50 10 AVEN * chr15 37933967 37933967 chr15 40396802 40396803 TCGA-KK-A7B0 DUP 36 10 TMCO5A * chr15 52062885 52062886 chr15 54615180 54615180 TCGA-KK-A7B0 DUP 42 19 MAPK6 UNC13C chr15 57680877 57680877 chr15 60532430 60532431 TCGA-KK-A7B0 DUP 48 12 GCOM1 RORA chr15 71997670 71997670 chr15 72634554 72634554 TCGA-KK-A7B0 DUP 49 40 MYO9A LINC02259 chr15 78540428 78540428 chr15 78961718 78961719 TCGA-KK-A7B0 DUP 9 23 PSMA4 RASGRF1 chr15 86563411 86563411 chr15 86794086 86794086 TCGA-KK-A7B0 DUP 45 21 AGBL1 AGBL1 chr15 97475252 97475253 chr15 101295925 101295925 TCGA-KK-A7B0 DUP 45 21 LINC02254 SNRPA1 chr15 97698616 97698616 chr17 20822308 20822308 TCGA-KK-A7B0 BND 34 26 LINC00923 ABHD17AP6 chr15 97698814 97698814 chr17 21271506 21271506 TCGA-KK-A7B0 BND 17 24 LINC00923 * chr15 97699896 97699896 chr15 99055979 99055979 TCGA-KK-A7B0 DUP 32 30 LINC00923 AC036108.1 chr15 97700805 97700805 chr17 21342777 21342777 TCGA-KK-A7B0 BND 32 15 LINC00923 * chr15 99055092 99055092 chr17 20822308 20822308 TCGA-KK-A7B0 BND 28 29 AC036108.1 ABHD17AP6 chr16 1894655 1894655 chr16 2280503 2280503 TCGA-KK-A7B0 DUP 48 36 * ABCA3 chr16 20312019 20312019 chr18 43202295 43202295 TCGA-KK-A7B0 BND 50 31 GP2 * chr16 2302435 2302435 chr16 3278636 3278636 TCGA-KK-A7B0 DUP 24 3 ABCA3 ZNF263 chr16 23906826 23906826 chr18 46660817 46660817 TCGA-KK-A7B0 BND 21 10 PRKCB * chr16 30292 30292 chrX 156009633 156009633 TCGA-KK-A7B0 BND 33 41 Z84723.1 IL9R chr16 53709211 53709211 chr13 40725224 40725224 TCGA-KK-A7B0 BND 1 22 FTO * chr16 55762195 55762195 chr16 55788603 55788603 TCGA-KK-A7B0 DEL 14 8 CES1P1 CES1P1 chr16 61106039 61106039 chr16 61240180 61240180 TCGA-KK-A7B0 DUP 19 31 * * chr16 70172063 70172063 chr16 70803840 70803840 TCGA-KK-A7B0 DUP 47 15 CLEC18C * chr16 72942122 72942122 chr16 80883475 80883475 TCGA-KK-A7B0 DUP 38 28 ZFHX3 ARLNC1 chr16 72942424 72942424 chr16 73206669 73206669 TCGA-KK-A7B0 INV 32 35 ZFHX3 ZFHX3 chr16 73206571 73206571 chr16 80404659 80404659 TCGA-KK-A7B0 DEL 48 27 ZFHX3 AC105411.1 chr16 73206642 73206642 chr16 80882583 80882584 TCGA-KK-A7B0 DEL 14 46 ZFHX3 ARLNC1 chr16 7914987 7914987 chr16 8178439 8178440 TCGA-KK-A7B0 DUP 50 28 * * chr16 8963811 8963811 chr16 10734037 10734038 TCGA-KK-A7B0 DUP 12 33 USP7 * chr17 16630740 16630740 chr17 19449414 19449414 TCGA-KK-A7B0 DUP 42 9 ZNF624 AC004448.2 chr17 21272496 21272496 chr17 21291187 21291187 TCGA-KK-A7B0 DEL 42 15 * MAP2K3 chr17 2462650 2462650 chr17 2831960 2831961 TCGA-KK-A7B0 DUP 10 16 METTL16 RAP1GAP2 chr17 35207202 35207202 chr17 35913253 35913253 TCGA-KK-A7B0 DUP 21 19 * LRRC37A9P chr17 35379677 35379677 chr17 35913203 35913203 TCGA-KK-A7B0 DUP 41 32 * LRRC37A9P chr17 37904729 37904729 chr17 40765569 40765569 TCGA-KK-A7B0 DUP 48 30 * * chr17 4786999 4786999 chr17 5606980 5606980 TCGA-KK-A7B0 DUP 49 46 VMO1 NLRP1 chr17 48268842 48268842 chr17 49652451 49652452 TCGA-KK-A7B0 DUP 30 18 SKAP1 SPOP chr17 48435407 48435407 chr17 52425225 52425225 TCGA-KK-A7B0 DUP 19 49 * LINC01982 chr17 58261435 58261435 chr17 60721024 60721025 TCGA-KK-A7B0 DUP 10 13 LPO BCAS3 chr17 74170479 74170479 chr17 77947381 77947382 TCGA-KK-A7B0 DUP 28 16 * * chr17 7679632 7679647 chr14 35668190 35668190 TCGA-KK-A7B0 BND 6 31 TP53 RALGAPA1 chr18 21732675 21732675 chr18 24954167 24954167 TCGA-KK-A7B0 DUP 39 25 MIB1 LINC01894 chr18 33591117 33591117 chr18 33823139 33823139 TCGA-KK-A7B0 DUP 31 30 ASXL3 * chr18 37629292 37629292 chr18 38059386 38059386 TCGA-KK-A7B0 DUP 4 26 AC009899.1 * chr18 4540465 4540468 chr8 33991719 33991722 TCGA-KK-A7B0 BND 27 34 * AF279873.3 chr18 58473502 58473502 chr18 58530433 58530433 TCGA-KK-A7B0 DEL 30 36 * ALPK2 chr18 62316430 62316431 chr18 65226032 65226045 TCGA-KK-A7B0 DUP 2 49 * * chr18 64800080 64800080 chr18 65521288 65521288 TCGA-KK-A7B0 DUP 28 14 * * chr18 72765137 72765137 chr18 73074402 73074403 TCGA-KK-A7B0 DUP 50 12 NETO1 * chr19 17015277 17015277 chr19 17066342 17066342 TCGA-KK-A7B0 DEL 39 45 CPAMD8 HAUS8 chr19 2177684 2177684 chr19 2698896 2698896 TCGA-KK-A7B0 DUP 45 9 DOT1L GNG7 chr19 29033214 29033214 chr19 29201948 29201948 TCGA-KK-A7B0 DUP 38 33 * * chr19 3618351 3618351 chr19 5237653 5237653 TCGA-KK-A7B0 DUP 36 49 CACTIN PTPRS chr19 36320117 36320118 chr19 36347826 36347826 TCGA-KK-A7B0 DEL 49 16 LINC00665 ZFP14 chr19 3635159 3635163 chr19 5138155 5138157 TCGA-KK-A7B0 DUP 25 35 PIP5K1C KDM4B chr19 44246366 44246366 chr19 45063630 45063631 TCGA-KK-A7B0 DUP 46 43 ZNF235 CLASRP chr19 52001410 52001411 chr19 52415703 52415703 TCGA-KK-A7B0 DUP 45 33 ZNF615 ZNF528 chr19 52087941 52087941 chr19 52201820 52201820 TCGA-KK-A7B0 INV 48 29 ZNF432 PPP2R1A chr19 52196254 52196254 chr19 52200488 52200488 TCGA-KK-A7B0 INV 11 29 PPP2R1A PPP2R1A chr19 52196596 52196596 chr19 52197716 52197716 TCGA-KK-A7B0 INV 12 1 PPP2R1A PPP2R1A chr19 52197425 52197425 chr19 52206301 52206301 TCGA-KK-A7B0 INV 46 5 PPP2R1A PPP2R1A chr19 52198585 52198585 chr19 52204876 52204876 TCGA-KK-A7B0 INV 12 38 PPP2R1A PPP2R1A chr19 52199192 52199192 chr19 52206944 52206944 TCGA-KK-A7B0 INV 12 9 PPP2R1A PPP2R1A chr19 52202272 52202272 chr19 52206566 52206569 TCGA-KK-A7B0 INV 33 28 PPP2R1A PPP2R1A chr19 53376648 53376648 chr19 53800043 53800044 TCGA-KK-A7B0 DUP 34 3 ZNF525 NLRP12 chr19 56575470 56575471 chr19 57375758 57375758 TCGA-KK-A7B0 DUP 43 45 ZNF470 ZNF547 chr19 9192811 9192812 chr19 10164506 10164506 TCGA-KK-A7B0 DUP 43 6 * DNMT1 chr1 101485901 101485901 chr1 101723170 101723170 TCGA-KK-A7B0 DUP 12 27 * LINC01709 chr1 107286497 107286497 chr1 110997067 110997067 TCGA-KK-A7B0 DUP 4 4 NTNG1 * chr1 119137586 119137586 chr1 144035250 144035250 TCGA-KK-A7B0 INV 27 14 WARS2 SRGAP2D chr1 149872080 149872080 chr1 150935724 150935724 TCGA-KK-A7B0 DUP 17 41 * SETDB1 chr1 150418713 150418714 chr1 150888343 150888343 TCGA-KK-A7B0 DUP 23 41 RPRD2 CTXND2 chr1 150751702 150751702 chr1 150751859 150751859 TCGA-KK-A7B0 INV 7 33 CTSS CTSS chr1 154332340 154332340 chr1 155261467 155261467 TCGA-KK-A7B0 DUP 32 11 ATP8B2 SCAMP3 chr1 161179422 161179422 chr1 161437184 161437184 TCGA-KK-A7B0 DUP 24 50 B4GALT3 AL592295.3 chr1 164203057 164203057 chr1 164538574 164538574 TCGA-KK-A7B0 DUP 5 8 * * chr1 171283742 171283742 chr1 171735348 171735348 TCGA-KK-A7B0 DUP 11 38 FMO1 VAMP4 chr1 171623362 171623362 chr1 172106381 172106381 TCGA-KK-A7B0 DUP 10 24 MYOCOS DNM3 chr1 17495389 17495390 chr1 20306654 20306654 TCGA-KK-A7B0 DUP 31 43 * VWA5B1 chr1 182486872 182486873 chr1 186666117 186666117 TCGA-KK-A7B0 DUP 46 18 RGSL1 * chr1 184896484 184896484 chr1 185706597 185706597 TCGA-KK-A7B0 DUP 46 27 NIBAN1 * chr1 187902305 187902305 chr9 79584634 79584634 TCGA-KK-A7B0 BND 34 48 * TLE4 chr1 190897797 190897797 chr1 193303993 193303994 TCGA-KK-A7B0 DUP 9 34 AL138927.1 LINC01031 chr1 203940985 203940985 chr1 205159354 205159354 TCGA-KK-A7B0 INV 32 18 * DSTYK chr1 216850588 216850588 chr1 220609233 220609233 TCGA-KK-A7B0 DUP 39 35 ESRRG MARK1 chr1 219546134 219546134 chr1 223137989 223137989 TCGA-KK-A7B0 DUP 8 31 * TLR5 chr1 227740934 227740934 chr1 230283934 230283934 TCGA-KK-A7B0 DUP 1 18 SNAP47 * chr1 234784311 234784311 chr1 237916285 237916285 TCGA-KK-A7B0 DUP 45 45 * AL359924.1 chr1 238490056 238490056 chr1 238661503 238661503 TCGA-KK-A7B0 DUP 38 13 KRT18P32 * chr1 238490308 238490308 chr1 238539783 238539783 TCGA-KK-A7B0 INV 7 21 KRT18P32 * chr1 238539547 238539548 chr1 238663139 238663140 TCGA-KK-A7B0 INV 6 33 * * chr1 239167094 239167094 chr1 241373122 241373123 TCGA-KK-A7B0 DUP 46 30 * * chr1 242205634 242205634 chr7 57657083 57657083 TCGA-KK-A7B0 BND 47 20 PLD5 * chr1 28004456 28004456 chr1 28050740 28050740 TCGA-KK-A7B0 INS 20 44 EYA3 EYA3 chr1 31376613 31376613 chr1 31838075 31838076 TCGA-KK-A7B0 DUP 33 12 FABP3 * chr1 33553864 33553864 chr1 33851965 33851965 TCGA-KK-A7B0 DUP 29 38 CSMD2 CSMD2 chr1 44274064 44274065 chr1 45390008 45390026 TCGA-KK-A7B0 DUP 49 20 ERI3 TESK2 chr1 46800398 46800398 chr1 48680572 48680572 TCGA-KK-A7B0 DUP 40 36 CYP4B1 AGBL4 chr1 50227600 50227600 chr1 53157627 53157628 TCGA-KK-A7B0 DUP 28 12 * * chr1 53997002 53997002 chr1 54089871 54089872 TCGA-KK-A7B0 DEL 41 42 * TCEANC2 chr1 58013611 58013611 chr1 60028764 60028765 TCGA-KK-A7B0 DUP 47 38 DAB1 C1orf87 chr1 6189021 6189021 chr21 39549030 39549030 TCGA-KK-A7B0 BND 23 2 RPL22 * chr1 69209607 69209607 chr1 71322212 71322212 TCGA-KK-A7B0 DUP 34 48 * ZRANB2-AS2 chr1 73153293 73153293 chr1 73421279 73421279 TCGA-KK-A7B0 DUP 19 24 * * chr1 85514447 85514447 chr1 145602010 145602010 TCGA-KK-A7B0 DUP 24 27 DDAH1 NBPF25P chr1 8659432 8659432 chr21 37376879 37376879 TCGA-KK-A7B0 BND 35 34 RERE DYRK1A chr1 8794089 8794089 chr1 9132753 9132753 TCGA-KK-A7B0 DUP 48 32 RERE * chr1 97850706 97850706 chr19 52287203 52287203 TCGA-KK-A7B0 BND 31 31 DPYD ZNF766 chr1 97851189 97851189 chr1 98061453 98061453 TCGA-KK-A7B0 DUP 22 43 DPYD * chr1 98062061 98062081 chr19 52171524 52171524 TCGA-KK-A7B0 BND 25 30 * AC011468.2 chr1 98062151 98062151 chr19 52206566 52206569 TCGA-KK-A7B0 BND 32 37 * PPP2R1A chr20 32548485 32548485 chr20 33959435 33959435 TCGA-KK-A7B0 DUP 30 47 NOL4L * chr20 38965120 38965120 chr20 39341193 39341194 TCGA-KK-A7B0 DUP 3 45 DHX35 * chr20 44896671 44896671 chr20 45324171 45324172 TCGA-KK-A7B0 DUP 24 24 YWHAB * chr20 47554574 47554574 chr20 47834167 47834167 TCGA-KK-A7B0 DUP 16 29 NCOA3 * chr20 47899337 47899337 chr20 48188001 48188001 TCGA-KK-A7B0 DUP 26 6 * * chr20 48688147 48688147 chr20 52031219 52031220 TCGA-KK-A7B0 DUP 45 39 PREX1 * chr20 53171397 53171400 chr20 54825014 54825014 TCGA-KK-A7B0 DUP 48 23 TSHZ2 * chr20 59723363 59723363 chr20 63377362 63377362 TCGA-KK-A7B0 DUP 36 2 PHACTR3 CHRNA4 chr21 14640585 14640586 chr21 16511567 16511567 TCGA-KK-A7B0 DUP 18 27 SAMSN1 MIR99AHG chr21 22638901 22638901 chr21 26708560 26708560 TCGA-KK-A7B0 DUP 30 14 * * chr21 27267168 27267168 chr21 27316937 27316937 TCGA-KK-A7B0 DUP 36 40 * * chr21 38494299 38494299 chr21 41502732 41502732 TCGA-KK-A7B0 DEL 18 23 ERG TMPRSS2 chr21 38613190 38613190 chr21 41502798 41502798 TCGA-KK-A7B0 DEL 43 1 ERG TMPRSS2 chr21 43336617 43336617 chr21 46090893 46090901 TCGA-KK-A7B0 INV 49 3 * * chr21 9906266 9906266 chr21 10149151 10149151 TCGA-KK-A7B0 DUP 14 14 * * chr22 32343341 32343341 chr22 32615929 32615930 TCGA-KK-A7B0 DUP 49 47 AL021937.3 SYN3 chr2 101940013 101940013 chr2 102189901 102189901 TCGA-KK-A7B0 DUP 7 30 * IL1RL2 chr2 103106598 103106598 chr2 103336287 103336287 TCGA-KK-A7B0 DUP 29 46 * * chr2 103361884 103361885 chr22 47379123 47379123 TCGA-KK-A7B0 BND 21 11 * * chr2 112304562 112304562 chr2 112921471 112921472 TCGA-KK-A7B0 DUP 35 24 ZC3H6 * chr2 117419945 117419945 chr2 119427969 119427970 TCGA-KK-A7B0 DUP 28 17 * * chr2 121478830 121478830 chr2 234514804 234514804 TCGA-KK-A7B0 INV 47 36 CLASP1 * chr2 123862682 123862682 chr2 124100775 124100775 TCGA-KK-A7B0 DUP 2 39 * CNTNAP5 chr2 125908028 125908028 chr2 126122268 126122268 TCGA-KK-A7B0 DUP 1 37 * * chr2 13224025 13224026 chr2 184398845 184398845 TCGA-KK-A7B0 DUP 7 43 AC093912.1 * chr2 13224025 13224026 chr2 13537820 13537820 TCGA-KK-A7B0 DUP 49 40 AC093912.1 AC073062.1 chr2 132377390 132377390 chr2 138942682 138942682 TCGA-KK-A7B0 DEL 23 24 * * chr2 132991589 132991589 chr2 132998133 132998133 TCGA-KK-A7B0 DEL 6 19 NCKAP5 NCKAP5 chr2 13495736 13495736 chr2 14396675 14396675 TCGA-KK-A7B0 DUP 33 23 * LINC00276 chr2 13538300 13538301 chr2 184397717 184397717 TCGA-KK-A7B0 DEL 44 10 AC073062.1 * chr2 13671368 13671368 chr2 14167817 14167817 TCGA-KK-A7B0 DUP 4 47 * LINC00276 chr2 13741485 13741485 chr2 14544329 14544330 TCGA-KK-A7B0 DUP 13 29 LINC00276 * chr2 137611582 137611582 chr2 145537040 145537040 TCGA-KK-A7B0 INS 47 47 THSD7B * chr2 138339247 138339247 chr2 144150954 144150954 TCGA-KK-A7B0 INS 20 13 * GTDC1 chr2 140296252 140296252 chr2 140515672 140515673 TCGA-KK-A7B0 DUP 48 42 LRP1B LRP1B chr2 151399444 151399444 chr2 152998278 152998278 TCGA-KK-A7B0 DUP 7 43 * * chr2 151731809 151731809 chr2 151736852 151736852 TCGA-KK-A7B0 DEL 26 47 NEB * chr2 152790279 152790279 chr2 152985485 152985485 TCGA-KK-A7B0 DUP 19 24 * * chr2 153279531 153279531 chr2 153608517 153608517 TCGA-KK-A7B0 DUP 14 8 * * chr2 159731003 159731004 chr2 159997881 159997881 TCGA-KK-A7B0 DUP 16 14 MARCHF7 PLA2R1 chr2 16336139 16336139 chr2 72831684 72831685 TCGA-KK-A7B0 DUP 28 1 * * chr2 165723465 165723465 chr2 168567520 168567520 TCGA-KK-A7B0 DUP 6 49 * CERS6 chr2 169503230 169503230 chr2 170915151 170915151 TCGA-KK-A7B0 DUP 19 18 BBS5 * chr2 180654403 180654403 chr2 184262940 184262940 TCGA-KK-A7B0 DUP 2 22 AC009478.1 * chr2 18120517 18120517 chr2 19242619 19242619 TCGA-KK-A7B0 DUP 31 44 KCNS3 LINC01376 chr2 183619713 183619713 chr2 185758681 185758690 TCGA-KK-A7B0 DUP 19 24 * FSIP2 chr2 20846634 20846634 chr2 68552812 68552812 TCGA-KK-A7B0 DEL 20 50 * APLF chr2 211719534 211719534 chr2 212053968 212053968 TCGA-KK-A7B0 DUP 18 20 ERBB4 ERBB4 chr2 216024770 216024770 chr2 221107907 221107907 TCGA-KK-A7B0 DUP 38 47 MREG * chr2 216028664 216028664 chr2 216071552 216071552 TCGA-KK-A7B0 DEL 21 41 MREG PECR chr2 223912966 223912966 chr8 126033329 126033329 TCGA-KK-A7B0 BND 13 10 WDFY1 * chr2 227277335 227277335 chr2 227719225 227719226 TCGA-KK-A7B0 DUP 28 39 COL4A3 SLC19A3 chr2 23629118 23629118 chr2 24872998 24872998 TCGA-KK-A7B0 DUP 9 6 KLHL29 ADCY3 chr2 2695808 2695808 chr2 3049860 3049860 TCGA-KK-A7B0 DUP 48 9 * LINC01250 chr2 30851843 30851843 chr2 31458612 31458612 TCGA-KK-A7B0 DUP 12 42 * * chr2 30993303 30993309 chr8 71934229 71934234 TCGA-KK-A7B0 BND 33 20 GALNT14 MSC-AS1 chr2 34166952 34166952 chr8 71716349 71716349 TCGA-KK-A7B0 BND 49 44 LINC01320 * chr2 40824225 40824225 chr2 40879576 40879576 TCGA-KK-A7B0 DEL 3 36 * * chr2 41021725 41021726 chr6 97178639 97178640 TCGA-KK-A7B0 BND 35 4 * MMS22L chr2 42268745 42268747 chr6 96103070 96103072 TCGA-KK-A7B0 BND 18 24 EML4 FUT9 chr2 43902241 43902244 chr6 81623726 81623729 TCGA-KK-A7B0 BND 49 9 LRPPRC TENT5A chr2 43920553 43920555 chr6 81625701 81625703 TCGA-KK-A7B0 BND 23 23 LRPPRC TENT5A chr2 56199985 56199985 chr2 56422066 56422066 TCGA-KK-A7B0 DUP 29 2 AC007744.1 * chr2 57473742 57473742 chr6 123423462 123423462 TCGA-KK-A7B0 BND 15 7 * TRDN chr2 57546390 57546390 chr6 96656637 96656637 TCGA-KK-A7B0 BND 48 19 * * chr2 62414333 62414333 chr2 62744048 62744049 TCGA-KK-A7B0 DUP 34 38 * EHBP1 chr2 63888423 63888424 chr2 68318161 68318162 TCGA-KK-A7B0 DUP 9 15 UGP2 CNRIP1 chr2 68373664 68373664 chr2 68373779 68373779 TCGA-KK-A7B0 DEL 37 45 PLEK PLEK chr2 70110031 70110032 chr2 70447889 70447889 TCGA-KK-A7B0 DUP 15 34 * TGFA chr2 70316255 70316255 chr2 70316410 70316410 TCGA-KK-A7B0 INV 8 9 * * chr2 72800488 72800488 chr2 74245049 74245049 TCGA-KK-A7B0 DUP 8 48 EXOC6B SLC4A5 chr2 74025307 74025307 chr2 74068712 74068712 TCGA-KK-A7B0 DEL 18 29 TET3 TET3 chr2 75688826 75688826 chr2 75880961 75880962 TCGA-KK-A7B0 DUP 43 40 MRPL19 * chr2 84250449 84250449 chr2 223706507 223706507 TCGA-KK-A7B0 INV 41 46 * * chr2 87305257 87305257 chr2 87587297 87587297 TCGA-KK-A7B0 DUP 20 34 * CYTOR chr2 88560931 88560931 chr8 127912253 127912253 TCGA-KK-A7B0 BND 24 12 EIF2AK3 PVT1 chr2 88561189 88561189 chr8 127912206 127912213 TCGA-KK-A7B0 BND 11 26 EIF2AK3 PVT1 chr2 91422016 91422016 chr2 91756193 91756193 TCGA-KK-A7B0 DUP 26 47 * AC027612.1 chr3 10011197 10011197 chr3 10349869 10349870 TCGA-KK-A7B0 DUP 46 19 EMC3 ATP2B2 chr3 107329367 107329367 chr3 110819393 110819394 TCGA-KK-A7B0 DUP 23 36 CSP2 * chr3 116687594 116687594 chr3 117956497 117956497 TCGA-KK-A7B0 INS 42 24 LSAMP AC092691.1 chr3 121841567 121841567 chr3 123161926 123161941 TCGA-KK-A7B0 DUP 20 1 EAF2 PDIA5 chr3 122504150 122504150 chr3 122833373 122833373 TCGA-KK-A7B0 DUP 29 33 KPNA1 SLC49A4 chr3 137712824 137712824 chr3 138725578 138725579 TCGA-KK-A7B0 DUP 47 26 * PIK3CB chr3 139805353 139805353 chr3 140133937 140133937 TCGA-KK-A7B0 DUP 18 12 * CLSTN2 chr3 149212609 149212609 chr3 149381768 149381769 TCGA-KK-A7B0 DUP 36 3 CP TM4SF1-AS1 chr3 150465789 150465789 chr3 150580664 150580665 TCGA-KK-A7B0 DUP 34 10 TSC22D2 SERP1 chr3 160382585 160382585 chr3 163130550 163130551 TCGA-KK-A7B0 DUP 41 44 IFT80 AC128685.1 chr3 161360658 161360658 chr3 162992370 162992370 TCGA-KK-A7B0 DUP 49 35 SPTSSB * chr3 161768925 161768925 chr3 164861113 164861113 TCGA-KK-A7B0 INS 34 28 * * chr3 165682655 165682655 chr3 165701711 165701711 TCGA-KK-A7B0 DEL 44 33 * * chr3 167716333 167716333 chr3 169580459 169580471 TCGA-KK-A7B0 DUP 24 12 PDCD10 MECOM chr3 167970106 167970106 chr3 168469073 168469073 TCGA-KK-A7B0 DUP 6 24 * EGFEM1P chr3 168950726 168950726 chr3 172207116 172207116 TCGA-KK-A7B0 DUP 39 11 * FNDC3B chr3 172207726 172207726 chr5 12202912 12202912 TCGA-KK-A7B0 BND 41 15 FNDC3B * chr3 180304080 180304080 chr3 182591454 182591454 TCGA-KK-A7B0 DUP 7 28 * * chr3 18451258 18451259 chr3 18696704 18696704 TCGA-KK-A7B0 DUP 50 47 SATB1-AS1 SATB1-AS1 chr3 191115796 191115796 chr3 191542361 191542361 TCGA-KK-A7B0 DUP 7 1 * AC073365.1 chr3 2435840 2435859 chr3 2845998 2845998 TCGA-KK-A7B0 DUP 34 31 CNTN4 CNTN4 chr3 2435928 2435928 chr3 10704575 10704575 TCGA-KK-A7B0 DUP 29 38 CNTN4 ATP2B2 chr3 2844153 2844153 chr3 7875129 7875129 TCGA-KK-A7B0 DEL 19 18 CNTN4 * chr3 2844268 2844268 chr3 10704974 10704974 TCGA-KK-A7B0 DUP 47 5 CNTN4 ATP2B2 chr3 5091999 5091999 chr3 5338299 5338299 TCGA-KK-A7B0 DUP 11 34 * * chr3 7657685 7657685 chr3 8036635 8036635 TCGA-KK-A7B0 DUP 26 3 GRM7 LMCD1-AS1 chr3 77403444 77403444 chr3 77900595 77900596 TCGA-KK-A7B0 DUP 16 45 ROBO2 * chr3 97904153 97904164 chr3 98723098 98723098 TCGA-KK-A7B0 DUP 13 9 CRYBG3 ST3GAL6-AS1 chr4 105193206 105193207 chr4 105573973 105573973 TCGA-KK-A7B0 DUP 5 38 TET2 ARHGEF38 chr4 105193206 105193207 chr4 105549157 105549157 TCGA-KK-A7B0 INV 31 45 TET2 AC004066.1 chr4 115640853 115640853 chr4 137399543 137399543 TCGA-KK-A7B0 DEL 9 4 * * chr4 119466644 119466644 chr4 123780091 123780091 TCGA-KK-A7B0 DUP 27 40 AC093752.1 LINC01091 chr4 120420915 120420915 chr4 120731686 120731686 TCGA-KK-A7B0 DUP 4 10 * PRDM5 chr4 122196938 122196938 chr4 122364741 122364741 TCGA-KK-A7B0 DEL 44 36 KIAA1109 * chr4 126332670 126332670 chr4 129085941 129085941 TCGA-KK-A7B0 DUP 44 18 * SCLT1 chr4 14888495 14888496 chr4 17870446 17870446 TCGA-KK-A7B0 DUP 9 5 LINC00504 LCORL chr4 149270927 149270927 chr4 152439684 152439685 TCGA-KK-A7B0 DUP 31 22 LINC02355 FBXW7 chr4 150281999 150282000 chr4 150475172 150475172 TCGA-KK-A7B0 DUP 5 16 LRBA LRBA chr4 153096503 153096503 chr4 153798536 153798536 TCGA-KK-A7B0 DEL 36 28 * * chr4 155746423 155746423 chr4 164046312 164046312 TCGA-KK-A7B0 DEL 20 27 * MARCHF1 chr4 1590569 1590569 chr4 1990319 1990319 TCGA-KK-A7B0 DUP 11 33 * NELFA chr4 163866467 163866467 chr4 165944385 165944385 TCGA-KK-A7B0 DUP 18 11 MARCHF1 TLL1 chr4 164153790 164153790 chr4 164160035 164160035 TCGA-KK-A7B0 DEL 38 22 MARCHF1 MARCHF1 chr4 164980170 164980170 chr4 166867317 166867317 TCGA-KK-A7B0 INS 28 50 * SPOCK3 chr4 165733807 165733807 chr4 168450266 168450266 TCGA-KK-A7B0 DEL 47 27 LINC01179 DDX60L chr4 170485788 170485788 chr4 170880228 170880228 TCGA-KK-A7B0 DEL 7 43 * * chr4 172639937 172639937 chr4 173416024 173416024 TCGA-KK-A7B0 DUP 6 3 GALNTL6 * chr4 17572723 17572723 chr4 17881112 17881113 TCGA-KK-A7B0 DUP 47 16 * LCORL chr4 180176792 180176800 chr4 180247122 180247122 TCGA-KK-A7B0 DUP 5 6 * * chr4 182829123 182829123 chr4 184855021 184855022 TCGA-KK-A7B0 DUP 50 48 * MIR3945HG chr4 183166636 183166636 chr4 183500291 183500291 TCGA-KK-A7B0 DUP 4 28 WWC2 AC107214.1 chr4 18806936 18806936 chr4 19176023 19176024 TCGA-KK-A7B0 DUP 7 10 * LINC02438 chr4 22412823 22412823 chr4 22710065 22710065 TCGA-KK-A7B0 DUP 15 44 ADGRA3 GBA3 chr4 23896578 23896578 chr4 24703779 24703780 TCGA-KK-A7B0 DUP 24 23 PPARGC1A * chr4 28079865 28079865 chr4 28461965 28461965 TCGA-KK-A7B0 DUP 23 41 * AC097480.1 chr4 28525545 28525545 chr4 28911949 28911949 TCGA-KK-A7B0 DUP 29 29 AC097480.1 * chr4 34536213 34536213 chr4 35203503 35203503 TCGA-KK-A7B0 DUP 31 34 * * chr4 46742582 46742582 chr4 46742852 46742852 TCGA-KK-A7B0 DEL 2 15 COX7B2 COX7B2 chr4 47179934 47179934 chr4 47520374 47520382 TCGA-KK-A7B0 DUP 4 36 GABRB1 ATP10D chr4 47187906 47187906 chr4 47503988 47503988 TCGA-KK-A7B0 DUP 16 4 GABRB1 ATP10D chr4 47814967 47814967 chr4 47816213 47816213 TCGA-KK-A7B0 DEL 31 33 CORIN CORIN chr4 68933320 68933320 chr4 69160583 69160583 TCGA-KK-A7B0 DUP 20 8 UGT2A3 * chr4 70620084 70620084 chr4 72397497 72397497 TCGA-KK-A7B0 DUP 32 12 * ADAMTS3 chr4 71271175 71271175 chr4 76519030 76519032 TCGA-KK-A7B0 DUP 9 12 SLC4A4 SHROOM3 chr4 76519030 76519032 chr9 98087787 98087787 TCGA-KK-A7B0 BND 43 14 SHROOM3 TRIM14 chr4 78206269 78206269 chr4 79123411 79123412 TCGA-KK-A7B0 DUP 23 23 FRAS1 LINC01088 chr4 78499482 78499482 chr4 79000620 79000620 TCGA-KK-A7B0 DUP 38 27 FRAS1 LINC01088 chr4 79949284 79949285 chr4 80144638 80144638 TCGA-KK-A7B0 DUP 15 35 ANTXR2 * chr4 98799856 98799857 chr4 102306764 102306764 TCGA-KK-A7B0 DUP 7 38 * SLC39A8 chr5 103380171 103380171 chr5 103802884 103802884 TCGA-KK-A7B0 DUP 30 22 * * chr5 104245436 104245436 chr5 105320807 105320807 TCGA-KK-A7B0 DUP 23 4 * AC099520.1 chr5 105255584 105255599 chr5 108049957 108049957 TCGA-KK-A7B0 DUP 29 21 AC099520.1 FBXL17 chr5 105466282 105466283 chr5 105654224 105654224 TCGA-KK-A7B0 DUP 39 45 * * chr5 107472988 107472988 chr5 107808833 107808833 TCGA-KK-A7B0 DUP 28 9 EFNA5 * chr5 110908524 110908524 chr5 115065716 115065717 TCGA-KK-A7B0 DUP 32 39 AC008782.1 * chr5 112756205 112756206 chr5 113097969 113097969 TCGA-KK-A7B0 DUP 9 28 APC MCC chr5 114182876 114182876 chr5 114424940 114424941 TCGA-KK-A7B0 DUP 40 22 KCNN2 KCNN2 chr5 11909859 11909859 chr5 12224045 12224045 TCGA-KK-A7B0 DUP 28 41 * * chr5 119794653 119794653 chr5 123373477 123373478 TCGA-KK-A7B0 DUP 37 35 * CEP120 chr5 12029440 12029440 chr5 13437320 13437320 TCGA-KK-A7B0 INV 34 50 * * chr5 145737811 145737811 chr5 151878575 151878575 TCGA-KK-A7B0 DUP 38 24 PRELID2 GLRA1 chr5 152546796 152546796 chr5 152553906 152553906 TCGA-KK-A7B0 DEL 39 28 * * chr5 159765640 159765640 chr5 160548224 160548224 TCGA-KK-A7B0 DUP 44 19 AC008691.1 * chr5 165274711 165274711 chr5 166374477 166374477 TCGA-KK-A7B0 DUP 9 24 * * chr5 167742934 167742936 chr5 173533216 173533216 TCGA-KK-A7B0 DUP 3 36 TENM2 * chr5 176481129 176481129 chr5 178881875 178881875 TCGA-KK-A7B0 DUP 6 24 FAF2 ZNF354B chr5 176505373 176505373 chr5 180360327 180360327 TCGA-KK-A7B0 DUP 22 14 FAF2 * chr5 19771193 19771193 chr5 20109119 20109119 TCGA-KK-A7B0 DEL 18 30 CDH18 CDH18 chr5 28810221 28810221 chr5 28939234 28939234 TCGA-KK-A7B0 DUP 31 22 AC008825.1 * chr5 50192966 50192966 chr5 51473603 51473603 TCGA-KK-A7B0 DUP 2 23 * * chr5 58376854 58376854 chr5 59256360 59256360 TCGA-KK-A7B0 DUP 24 12 * PDE4D chr5 60578276 60578276 chr5 61255460 61255464 TCGA-KK-A7B0 DUP 11 38 * LINC02057 chr5 71242487 71242487 chr5 73250488 73250488 TCGA-KK-A7B0 DUP 11 29 GUSBP17 AC116345.1 chr5 76036321 76036321 chr5 80599704 80599705 TCGA-KK-A7B0 DUP 13 13 * * chr5 76623181 76623181 chr5 77480032 77480032 TCGA-KK-A7B0 DUP 13 32 IQGAP2 WDR41 chr5 80599704 80599705 chr8 78744242 78744242 TCGA-KK-A7B0 BND 15 39 * IL7 chr5 821795 821795 chr5 126662565 126662565 TCGA-KK-A7B0 INV 20 26 ZDHHC11 * chr5 98778161 98778161 chr5 98778161 98778161 TCGA-KK-A7B0 DEL 14 30 RGMB RGMB chr6 102643700 102643701 chr6 102849457 102849457 TCGA-KK-A7B0 DUP 12 9 * * chr6 105893247 105893247 chr6 106705037 106705037 TCGA-KK-A7B0 DUP 42 49 AL591518.1 * chr6 107710291 107710291 chr6 107920495 107920495 TCGA-KK-A7B0 DUP 17 43 SCML4 SEC63 chr6 120331723 120331723 chr6 120456274 120456274 TCGA-KK-A7B0 DUP 18 29 * * chr6 122138796 122138796 chr6 124673920 124673920 TCGA-KK-A7B0 DUP 38 4 * NKAIN2 chr6 123348867 123348867 chr2 42021845 42021845 TCGA-KK-A7B0 BND 29 22 TRDN AC013480.1 chr6 129393265 129393265 chr6 129712462 129712462 TCGA-KK-A7B0 DUP 47 9 LAMA2 * chr6 133874549 133874549 chr6 134042027 134042028 TCGA-KK-A7B0 DUP 6 12 TARID SLC2A12 chr6 134063787 134063787 chr6 134330463 134330463 TCGA-KK-A7B0 DUP 49 5 * * chr6 135199635 135199635 chr6 138287146 138287146 TCGA-KK-A7B0 DUP 38 12 MYB ARFGEF3 chr6 152118506 152118506 chr6 152533602 152533602 TCGA-KK-A7B0 DUP 15 10 ESR1 SYNE1 chr6 156330451 156330451 chr6 158870911 158870911 TCGA-KK-A7B0 DUP 21 37 * C6orf99 chr6 156612827 156612827 chr6 159239349 159239349 TCGA-KK-A7B0 DUP 21 11 * FNDC1 chr6 160373172 160373172 chr6 160535515 160535515 TCGA-KK-A7B0 DUP 18 35 SLC22A3 LPA chr6 167323563 167323563 chr6 167324547 167324547 TCGA-KK-A7B0 DEL 9 16 * TTLL2 chr6 17256878 17256878 chr6 20336816 20336833 TCGA-KK-A7B0 DUP 23 43 * * chr6 23441946 23441946 chr6 23946558 23946559 TCGA-KK-A7B0 DUP 3 45 * * chr6 24156459 24156459 chr6 25509144 25509144 TCGA-KK-A7B0 DUP 24 26 * CARMIL1 chr6 28803887 28803887 chr6 29043048 29043048 TCGA-KK-A7B0 DUP 36 27 * AL662791.2 chr6 32476553 32476553 chr6 32564579 32564579 TCGA-KK-A7B0 DEL 43 44 * * chr6 37725468 37725468 chr6 39638335 39638335 TCGA-KK-A7B0 DUP 6 50 * KIF6 chr6 55333519 55333519 chr6 55601375 55601375 TCGA-KK-A7B0 DUP 16 50 GFRAL * chr6 63164848 63164848 chr6 64645412 64645412 TCGA-KK-A7B0 DUP 38 17 * EYS chr6 65013208 65013208 chr6 65247962 65247962 TCGA-KK-A7B0 DEL 40 25 EYS EYS chr6 69340297 69340298 chr6 71736280 71736280 TCGA-KK-A7B0 DUP 4 50 ADGRB3 * chr6 77707911 77707911 chr6 104191929 104191929 TCGA-KK-A7B0 INV 22 30 MEI4 * chr6 80266339 80266340 chr6 104647857 104647858 TCGA-KK-A7B0 INV 21 9 BCKDHB * chr6 81459213 81459213 chr2 43904544 43904544 TCGA-KK-A7B0 BND 7 31 * LRPPRC chr6 81623726 81623729 chr2 43902241 43902244 TCGA-KK-A7B0 BND 29 5 TENT5A LRPPRC chr6 82088038 82088038 chr6 95572290 95572290 TCGA-KK-A7B0 DEL 30 35 * * chr6 83196042 83196042 chr7 146447551 146447551 TCGA-KK-A7B0 BND 4 15 RWDD2A CNTNAP2 chr6 83542096 83542096 chr7 146445656 146445656 TCGA-KK-A7B0 BND 31 23 * CNTNAP2 chr6 83614688 83614688 chr2 44826390 44826390 TCGA-KK-A7B0 BND 27 12 SNAP91 * chr6 88480316 88480316 chr6 92862261 92862261 TCGA-KK-A7B0 INS 43 32 * * chr6 88874500 88874500 chr6 89196947 89196947 TCGA-KK-A7B0 DUP 15 11 RNGTT GABRR1 chr6 96330169 96330169 chr2 43234333 43234333 TCGA-KK-A7B0 BND 3 44 * THADA chr6 96592079 96592079 chr6 122999861 122999861 TCGA-KK-A7B0 DEL 9 24 FHL5 CLVS2 chr6 97178639 97178640 chr2 41021725 41021726 TCGA-KK-A7B0 BND 7 50 MMS22L * chr7 101985181 101985181 chr11 45395830 45395831 TCGA-KK-A7B0 BND 8 30 CUX1 AC103855.3 chr7 101986066 101986066 chr11 45168117 45168117 TCGA-KK-A7B0 BND 35 29 CUX1 PRDM11 chr7 102930781 102930781 chr7 106105395 106105396 TCGA-KK-A7B0 DUP 35 31 FBXL13 SYPL1 chr7 103897549 103897549 chr11 45395830 45395831 TCGA-KK-A7B0 BND 20 19 RELN AC103855.3 chr7 105885641 105885642 chr7 118590978 118590978 TCGA-KK-A7B0 DEL 6 42 CDHR3 * chr7 114279045 114279045 chr7 114622009 114622009 TCGA-KK-A7B0 DUP 35 38 FOXP2 FOXP2 chr7 140962170 140962170 chr7 141084692 141084692 TCGA-KK-A7B0 DUP 1 50 * TMEM178B chr7 146451482 146451482 chr7 149523310 149523311 TCGA-KK-A7B0 DUP 50 28 CNTNAP2 * chr7 151937008 151937008 chr7 153964027 153964027 TCGA-KK-A7B0 DUP 49 12 * DPP6 chr7 25946310 25946311 chr7 30002962 30002962 TCGA-KK-A7B0 DUP 32 24 * FKBP14-AS1 chr7 41673226 41673227 chr7 44870076 44870076 TCGA-KK-A7B0 DUP 45 21 INHBA * chr7 6060095 6060095 chr7 6603806 6603806 TCGA-KK-A7B0 DUP 45 33 EIF2AK1 C7orf26 chr7 66205255 66205255 chr7 66481229 66481229 TCGA-KK-A7B0 INV 44 5 TPST1 LINC00174 chr7 68528747 68528747 chr7 68849446 68849446 TCGA-KK-A7B0 DUP 18 8 * * chr7 77397065 77397065 chr7 77614510 77614511 TCGA-KK-A7B0 DUP 2 3 GSAP PTPN12 chr7 84584301 84584301 chr13 67722618 67722618 TCGA-KK-A7B0 BND 50 11 AC003984.1 * chr7 87458551 87458551 chr7 87753595 87753595 TCGA-KK-A7B0 DUP 44 49 ABCB4 RUNDC3B chr7 91089608 91089608 chr7 92171187 92171187 TCGA-KK-A7B0 DUP 37 6 CDK14 LRRD1 chr7 92819141 92819141 chr7 93381916 93381917 TCGA-KK-A7B0 DUP 5 11 CDK6 * chr7 97755009 97755010 chr7 97855218 97855218 TCGA-KK-A7B0 DUP 4 26 * ASNS chr7 97755009 97755010 chr14 44171240 44171240 TCGA-KK-A7B0 BND 48 34 * LINC02307 chr7 97756823 97756824 chr14 44172033 44172034 TCGA-KK-A7B0 BND 28 33 * LINC02307 chr7 97756823 97756824 chr7 97853325 97853326 TCGA-KK-A7B0 DEL 45 44 * ASNS chr7 97853325 97853326 chr14 44172033 44172034 TCGA-KK-A7B0 BND 28 44 ASNS LINC02307 chr8 107735527 107735527 chr8 109896515 109896515 TCGA-KK-A7B0 DUP 19 21 * * chr8 109822698 109822698 chr8 110459575 110459576 TCGA-KK-A7B0 DUP 4 47 * * chr8 124351705 124351705 chr8 128137962 128137962 TCGA-KK-A7B0 DUP 23 50 TMEM65 * chr8 125001203 125001203 chr8 126008850 126008851 TCGA-KK-A7B0 DUP 4 13 SQLE * chr8 135202509 135202509 chr8 135467970 135467971 TCGA-KK-A7B0 DUP 42 10 * KHDRBS3 chr8 137591003 137591003 chrX 66541751 66541751 TCGA-KK-A7B0 BND 27 47 AC105213.1 * chr8 138202031 138202031 chrX 66762433 66762433 TCGA-KK-A7B0 BND 21 36 FAM135B * chr8 139146605 139146605 chr8 140312902 140312903 TCGA-KK-A7B0 DUP 37 3 * TRAPPC9 chr8 143596853 143596853 chr8 144233735 144233735 TCGA-KK-A7B0 DUP 27 17 EEF1D MROH1 chr8 22908506 22908506 chr8 25209095 25209096 TCGA-KK-A7B0 DUP 22 9 PEBP4 DOCK5 chr8 37613330 37613330 chr8 48212562 48212562 TCGA-KK-A7B0 INV 13 28 AC137579.2 * chr8 39539188 39539188 chr8 39789326 39789326 TCGA-KK-A7B0 DEL 43 4 AC123767.1 ADAM2 chr8 46104516 46104516 chr8 47784803 47784803 TCGA-KK-A7B0 DUP 17 39 * PRKDC chr8 50857755 50857756 chr8 53487758 53487772 TCGA-KK-A7B0 DUP 26 33 * * chr8 6131457 6131457 chr8 43515750 43515750 TCGA-KK-A7B0 DEL 12 16 AC009435.1 * chr8 62749717 62749717 chr8 63317488 63317489 TCGA-KK-A7B0 DUP 43 9 NKAIN3 * chr8 64265878 64265878 chr8 64391720 64391720 TCGA-KK-A7B0 DUP 29 22 LINC01414 * chr8 71004768 71004768 chr8 71200206 71200206 TCGA-KK-A7B0 DEL 17 7 AC015687.1 AC015687.1 chr8 75142732 75142732 chr8 76098319 76098320 TCGA-KK-A7B0 DUP 8 35 * * chr8 78323879 78323879 chr8 80834348 80834348 TCGA-KK-A7B0 DUP 9 17 * ZNF704 chr8 85965296 85965296 chr8 87424577 87424577 TCGA-KK-A7B0 DUP 28 4 * CNBD1 chr8 9011350 9011350 chr8 12178524 12178524 TCGA-KK-A7B0 INV 27 14 ERI1 ALG1L11P chr8 98287229 98287229 chr8 98989989 98989989 TCGA-KK-A7B0 DUP 46 14 NIPAL2 * chr9 103921088 103921088 chr9 104281459 104281459 TCGA-KK-A7B0 DUP 12 15 * TOPORSLP chr9 106264606 106264606 chr9 106440142 106440142 TCGA-KK-A7B0 DUP 28 30 LINC01505 LINC01505 chr9 106534532 106534533 chr9 108478513 108478513 TCGA-KK-A7B0 DUP 23 41 LINC01505 * chr9 108028650 108028650 chr9 111994620 111994620 TCGA-KK-A7B0 DUP 6 49 * * chr9 12505882 12505882 chr9 12846751 12846751 TCGA-KK-A7B0 DUP 20 22 * * chr9 130082409 130082409 chr20 33630817 33630817 TCGA-KK-A7B0 BND 50 3 GPR107 CBFA2T2 chr9 130082975 130082978 chr20 33631362 33631362 TCGA-KK-A7B0 BND 45 50 GPR107 CBFA2T2 chr9 130083028 130083028 chr9 130512345 130512345 TCGA-KK-A7B0 INV 12 12 GPR107 * chr9 13479858 13479858 chr9 13616501 13616502 TCGA-KK-A7B0 DUP 34 38 AL583785.1 * chr9 35072041 35072041 chr9 37718512 37718512 TCGA-KK-A7B0 DUP 6 5 VCP AL138752.2 chr9 4259650 4259650 chr9 5243301 5243302 TCGA-KK-A7B0 DUP 7 35 GLIS3 * chr9 61534621 61534621 chr9 61992537 61992537 TCGA-KK-A7B0 DEL 1 50 * * chr9 74117563 74117563 chr9 74498590 74498590 TCGA-KK-A7B0 DUP 33 41 * RORB chr9 84763438 84763439 chr9 87951190 87951190 TCGA-KK-A7B0 DUP 27 44 NTRK2 * chr9 86854382 86854382 chr9 90705849 90705858 TCGA-KK-A7B0 DUP 19 49 * * chr9 87292362 87292363 chr18 28407299 28407300 TCGA-KK-A7B0 BND 1 42 * * chr9 87675238 87675238 chr9 88070842 88070842 TCGA-KK-A7B0 DUP 6 11 DAPK1 * chr9 87809577 87809577 chr9 88069527 88069527 TCGA-KK-A7B0 DEL 36 22 AL772337.4 * chr9 87809599 87809599 chr9 88068511 88068519 TCGA-KK-A7B0 INV 38 44 AL772337.4 * chr9 87810171 87810171 chr9 88068511 88068519 TCGA-KK-A7B0 INV 1 27 AL772337.4 * chr9 88390679 88390679 chr18 25311043 25311043 TCGA-KK-A7B0 BND 42 38 SPIN1 ZNF521 chr9 97770973 97770973 chr9 98087759 98087759 TCGA-KK-A7B0 DUP 18 10 PTCSC2 TRIM14 chr9 99894176 99894176 chr9 101928667 101928667 TCGA-KK-A7B0 DUP 43 49 STX17-AS1 * chrX 101187869 101187870 chrX 101604005 101604005 TCGA-KK-A7B0 DUP 17 4 * * chrX 1074738 1074738 chrX 1085217 1085217 TCGA-KK-A7B0 DEL 15 44 * * chrX 111294719 111294719 chrX 114036555 114036555 TCGA-KK-A7B0 DUP 48 48 DCX XACT chrX 114777829 114777829 chrX 117219315 117219315 TCGA-KK-A7B0 DUP 4 50 HTR2C * chrX 119050263 119050263 chrX 121070638 121070638 TCGA-KK-A7B0 DUP 10 50 * * chrX 136235616 136235617 chrX 136778627 136778627 TCGA-KK-A7B0 DUP 24 40 MAP7D3 ARHGEF6 chrX 136571793 136571793 chrX 136746813 136746813 TCGA-KK-A7B0 INV 39 10 Y_RNA ARHGEF6 chrX 136613842 136613842 chrX 136903152 136903152 TCGA-KK-A7B0 INV 39 4 * * chrX 153061762 153061762 chrX 153083526 153083526 TCGA-KK-A7B0 DEL 1 25 * * chrX 16086853 16086853 chrX 19271070 19271071 TCGA-KK-A7B0 DUP 17 48 * * chrX 25132161 25132161 chrX 25581070 25581070 TCGA-KK-A7B0 DUP 30 47 * * chrX 30904806 30904809 chrX 33487367 33487370 TCGA-KK-A7B0 DUP 5 11 TAB3 * chrX 32518976 32518977 chrX 34941454 34941457 TCGA-KK-A7B0 DUP 46 39 DMD FAM47B chrX 39678799 39678799 chrX 43193787 43193787 TCGA-KK-A7B0 DUP 33 50 * PINCR chrX 46636905 46636905 chrX 46878935 46878935 TCGA-KK-A7B0 DUP 34 29 SLC9A7 RP2 chrX 47564881 47564881 chrX 47900981 47900981 TCGA-KK-A7B0 DUP 40 41 ARAF ZNF81 chrX 66545533 66545533 chrX 70400099 70400099 TCGA-KK-A7B0 DUP 41 11 * KIF4A chrX 66895147 66895147 chrX 67344558 67344558 TCGA-KK-A7B0 DUP 46 32 * * chrX 67256417 67256417 chrX 70438304 70438304 TCGA-KK-A7B0 DUP 37 11 * * chrX 7451870 7451870 chrX 30130783 30130783 TCGA-KK-A7B0 DUP 33 25 * * chrX 7574003 7574003 chrX 7730539 7730539 TCGA-KK-A7B0 DUP 50 49 * * chrX 7659236 7659236 chrX 7795795 7795795 TCGA-KK-A7B0 DUP 22 28 * * chr10 105157800 105157805 chr2 49050050 49050055 TCGA-J4-A83J BND 5 8 SORCS3 AC009975.1 chr10 108027572 108027572 chr10 108295892 108295892 TCGA-J4-A83J DEL 35 43 LINC01435 PTGES3P5 chr10 108030912 108030912 chr10 110115140 110115157 TCGA-J4-A83J INS 3 1 LINC01435 ADD3 chr10 108263987 108263987 chr10 109121910 109121910 TCGA-J4-A83J DEL 11 28 * * chr10 112034668 112034668 chr10 125121096 125121096 TCGA-J4-A83J DEL 9 1 * CTBP2 chr10 125283257 125283264 chr4 171234067 171234074 TCGA-J4-A83J BND 39 9 * * chr10 132328505 132328505 chr3 149892347 149892347 TCGA-J4-A83J BND 1 35 STK32C ANKUB1 chr10 20539450 20539450 chr10 20572515 20572515 TCGA-J4-A83J INV 40 34 * * chr10 65532966 65532966 chr14 85512483 85512483 TCGA-J4-A83J BND 5 37 * AL049775.2 chr10 66093358 66093359 chr14 84912517 84912518 TCGA-J4-A83J BND 41 4 CTNNA3 * chr10 80489163 80489163 chr4 154808371 154808371 TCGA-J4-A83J BND 39 1 TSPAN14 RBM46 chr10 87868213 87868213 chr10 96396049 96396049 TCGA-J4-A83J DEL 7 9 PTEN TLL2 chr10 87897953 87897953 chr10 91245977 91245977 TCGA-J4-A83J INV 17 10 PTEN PCGF5 chr10 90152006 90152006 chr7 22806003 22806003 TCGA-J4-A83J BND 6 50 * * chr10 90395745 90395745 chr10 91308901 91308901 TCGA-J4-A83J DEL 28 18 * * chr10 96125702 96125702 chr10 125299052 125299052 TCGA-J4-A83J DEL 21 37 * * chr11 105541685 105541685 chr11 105584918 105584918 TCGA-J4-A83J DEL 2 2 * * chr11 17081939 17081939 chr18 33828547 33828547 TCGA-J4-A83J BND 28 11 PIK3C2A * chr11 42633027 42633027 chr18 74562063 74562063 TCGA-J4-A83J BND 50 8 * CNDP1 chr11 44019012 44019012 chr18 74562096 74562096 TCGA-J4-A83J BND 49 37 * CNDP1 chr11 46183798 46183798 chr18 72761226 72761226 TCGA-J4-A83J BND 38 17 * NETO1 chr11 50116350 50116350 chr11 50343829 50343829 TCGA-J4-A83J INV 5 32 * AC024405.2 chr11 57323745 57323745 chr9 104777228 104777228 TCGA-J4-A83J BND 46 33 TNKS1BP1 NIPSNAP3B chr11 57323908 57323908 chr18 48472044 48472044 TCGA-J4-A83J BND 5 25 TNKS1BP1 * chr11 58907422 58907428 chr3 180279519 180279520 TCGA-J4-A83J BND 27 35 GLYATL1 * chr11 5936945 5936945 chr9 124949565 124949565 TCGA-J4-A83J BND 6 2 TRIM5 GOLGA1 chr11 5948442 5948442 chr11 42651687 42651687 TCGA-J4-A83J DEL 47 50 OR56A3 * chr11 6958069 6958069 chr18 33846396 33846396 TCGA-J4-A83J BND 7 17 ZNF215 * chr11 7511405 7511407 chr18 45637689 45637691 TCGA-J4-A83J BND 12 47 AC107884.1 SLC14A2 chr11 7524990 7524990 chr18 33264595 33264595 TCGA-J4-A83J BND 45 2 PPFIBP2 CCDC178 chr11 8613771 8613773 chr18 45637778 45637780 TCGA-J4-A83J BND 5 44 TRIM66 SLC14A2 chr12 122036164 122036164 chr12 122107335 122107335 TCGA-J4-A83J DUP 20 31 BCL7A MLXIP chr12 123210192 123210192 chr12 123566534 123566534 TCGA-J4-A83J DUP 39 10 MPHOSPH9 * chr12 38130088 38130088 chr12 38156841 38156841 TCGA-J4-A83J DEL 37 2 * * chr12 38508084 38508084 chrY 21289805 21289805 TCGA-J4-A83J BND 29 50 * * chr12 40652614 40652614 chr12 40715904 40715904 TCGA-J4-A83J DEL 30 50 * CNTN1 chr12 61975012 61975012 chr12 61976446 61976446 TCGA-J4-A83J DEL 50 12 TAFA2 TAFA2 chr12 8998781 8998781 chr12 18057754 18057754 TCGA-J4-A83J DEL 42 40 KLRG1 * chr13 82180696 82180696 chr13 84731572 84731572 TCGA-J4-A83J DEL 1 24 * * chr14 81113263 81113264 chr14 81929288 81929288 TCGA-J4-A83J INS 23 48 TSHR AL355838.1 chr14 83073688 83073688 chr14 85061482 85061482 TCGA-J4-A83J INS 3 26 * * chr14 83089589 83089589 chr14 83978218 83978218 TCGA-J4-A83J DEL 23 15 * * chr14 84912517 84912518 chr10 66093358 66093359 TCGA-J4-A83J BND 29 39 * CTNNA3 chr14 85647888 85647888 chr14 85946214 85946214 TCGA-J4-A83J INS 4 5 FLRT2 LINC02328 chr14 85656312 85656312 chr14 87591426 87591426 TCGA-J4-A83J DEL 18 32 * * chr16 32317727 32317739 chr20 53866928 53866928 TCGA-J4-A83J BND 4 25 * * chr17 42431137 42431137 chr11 1445944 1445944 TCGA-J4-A83J BND 32 2 * BRSK2 chr17 67152847 67152847 chr17 67243631 67243631 TCGA-J4-A83J DUP 50 6 HELZ HELZ chr17 7682581 7682581 chr12 55724819 55724819 TCGA-J4-A83J BND 19 19 TP53 * chr18 33282234 33282234 chr9 122015612 122015612 TCGA-J4-A83J BND 36 27 CCDC178 TTLL11 chr18 33725015 33725015 chr18 36491875 36491875 TCGA-J4-A83J DEL 19 36 ASXL3 FHOD3 chr18 33870218 33870218 chr9 110140550 110140550 TCGA-J4-A83J BND 14 42 NOL4 PALM2AKAP2 chr18 36499194 36499194 chr11 46190529 46190529 TCGA-J4-A83J BND 34 24 FHOD3 * chr18 45637689 45637691 chr11 7511405 7511407 TCGA-J4-A83J BND 44 38 SLC14A2 AC107884.1 chr18 48466014 48466014 chr11 8613854 8613854 TCGA-J4-A83J BND 29 16 * TRIM66 chr18 72765047 72765047 chr11 5942954 5942954 TCGA-J4-A83J BND 18 45 NETO1 OR56A3 chr18 79307889 79307893 chr9 122011663 122011667 TCGA-J4-A83J BND 39 27 ATP9B TTLL11 chr19 20556215 20556215 chr19 20700849 20700849 TCGA-J4-A83J DUP 12 30 ZNF737 * chr1 166667752 166667752 chr1 166685790 166685790 TCGA-J4-A83J DEL 23 3 FMO10P * chr1 241734360 241734360 chr1 241765119 241765119 TCGA-J4-A83J DEL 39 16 WDR64 WDR64 chr1 246822289 246822289 chr14 50360721 50360721 TCGA-J4-A83J BND 16 28 KIF28P CDKL1 chr21 38496730 38496730 chr21 41506126 41506126 TCGA-J4-A83J DEL 8 20 ERG TMPRSS2 chr21 38505818 38505818 chr21 41506230 41506230 TCGA-J4-A83J DEL 16 25 ERG TMPRSS2 chr21 41506630 41506630 chr17 43548058 43548058 TCGA-J4-A83J BND 8 47 TMPRSS2 DHX8 chr2 103986500 103986500 chr2 104115836 104115836 TCGA-J4-A83J DEL 17 28 LINC01965 * chr2 117856589 117856589 chr2 117867413 117867413 TCGA-J4-A83J DEL 38 28 * HTR5BP chr2 124687897 124687897 chr2 127572689 127572689 TCGA-J4-A83J DEL 24 11 CNTNAP5 MYO7B chr2 136486141 136486141 chr2 143553306 143553306 TCGA-J4-A83J DEL 19 12 * ARHGAP15 chr2 136492007 136492007 chr2 142065266 142065266 TCGA-J4-A83J INS 30 25 * LRP1B chr2 137135996 137135996 chr2 137845322 137845322 TCGA-J4-A83J DEL 39 29 THSD7B * chr2 138466134 138466134 chr2 143533386 143533386 TCGA-J4-A83J INS 19 15 AC114763.1 ARHGAP15 chr2 144030819 144030819 chr2 144056135 144056135 TCGA-J4-A83J DEL 13 14 GTDC1 GTDC1 chr2 185707453 185707453 chr2 198108811 198108811 TCGA-J4-A83J DEL 26 35 * PLCL1 chr2 189680480 189680480 chr2 189680945 189680945 TCGA-J4-A83J DEL 44 6 ANKAR ANKAR chr2 198088388 198088388 chr2 198276777 198276777 TCGA-J4-A83J DEL 34 18 PLCL1 PLCL1 chr2 231005555 231005555 chr12 109634875 109634875 TCGA-J4-A83J BND 5 20 SPATA3 * chr2 25757466 25757466 chr2 25808375 25808375 TCGA-J4-A83J DEL 6 24 ASXL2 ASXL2 chr2 55959791 55959791 chr2 102732012 102732012 TCGA-J4-A83J DEL 46 32 AC011306.1 MFSD9 chr2 71204073 71204073 chr10 112182548 112182548 TCGA-J4-A83J BND 42 12 PAIP2B GPAM chr2 79570201 79570201 chr2 143270111 143270111 TCGA-J4-A83J DEL 19 43 CTNNA2 ARHGAP15 chr2 79570338 79570338 chr2 140109028 140109028 TCGA-J4-A83J INS 39 44 CTNNA2 LINC01853 chr2 81512712 81512712 chr10 89223587 89223587 TCGA-J4-A83J BND 24 38 * LIPA chr2 81626994 81626994 chr3 164129084 164129084 TCGA-J4-A83J BND 48 7 * * chr2 82194652 82194656 chr4 172617909 172617933 TCGA-J4-A83J BND 18 3 * GALNTL6 chr2 84421940 84421940 chr3 100937854 100937854 TCGA-J4-A83J BND 45 3 * ABI3BP chr2 84460290 84460290 chr3 164668531 164668531 TCGA-J4-A83J BND 50 50 SUCLG1 * chr3 100921138 100921138 chr2 144748404 144748404 TCGA-J4-A83J BND 50 14 ABI3BP TEX41 chr3 145197775 145197775 chr3 145198080 145198080 TCGA-J4-A83J DEL 49 19 * * chr3 146113015 146113015 chr3 146138282 146138282 TCGA-J4-A83J DEL 32 19 PLOD2 PLOD2 chr3 149374375 149374375 chr10 86903362 86903362 TCGA-J4-A83J BND 1 8 TM4SF1 BMPR1A chr3 164095479 164095479 chr2 82267800 82267800 TCGA-J4-A83J BND 7 17 * * chr3 164629227 164629228 chr2 84479459 84479460 TCGA-J4-A83J BND 25 50 * * chr3 164785339 164785339 chr2 81630358 81630358 TCGA-J4-A83J BND 44 32 LINC01324 * chr3 180279575 180279575 chr3 180332540 180332540 TCGA-J4-A83J DEL 6 11 * * chr3 180332447 180332447 chr11 58907422 58907428 TCGA-J4-A83J BND 26 25 * GLYATL1 chr3 191399715 191399715 chr3 191400981 191400981 TCGA-J4-A83J DEL 13 45 * * chr3 2723328 2723328 chr3 79833878 79833878 TCGA-J4-A83J DEL 12 37 CNTN4 * chr3 2957400 2957400 chr3 2975233 2975233 TCGA-J4-A83J DEL 30 3 CNTN4 CNTN4 chr3 79398430 79398430 chr3 82724216 82724216 TCGA-J4-A83J INS 33 15 ROBO1 * chr3 84471249 84471249 chr3 164352375 164352375 TCGA-J4-A83J INS 48 7 * * chr3 98849217 98849217 chr3 98853443 98853443 TCGA-J4-A83J DEL 34 34 DCBLD2 DCBLD2 chr3 99313217 99313217 chr3 99314236 99314236 TCGA-J4-A83J DEL 6 29 * * chr4 127700179 127700179 chr4 134498993 134498993 TCGA-J4-A83J INS 18 22 INTU * chr4 163293017 163293017 chr4 172918551 172918551 TCGA-J4-A83J DEL 25 12 * GALNTL6 chr4 170085664 170085682 chr2 82192593 82192610 TCGA-J4-A83J BND 10 47 AADAT * chr4 172617909 172617933 chr2 81595753 81595753 TCGA-J4-A83J BND 49 27 GALNTL6 * chr4 172621265 172621265 chr2 71192023 71192023 TCGA-J4-A83J BND 27 35 GALNTL6 PAIP2B chr4 173191036 173191036 chr4 175357521 175357521 TCGA-J4-A83J DEL 49 39 GALNT7 AC095050.1 chr4 174291169 174291169 chr4 180455403 180455403 TCGA-J4-A83J INS 6 20 CEP44 * chr4 182819600 182819600 chr4 182821972 182821972 TCGA-J4-A83J DEL 4 3 * * chr4 21405012 21405012 chr4 21568158 21568158 TCGA-J4-A83J DEL 6 15 KCNIP4 KCNIP4 chr4 21456934 21456934 chr4 33292428 33292428 TCGA-J4-A83J INS 6 49 KCNIP4 * chr4 21572689 21572689 chr4 33296671 33296671 TCGA-J4-A83J DEL 12 11 KCNIP4 * chr4 63517578 63517578 chr4 63520421 63520421 TCGA-J4-A83J DEL 34 34 * * chr4 83912562 83912562 chr4 83912668 83912668 TCGA-J4-A83J DEL 34 44 AC079160.1 AC079160.1 chr4 89934117 89934117 chr4 90102348 90102348 TCGA-J4-A83J INS 13 37 MMRN1 * chr4 95300848 95300848 chr4 98506741 98506741 TCGA-J4-A83J DEL 22 10 UNC5C TSPAN5 chr4 96150326 96150326 chr4 96847144 96847144 TCGA-J4-A83J DEL 48 6 * * chr4 98586651 98586651 chr4 178733719 178733719 TCGA-J4-A83J DEL 4 14 TSPAN5 * chr5 104321537 104321537 chr5 105233508 105233508 TCGA-J4-A83J INS 23 18 * AC099520.1 chr5 104851125 104851125 chr6 122763928 122763928 TCGA-J4-A83J BND 15 8 AC099520.1 * chr5 109778964 109778964 chr5 112115747 112115747 TCGA-J4-A83J DEL 6 11 MAN2A1 * chr5 13202380 13202380 chr5 13207384 13207384 TCGA-J4-A83J DEL 29 15 * * chr5 2442133 2442133 chr5 2497698 2497698 TCGA-J4-A83J DEL 39 43 * * chr5 24679668 24679668 chr5 24685685 24685685 TCGA-J4-A83J DEL 30 6 * * chr5 51138743 51138743 chr5 110381975 110381975 TCGA-J4-A83J DEL 24 33 * TMEM232 chr5 85247961 85247961 chr5 85249037 85249037 TCGA-J4-A83J DEL 6 7 * * chr5 96942334 96942334 chr5 98387075 98387075 TCGA-J4-A83J INS 33 36 LNPEP * chr6 121628082 121628084 chr5 104887810 104887812 TCGA-J4-A83J BND 29 30 * AC099520.1 chr6 122862234 122862234 chr6 125445684 125445684 TCGA-J4-A83J DEL 50 50 * AL450332.1 chr6 32442310 32442310 chr6 32577647 32577647 TCGA-J4-A83J DUP 24 43 HLA-DRA * chr6 65687552 65687552 chr6 65691930 65691930 TCGA-J4-A83J DEL 31 12 EYS EYS chr6 66266365 66266365 chr6 66291728 66291728 TCGA-J4-A83J DEL 40 5 * * chr6 69636276 69636276 chr6 69636963 69636963 TCGA-J4-A83J DEL 5 11 * * chr6 94860148 94860148 chr6 98465095 98465095 TCGA-J4-A83J INS 26 33 * * chr6 96402507 96402507 chr6 119414731 119414731 TCGA-J4-A83J DEL 21 20 UFL1-AS1 * chr6 98521364 98521364 chr6 119416724 119416724 TCGA-J4-A83J INS 20 13 * * chr6 98595996 98595996 chr6 98610385 98610385 TCGA-J4-A83J DEL 45 43 * * chr7 115024238 115024238 chr7 115689568 115689568 TCGA-J4-A83J INS 45 10 * * chr7 18177360 18177360 chr7 18180186 18180186 TCGA-J4-A83J DEL 15 34 HDAC9 HDAC9 chr7 53587154 53587154 chr7 54832349 54832349 TCGA-J4-A83J DEL 13 17 * * chr7 54220299 54220299 chr7 54308287 54308306 TCGA-J4-A83J INV 19 16 * * chr7 57692600 57692600 chr12 37463004 37463004 TCGA-J4-A83J BND 41 26 * * chr7 79765224 79765224 chr7 82325950 82325950 TCGA-J4-A83J INS 12 48 * CACNA2D1 chr7 81280729 81280729 chr7 82442252 82442252 TCGA-J4-A83J DEL 6 32 * CACNA2D1 chr7 82326129 82326129 chr7 88112026 88112026 TCGA-J4-A83J INS 40 46 CACNA2D1 ADAM22 chr7 83039290 83039290 chr7 88560950 88560950 TCGA-J4-A83J INS 20 50 PCLO * chr7 88125754 88125754 chr7 88656332 88656332 TCGA-J4-A83J INS 28 35 ADAM22 * chr8 104642215 104642215 chrX 1514607 1514607 TCGA-J4-A83J BND 34 17 ZFPM2 P2RY8 chr8 109515651 109515651 chr8 110635528 110635528 TCGA-J4-A83J DEL 30 19 PKHD1L1 * chr8 113107143 113107143 chr8 113107499 113107499 TCGA-J4-A83J INV 13 44 CSMD3 CSMD3 chr8 113713191 113713191 chr8 116588177 116588177 TCGA-J4-A83J INS 47 43 * * chr8 113750869 113750869 chr8 113754438 113754438 TCGA-J4-A83J DEL 5 16 * * chr8 5416809 5416809 chr8 5417085 5417085 TCGA-J4-A83J DEL 7 35 * * chr8 72917070 72917070 chr8 72919855 72919855 TCGA-J4-A83J DEL 21 16 KCNB2 KCNB2 chr8 82598659 82598659 chr8 82652018 82652018 TCGA-J4-A83J DEL 11 27 AC060765.1 AC060765.1 chr8 83151970 83151970 chr8 83536583 83536583 TCGA-J4-A83J DEL 11 21 * * chr8 83460802 83460802 chr18 72764461 72764461 TCGA-J4-A83J BND 19 17 * NETO1 chr8 83817851 83817851 chr8 86746201 86746201 TCGA-J4-A83J DEL 39 33 * AC090572.3 chr8 83827836 83827836 chr8 116973283 116973283 TCGA-J4-A83J INS 3 11 * SLC30A8 chr8 84254707 84254707 chr8 116686155 116686155 TCGA-J4-A83J INS 49 23 RALYL EIF3H chr8 84662057 84662057 chr8 113709806 113709806 TCGA-J4-A83J INS 19 44 RALYL * chr8 84742610 84742610 chr8 84775544 84775544 TCGA-J4-A83J DEL 16 24 RALYL RALYL chr8 87592345 87592345 chr8 114899919 114899919 TCGA-J4-A83J INS 38 49 CNBD1 * chr9 122011663 122011667 chr18 79307889 79307893 TCGA-J4-A83J BND 5 21 TTLL11 ATP9B chr9 122011814 122011814 chr11 5932944 5932944 TCGA-J4-A83J BND 50 2 TTLL11 TRIM5 chr9 122015612 122015612 chr18 33282234 33282234 TCGA-J4-A83J BND 33 39 TTLL11 CCDC178 chr9 127018426 127018426 chr17 42459205 42459205 TCGA-J4-A83J BND 42 44 RALGPS1 ATP6V0A1 chr9 21980991 21980991 chr6 3634976 3634976 TCGA-J4-A83J BND 40 7 AL359922.1 * chr9 95270542 95270542 chr9 127013457 127013457 TCGA-J4-A83J DEL 45 47 FANCC RALGPS1 chr9 99892311 99892311 chr9 99896624 99896624 TCGA-J4-A83J DEL 5 17 STX17-AS1 STX17-AS1 chrX 105688189 105688189 chrX 105695750 105695750 TCGA-J4-A83J DEL 1 43 IL1RAPL2 IL1RAPL2 chrX 109034936 109034936 chrX 109036622 109036622 TCGA-J4-A83J DEL 13 36 * * chrX 68245388 68245388 chrX 68247123 68247123 TCGA-J4-A83J INV 4 31 OPHN1 OPHN1 chrX 83049774 83049774 chrX 83058715 83058715 TCGA-J4-A83J DEL 7 29 * * chrX 83354299 83354299 chrX 83354712 83354712 TCGA-J4-A83J DEL 46 34 * * chrX 83484318 83484318 chrX 83529549 83529549 TCGA-J4-A83J DEL 29 48 * * chrX 88426665 88426665 chrX 88472738 88472738 TCGA-J4-A83J DEL 13 38 * * chrY 19984425 19984425 chr12 40154674 40154674 TCGA-J4-A83J BND 2 1 * LINC02471 chrY 21150603 21150603 chr12 38795649 38795649 TCGA-J4-A83J BND 33 33 * CPNE8 chr10 13855232 13855232 chr10 15621990 15621990 TCGA-VP-A878 INS 42 24 FRMD4A ITGA8 chr10 24694031 24694031 chr10 25039504 25039504 TCGA-VP-A878 INS 39 39 ARHGAP21 AL512598.2 chr11 110438669 110438669 chr11 110761170 110761170 TCGA-VP-A878 INS 27 9 FDX1 * chr11 120544434 120544434 chr11 120870208 120870208 TCGA-VP-A878 INS 4 5 GRIK4 GRIK4 chr11 124937985 124937985 chr11 125785536 125785536 TCGA-VP-A878 INS 3 19 * * chr11 134219409 134219409 chr11 134663423 134663423 TCGA-VP-A878 INS 32 8 NCAPD3 * chr11 16679097 16679097 chr11 18268790 18268790 TCGA-VP-A878 INS 6 25 SOX6 SAA1 chr11 19993998 19993998 chr11 22340890 22340890 TCGA-VP-A878 INS 50 25 NAV2 SLC17A6 chr11 26437175 26437175 chr11 26678844 26678844 TCGA-VP-A878 INS 6 31 ANO3 SLC5A12 chr11 26574047 26574047 chr11 27017778 27017778 TCGA-VP-A878 INS 4 36 ANO3 * chr11 29612148 29612148 chr11 29979046 29979046 TCGA-VP-A878 INS 43 36 LINC02546 * chr11 77786436 77786436 chr11 80076210 80076210 TCGA-VP-A878 INS 12 46 RSF1 * chr11 84485590 84485590 chr11 86374330 86374330 TCGA-VP-A878 INS 39 30 DLG2 CCDC81 chr11 86026952 86026952 chr11 89074944 89074944 TCGA-VP-A878 INS 4 43 PICALM * chr11 93522744 93522744 chr11 95229298 95229298 TCGA-VP-A878 INS 33 43 SMCO4 SESN3 chr11 93740882 93740882 chr11 95130983 95130983 TCGA-VP-A878 DEL 35 34 TAF1D ENDOD1 chr12 101517687 101517687 chr12 104414116 104414116 TCGA-VP-A878 INS 14 31 * * chr12 109046984 109046984 chr12 109634926 109634926 TCGA-VP-A878 INS 47 41 USP30 * chr12 128364434 128364434 chr12 130415848 130415848 TCGA-VP-A878 INS 27 6 TMEM132C RIMBP2 chr12 130629270 130629270 chr12 131337856 131337856 TCGA-VP-A878 INS 37 36 RIMBP2 * chr12 14090582 14090582 chr12 15739595 15739595 TCGA-VP-A878 INS 23 33 * EPS8 chr12 43397312 43397312 chr12 45369466 45369466 TCGA-VP-A878 INS 40 24 ADAMTS20 ANO6 chr12 71523234 71523234 chr12 73935189 73935189 TCGA-VP-A878 INS 31 12 LGR5 * chr12 91770597 91770597 chr9 71360337 71360337 TCGA-VP-A878 BND 48 39 * TRPM3 chr13 46388968 46388968 chr13 46595099 46595099 TCGA-VP-A878 INS 4 41 RUBCNL LRCH1 chr13 51314864 51314864 chr13 51352620 51352620 TCGA-VP-A878 DEL 38 6 * SERPINE3 chr13 88713890 88713890 chr13 89039535 89039535 TCGA-VP-A878 INS 42 41 * * chr13 94267894 94267894 chr13 95142411 95142411 TCGA-VP-A878 INS 18 39 GPC6 ABCC4 chr14 24377600 24377600 chr14 24577850 24577850 TCGA-VP-A878 INS 26 24 NFATC4 * chr14 27899349 27899349 chr14 31440278 31440278 TCGA-VP-A878 INS 25 19 * AL139353.1 chr14 36711070 36711070 chr14 37613568 37613568 TCGA-VP-A878 INS 26 40 SLC25A21 TTC6 chr14 49417189 49417189 chr14 50638160 50638160 TCGA-VP-A878 INS 31 47 * SAV1 chr14 49648480 49648480 chr14 50001923 50001923 TCGA-VP-A878 INS 15 4 POLE2 LINC01588 chr14 57235119 57235119 chr14 61811591 61811591 TCGA-VP-A878 INS 12 17 EXOC5 SYT16 chr14 90526826 90526826 chr14 90909710 90909710 TCGA-VP-A878 DEL 44 30 TTC7B RPS6KA5 chr15 26040708 26040708 chr12 131262087 131262087 TCGA-VP-A878 BND 50 5 LINC02346 * chr15 65199838 65199845 chr15 67046477 67046477 TCGA-VP-A878 INS 49 34 CILP AC087482.1 chr16 81008334 81008334 chr16 81332709 81332709 TCGA-VP-A878 INS 36 7 CMC2 GAN chr17 41911420 41911420 chr17 44099802 44099802 TCGA-VP-A878 INS 19 41 ACLY HDAC5 chr17 59946227 59946227 chr17 60217868 60217868 TCGA-VP-A878 INS 30 49 RPS6KB1 USP32 chr17 61936090 61936090 chr17 62157122 62157122 TCGA-VP-A878 INS 24 48 * * chr17 63827195 63827195 chr17 64161407 64161407 TCGA-VP-A878 INS 26 18 FTSJ3 TEX2 chr17 75209908 75209908 chr17 78291848 78291851 TCGA-VP-A878 INS 34 36 NUP85 * chr18 4866581 4866581 chr18 5108407 5108407 TCGA-VP-A878 INS 21 23 AP005203.1 * chr18 75272430 75272430 chr18 76553711 76553711 TCGA-VP-A878 INS 7 34 TSHZ1 * chr18 76223834 76223834 chr18 77794530 77794530 TCGA-VP-A878 INS 6 37 * * chr18 8460852 8460852 chr18 9962103 9962103 TCGA-VP-A878 INS 22 39 * * chr19 14623975 14623975 chr19 15642444 15642444 TCGA-VP-A878 INS 17 14 ADGRE3 CYP4F3 chr19 27613198 27613198 chr19 32569120 32569120 TCGA-VP-A878 INS 37 37 * * chr19 5909063 5909063 chr19 8387022 8387022 TCGA-VP-A878 INS 27 43 VMAC RAB11B-AS1 chr19 9535954 9535954 chr19 9820889 9820889 TCGA-VP-A878 INS 14 24 ZNF426 FBXL12 chr1 111649437 111649437 chr1 111999945 111999945 TCGA-VP-A878 INS 40 36 RAP1A * chr1 112292460 112292460 chr1 112295039 112295039 TCGA-VP-A878 DEL 4 11 LINC02884 LINC02884 chr1 150230163 150230163 chr1 151073683 151073683 TCGA-VP-A878 INS 32 13 ANP32E GABPB2 chr1 150397736 150397736 chr1 150559247 150559247 TCGA-VP-A878 DEL 2 35 RPRD2 ADAMTSL4 chr1 163258992 163258992 chr1 165791600 165791600 TCGA-VP-A878 INS 32 16 RGS5 TMCO1 chr1 168151336 168151336 chr1 168862506 168862506 TCGA-VP-A878 INS 38 35 * AL135926.1 chr1 168185514 168185514 chr1 169200279 169200279 TCGA-VP-A878 INS 37 45 TIPRL NME7 chr1 203261155 203261155 chr1 205628572 205628572 TCGA-VP-A878 INS 19 19 CHIT1 ELK4 chr1 214464876 214464876 chr1 214743946 214743946 TCGA-VP-A878 INS 17 31 PTPN14 * chr1 32275985 32275985 chr1 35265735 35265735 TCGA-VP-A878 INS 35 8 LCK * chr1 33239946 33239946 chr1 33774479 33774479 TCGA-VP-A878 INS 20 43 * CSMD2 chr1 47463707 47463707 chr1 47616125 47616125 TCGA-VP-A878 INS 23 7 * * chr1 57045987 57045987 chr1 59341177 59341177 TCGA-VP-A878 INS 32 28 DAB1 FGGY chr1 60073077 60073077 chr1 61764980 61764980 TCGA-VP-A878 INS 49 8 C1orf87 PATJ chr20 21515098 21515098 chr7 151396971 151396971 TCGA-VP-A878 BND 26 34 NKX2-2 WDR86 chr20 733566 733566 chr20 1217065 1217065 TCGA-VP-A878 INS 15 35 * * chr22 38153646 38153646 chr22 38505529 38505529 TCGA-VP-A878 INS 16 3 PLA2G6 DDX17 chr22 38849043 38849043 chr22 39144902 39144902 TCGA-VP-A878 INS 9 19 * CBX7 chr2 116045533 116045533 chr2 118217805 118217805 TCGA-VP-A878 INS 41 49 * THORLNC chr2 177842385 177842385 chr2 180343058 180343058 TCGA-VP-A878 INS 12 11 PDE11A * chr2 18978570 18978570 chr2 19304039 19304039 TCGA-VP-A878 INS 21 17 * LINC01376 chr2 229910477 229910477 chr2 230321906 230321906 TCGA-VP-A878 INS 32 25 TRIP12 * chr2 26108634 26108634 chr2 26546979 26546979 TCGA-VP-A878 INS 27 12 RAB10 OTOF chr2 2815388 2815388 chr2 4422995 4422995 TCGA-VP-A878 INS 50 8 * * chr2 42914612 42914612 chr2 44813798 44813798 TCGA-VP-A878 INS 40 10 * * chr2 65519342 65519342 chr5 43089177 43089177 TCGA-VP-A878 BND 34 40 AC007389.1 ZNF131 chr3 107518155 107518155 chr3 107637775 107637775 TCGA-VP-A878 INS 33 14 * BBX chr3 107519632 107519632 chr3 107541041 107541041 TCGA-VP-A878 INS 38 47 * BBX chr3 12388385 12388385 chr3 12928074 12928074 TCGA-VP-A878 INS 23 49 PPARG IQSEC1 chr3 151690473 151690473 chr3 152222374 152222374 TCGA-VP-A878 INS 25 12 * * chr3 155680329 155680329 chr3 155854139 155854139 TCGA-VP-A878 INS 35 41 PLCH1 SLC33A1 chr3 20056450 20056450 chr3 21882295 21882295 TCGA-VP-A878 INS 48 25 KAT2B ZNF385D chr3 33954504 33954504 chr3 34208578 34208578 TCGA-VP-A878 INS 11 23 * LINC01811 chr3 40398886 40398886 chr3 40562947 40562947 TCGA-VP-A878 INS 32 4 ENTPD3-AS1 ZNF621 chr3 47190431 47190434 chr3 48253688 48253688 TCGA-VP-A878 INS 41 39 KIF9-AS1 ZNF589 chr3 47195335 47195335 chr3 48027012 48027012 TCGA-VP-A878 DEL 29 34 KIF9-AS1 MAP4 chr3 95917052 95917052 chr3 97367768 97367768 TCGA-VP-A878 INS 20 19 * EPHA6 chr4 139711697 139711697 chr4 142228265 142228265 TCGA-VP-A878 INS 31 35 MGST2 INPP4B chr4 154127132 154127132 chr4 156087009 156087009 TCGA-VP-A878 INS 3 22 * * chr4 158558488 158558488 chr4 160141146 160141146 TCGA-VP-A878 INS 15 27 RXFP1 * chr4 158559567 158559567 chr4 158560683 158560683 TCGA-VP-A878 DEL 21 42 RXFP1 RXFP1 chr4 164884679 164884679 chr4 166671953 166671953 TCGA-VP-A878 INS 24 20 APELA * chr4 179225779 179225779 chr4 180551435 180551435 TCGA-VP-A878 INS 22 28 * * chr4 22180450 22180450 chr4 22778667 22778667 TCGA-VP-A878 INS 9 6 AC096719.1 GBA3 chr4 27256433 27256433 chr4 30413444 30413444 TCGA-VP-A878 INS 17 4 LINC02261 * chr5 126897177 126897177 chr5 127349251 127349251 TCGA-VP-A878 INS 50 37 MARCHF3 MEGF10 chr5 127331049 127331049 chr5 127599506 127599506 TCGA-VP-A878 INS 13 41 MEGF10 * chr5 139406138 139406138 chr5 139782390 139782390 TCGA-VP-A878 INS 45 25 * * chr5 36754592 36754592 chr5 37436431 37436431 TCGA-VP-A878 INS 29 36 * WDR70 chr5 53650762 53650762 chr5 56219012 56219012 TCGA-VP-A878 INS 44 31 NDUFS4 ANKRD55 chr5 90234106 90234106 chr5 90721840 90721840 TCGA-VP-A878 INS 50 8 LINC01339 ADGRV1 chr6 10248202 10248202 chr6 12040076 12040076 TCGA-VP-A878 INS 18 3 * HIVEP1 chr6 11114150 11114150 chr6 11783473 11783473 TCGA-VP-A878 INS 17 25 SMIM13 ADTRP chr6 112094610 112094610 chr6 112464280 112464280 TCGA-VP-A878 INS 25 34 FAM229B * chr6 116165477 116165477 chr6 116804190 116804190 TCGA-VP-A878 INS 33 3 NT5DC1 GPRC6A chr6 153756885 153756885 chr6 156514149 156514149 TCGA-VP-A878 INS 50 13 * * chr6 23393035 23393035 chr6 24624979 24624979 TCGA-VP-A878 INS 24 14 * KIAA0319 chr6 26756689 26756689 chr6 26757955 26757955 TCGA-VP-A878 DEL 8 34 * * chr6 36631439 36631439 chr6 37968583 37968583 TCGA-VP-A878 INS 3 10 * ZFAND3 chr6 6150752 6150752 chr6 8658372 8658372 TCGA-VP-A878 INS 27 29 F13A1 AL355499.2 chr6 84747279 84747279 chr6 86580853 86580853 TCGA-VP-A878 INS 41 41 TBX18 * chr6 86503425 86503425 chr6 88070626 88070626 TCGA-VP-A878 INS 19 15 * * chr7 130005996 130005996 chr7 132786684 132786684 TCGA-VP-A878 INS 18 20 AC073320.1 CHCHD3 chr7 149843272 149843272 chr7 152307804 152307804 TCGA-VP-A878 INS 44 23 ZNF862 KMT2C chr7 151647218 151647218 chr20 21515992 21515992 TCGA-VP-A878 BND 2 1 PRKAG2 * chr7 152346307 152346307 chr7 152495345 152495345 TCGA-VP-A878 INS 31 40 KMT2C * chr7 25897411 25897411 chr7 26172046 26172046 TCGA-VP-A878 INS 28 31 * NFE2L3 chr7 4744847 4744847 chr7 6396071 6396071 TCGA-VP-A878 INS 41 30 FOXK1 RAC1 chr7 90380937 90380937 chr7 90978145 90978145 TCGA-VP-A878 INS 34 21 GTPBP10 CDK14 chr7 90702569 90702569 chr18 2025883 2025883 TCGA-VP-A878 BND 48 33 CDK14 AP005230.1 chr8 122830373 122830373 chr8 123399525 123399525 TCGA-VP-A878 INS 46 47 ZHX2 ATAD2 chr8 140824356 140824356 chr8 141327667 141327667 TCGA-VP-A878 INS 30 12 PTK2 * chr8 16571069 16571069 chr8 17577856 17577856 TCGA-VP-A878 INS 38 18 * PDGFRL chr8 29964617 29964617 chr8 32527863 32527863 TCGA-VP-A878 INS 32 39 * NRG1 chr8 65807090 65807090 chr8 66087182 66087182 TCGA-VP-A878 INS 26 30 PDE7A DNAJC5B chr8 95888321 95888321 chr8 98443066 98443066 TCGA-VP-A878 INS 40 45 * STK3 chr8 99560177 99560177 chr8 101311978 101311978 TCGA-VP-A878 INS 46 49 VPS13B * chr9 111539167 111539167 chr9 115553186 115553186 TCGA-VP-A878 INS 32 14 ZNF483 AL691420.1 chr9 119177429 119177429 chr9 121556098 121556098 TCGA-VP-A878 INS 26 14 BRINP1 * chr9 13482435 13482435 chr9 13669069 13669069 TCGA-VP-A878 INS 50 30 AL583785.1 * chr9 72385890 72385890 chr4 71885108 71885108 TCGA-VP-A878 BND 16 40 * * chr9 85215101 85215101 chr9 86803929 86803929 TCGA-VP-A878 INS 10 1 * * chr9 8910746 8910746 chr9 9022774 9022774 TCGA-VP-A878 DEL 10 36 PTPRD PTPRD chr9 9023259 9023259 chr9 9024715 9024715 TCGA-VP-A878 DEL 44 48 PTPRD PTPRD chr9 9282420 9282420 chr9 9505618 9505618 TCGA-VP-A878 DEL 41 50 PTPRD PTPRD chr9 93417136 93417136 chr9 95906717 95906717 TCGA-VP-A878 INS 42 46 Y_RNA ERCC6L2 chrX 107298378 107298378 chrX 108714287 108714287 TCGA-VP-A878 INS 3 11 * * chrX 108111412 108111412 chrX 108969675 108969675 TCGA-VP-A878 INS 41 15 ATG4A * chrX 117912123 117912123 chrX 118087550 118087550 TCGA-VP-A878 INS 30 27 KLHL13 KLHL13 chrX 143435796 143435796 chrX 143701277 143701277 TCGA-VP-A878 INS 27 31 AC239727.1 * chrX 42376795 42376795 chrX 44784128 44784128 TCGA-VP-A878 INS 12 46 Z93403.1 * chrX 48824376 48824376 chrX 48993205 48993205 TCGA-VP-A878 INS 13 3 HDAC6 GRIPAP1 chrX 75735560 75735560 chrX 76426274 76426274 TCGA-VP-A878 INS 49 49 * MAGEE1 chrX 82514988 82514988 chrX 83006906 83006906 TCGA-VP-A878 INS 26 13 * * chrX 9714821 9714821 chrX 12014366 12014366 TCGA-VP-A878 INS 40 44 TBL1X * chr10 105905211 105905211 chr10 106110504 106110504 TCGA-HC-A6AP DUP 41 17 * * chr10 10856873 10856873 chr10 14192085 14192085 TCGA-HC-A6AP DUP 24 8 CELF2 FRMD4A chr10 116953221 116953221 chr10 116987344 116987344 TCGA-HC-A6AP DUP 16 49 SHTN1 SHTN1 chr10 14897097 14897097 chr10 15737017 15737017 TCGA-HC-A6AP DUP 12 7 SUV39H2 * chr10 1823745 1823745 chr10 3216989 3216989 TCGA-HC-A6AP DUP 49 28 * * chr10 20176768 20176768 chr10 20448370 20448370 TCGA-HC-A6AP DUP 18 50 PLXDC2 * chr10 20516581 20516581 chr10 20728655 20728655 TCGA-HC-A6AP INV 44 36 * * chr10 20624537 20624537 chr10 20770630 20770630 TCGA-HC-A6AP INV 20 13 * * chr10 46490646 46490646 chr10 46526440 46526440 TCGA-HC-A6AP DEL 1 44 AC244230.2 AC244230.2 chr10 61475497 61475497 chr10 61861754 61861754 TCGA-HC-A6AP DUP 15 8 TMEM26-AS1 * chr10 63572672 63572672 chr5 150236583 150236583 TCGA-HC-A6AP BND 30 24 REEP3 CAMK2A chr10 77628346 77628346 chr10 78014233 78014233 TCGA-HC-A6AP DUP 48 32 KCNMA1 POLR3A chr10 85469470 85469470 chr10 85689185 85689185 TCGA-HC-A6AP DUP 38 21 LINC01520 GRID1 chr10 85735940 85735940 chr13 83380534 83380534 TCGA-HC-A6AP BND 35 44 GRID1 * chr10 86372354 86372354 chr10 86850553 86850553 TCGA-HC-A6AP DUP 15 14 * BMPR1A chr10 90646093 90646093 chr10 90931361 90931361 TCGA-HC-A6AP DUP 8 50 * * chr11 128081106 128081106 chr11 128191905 128191905 TCGA-HC-A6AP DUP 11 34 * * chr11 34593781 34593781 chr11 36248677 36248677 TCGA-HC-A6AP DEL 23 34 * * chr11 43191794 43191794 chr11 43579008 43579008 TCGA-HC-A6AP DUP 17 42 HNRNPKP3 AC068205.1 chr11 4496460 4496460 chr11 5213749 5213749 TCGA-HC-A6AP DUP 44 36 * * chr11 5409782 5409782 chr11 8262944 8262944 TCGA-HC-A6AP INV 37 13 HBG2 LMO1 chr11 65925557 65925557 chr11 65925675 65925675 TCGA-HC-A6AP INV 25 42 * * chr11 67822673 67822673 chr11 67822755 67822755 TCGA-HC-A6AP INV 38 35 ENPP7P7 ENPP7P7 chr11 91608802 91608802 chr11 91736558 91736558 TCGA-HC-A6AP DUP 9 46 * * chr11 97185689 97185689 chr11 116742559 116742559 TCGA-HC-A6AP DEL 31 28 * * chr12 12719327 12719327 chr11 9756527 9756527 TCGA-HC-A6AP BND 30 21 CDKN1B LINC02709 chr12 21811041 21811041 chr12 25582534 25582534 TCGA-HC-A6AP DUP 12 7 ABCC9 LMNTD1 chr12 28660468 28660468 chr12 32014656 32014656 TCGA-HC-A6AP DUP 4 44 * * chr12 38118756 38118756 chr12 38119767 38119767 TCGA-HC-A6AP INV 6 22 * * chr12 42598446 42598446 chr12 42758608 42758608 TCGA-HC-A6AP DUP 30 19 * * chr12 52548406 52548406 chr12 55944551 55944551 TCGA-HC-A6AP DUP 24 50 KRT71 DGKA chr12 56853261 56853261 chr22 42793559 42793559 TCGA-HC-A6AP BND 25 22 AC121758.2 AL049757.1 chr12 58328083 58328083 chr12 58336637 58336637 TCGA-HC-A6AP INS 4 37 * * chr12 59207007 59207007 chr12 61547587 61547587 TCGA-HC-A6AP INV 27 25 * * chr12 71417124 71417124 chr12 71955434 71955434 TCGA-HC-A6AP DUP 7 7 TSPAN8 TPH2 chr12 79774716 79774716 chr12 80154639 80154639 TCGA-HC-A6AP DUP 28 25 PPP1R12A OTOGL chr13 20762319 20762319 chr13 21229214 21229214 TCGA-HC-A6AP DUP 11 9 EEF1AKMT1 * chr13 23960666 23960666 chr13 24427494 24427494 TCGA-HC-A6AP DUP 10 50 * TPTE2P6 chr13 29240026 29240026 chr13 29509062 29509062 TCGA-HC-A6AP DUP 8 37 MTUS2 * chr13 38346000 38346000 chr13 38462559 38462559 TCGA-HC-A6AP DUP 24 22 * * chr13 38523819 38523819 chr13 38599755 38599755 TCGA-HC-A6AP DUP 25 31 * * chr13 47385871 47385871 chr13 47737800 47737800 TCGA-HC-A6AP DUP 31 15 * * chr13 52545048 52545048 chr13 52708637 52708637 TCGA-HC-A6AP DUP 16 37 AL137058.1 CNMD chr13 67790124 67790124 chr13 69336853 69336853 TCGA-HC-A6AP DUP 26 20 BCRP9 * chr13 89993241 89993241 chr13 95058567 95058567 TCGA-HC-A6AP DEL 37 30 * ABCC4 chr14 103222403 103222403 chr14 103843610 103843610 TCGA-HC-A6AP DUP 29 38 * PPP1R13B chr14 105564847 105564847 chr14 105684257 105684277 TCGA-HC-A6AP INV 10 26 * * chr14 105573444 105573444 chr14 105693927 105693927 TCGA-HC-A6AP DEL 4 23 * * chr14 23973924 23973924 chr14 24016601 24016601 TCGA-HC-A6AP DUP 11 32 DHRS4-AS1 AL136419.1 chr14 25980876 25980876 chr14 26086504 26086504 TCGA-HC-A6AP DUP 22 1 LINC02306 LINC02306 chr14 34109764 34109764 chr14 34112647 34112647 TCGA-HC-A6AP INV 19 46 EGLN3 EGLN3 chr14 37414778 37414778 chr14 37680918 37680918 TCGA-HC-A6AP DUP 8 4 MIPOL1 TTC6 chr14 41970389 41970389 chr14 42139792 42139792 TCGA-HC-A6AP DUP 9 49 * * chr14 60145934 60145934 chr20 52850637 52850637 TCGA-HC-A6AP BND 45 39 PCNX4 * chr14 69400001 69400001 chr14 69401271 69401271 TCGA-HC-A6AP INV 49 48 ERH SLC39A9 chr14 71916384 71916384 chr14 73022328 73022328 TCGA-HC-A6AP DEL 36 40 * ZFYVE1 chr14 79639948 79639948 chr14 79648707 79648707 TCGA-HC-A6AP INS 16 15 NRXN3 NRXN3 chr14 80725401 80725401 chr14 80772492 80772492 TCGA-HC-A6AP DUP 41 32 CEP128 CEP128 chr15 20534301 20534319 chr15 23130283 23130283 TCGA-HC-A6AP DUP 22 47 GOLGA6L6 GOLGA6L1 chr15 40024461 40024461 chr15 40489568 40489568 TCGA-HC-A6AP DUP 49 14 EIF2AK4 AC091045.1 chr15 63390292 63390292 chr15 63547807 63547807 TCGA-HC-A6AP DUP 18 6 LINC02568 USP3 chr16 4937516 4937516 chr16 81819091 81819091 TCGA-HC-A6AP INV 6 21 PPL PLCG2 chr16 60028385 60028385 chr16 60145790 60145790 TCGA-HC-A6AP DUP 35 34 LINC02141 * chr16 60828589 60828589 chr16 60924395 60924395 TCGA-HC-A6AP DUP 43 45 * * chr16 71326294 71326294 chr16 71689501 71689501 TCGA-HC-A6AP DUP 25 12 * PHLPP2 chr16 72583092 72583092 chr16 72685180 72685180 TCGA-HC-A6AP DEL 34 28 LINC01572 AC004943.2 chr17 1244830 1244830 chr17 3324737 3324737 TCGA-HC-A6AP DUP 13 49 AC144836.1 OR3A2 chr17 39698643 39698643 chr17 40041113 40041113 TCGA-HC-A6AP DUP 42 22 ERBB2 MED24 chr17 48613157 48613157 chr17 49058586 49058586 TCGA-HC-A6AP DUP 48 7 HOXB7 * chr17 61215371 61215371 chr17 61632862 61632862 TCGA-HC-A6AP DUP 35 28 BCAS3 * chr17 64573150 64573150 chr19 14763671 14763671 TCGA-HC-A6AP BND 36 22 SMURF2 ADGRE2 chr17 7685121 7685121 chr12 69887372 69887372 TCGA-HC-A6AP BND 22 33 TP53 MYRFL chr18 27168220 27168220 chr18 27320538 27320538 TCGA-HC-A6AP DUP 38 11 AQP4-AS1 * chr18 53547013 53547013 chr18 53731695 53731695 TCGA-HC-A6AP DUP 12 7 LINC01917 * chr18 54799950 54799950 chr18 55059636 55059636 TCGA-HC-A6AP DUP 49 40 RAB27B * chr18 64424853 64424853 chr18 64514980 64514980 TCGA-HC-A6AP DUP 48 5 * * chr18 65661926 65661926 chr18 66407337 66407337 TCGA-HC-A6AP DUP 22 6 * * chr18 69202985 69202985 chr18 69326639 69326639 TCGA-HC-A6AP DUP 24 9 * * chr18 71247358 71247358 chr18 71465195 71465195 TCGA-HC-A6AP DUP 16 9 * * chr19 13960757 13960757 chr19 14740682 14740682 TCGA-HC-A6AP DUP 7 9 DCAF15 ADGRE2 chr19 33261084 33261084 chr19 33488320 33488320 TCGA-HC-A6AP DUP 4 14 * PEPD chr19 37836057 37836057 chr19 38159270 38159270 TCGA-HC-A6AP DUP 25 43 AC016582.1 SIPA1L3 chr19 48068914 48068914 chr19 50964001 50964001 TCGA-HC-A6AP DUP 39 16 PLA2G4C KLK6 chr19 54181883 54181883 chr20 53837914 53837914 TCGA-HC-A6AP BND 43 50 MBOAT7 * chr1 101900495 101900495 chr1 102001161 102001161 TCGA-HC-A6AP DUP 17 44 OLFM3 * chr1 117744241 117744241 chr1 117958950 117958950 TCGA-HC-A6AP DUP 11 17 * WDR3 chr1 164529132 164529132 chr1 164672234 164672234 TCGA-HC-A6AP DUP 45 42 * PBX1 chr1 171668121 171668121 chr1 171869694 171869694 TCGA-HC-A6AP DUP 27 29 * DNM3 chr1 191469185 191469185 chr1 191783566 191783566 TCGA-HC-A6AP DUP 34 22 * * chr1 196442313 196442313 chr1 196669050 196669050 TCGA-HC-A6AP DUP 47 34 KCNT2 CFH chr1 200673836 200673836 chr1 205591951 205591951 TCGA-HC-A6AP DUP 44 38 DDX59-AS1 MFSD4A chr1 205269156 205269156 chr17 43545140 43545140 TCGA-HC-A6AP BND 48 45 TMCC2 DHX8 chr1 214037803 214037803 chr1 214237455 214237455 TCGA-HC-A6AP DUP 13 15 PROX1 * chr1 215087774 215087774 chr1 215198309 215198309 TCGA-HC-A6AP DUP 26 5 KCNK2 KCNK2 chr1 21775976 21775976 chr9 107407039 107407039 TCGA-HC-A6AP BND 39 50 USP48 * chr1 223318760 223318760 chrX 83547169 83547169 TCGA-HC-A6AP BND 10 49 SUSD4 * chr1 228161538 228161538 chr1 228299799 228299799 TCGA-HC-A6AP DUP 42 29 * OBSCN chr1 230252402 230252402 chr1 230548817 230548817 TCGA-HC-A6AP DUP 9 10 GALNT2 * chr1 230392867 230392867 chr1 230395351 230395351 TCGA-HC-A6AP INV 21 3 PGBD5 PGBD5 chr1 45300411 45300411 chr1 46692365 46692365 TCGA-HC-A6AP DUP 47 9 ZSWIM5 EFCAB14 chr1 71503638 71503638 chr1 71926827 71926827 TCGA-HC-A6AP DUP 48 4 NEGR1 NEGR1 chr1 75984865 75984865 chr1 79198918 79198918 TCGA-HC-A6AP DUP 5 50 AC092813.1 * chr1 91220972 91220972 chr1 91542618 91542618 TCGA-HC-A6AP DUP 31 40 * * chr1 96657947 96657947 chr1 96761436 96761436 TCGA-HC-A6AP DUP 42 4 * PTBP2 chr20 19326024 19326024 chr20 20106401 20106401 TCGA-HC-A6AP DUP 11 37 SLC24A3 CFAP61 chr20 22566906 22566906 chr21 22092408 22092408 TCGA-HC-A6AP BND 36 16 LINC00261 LINC01687 chr20 48618394 48618394 chr20 48870727 48870727 TCGA-HC-A6AP DUP 12 27 * * chr20 58068857 58068857 chr20 58270756 58270756 TCGA-HC-A6AP DUP 30 33 * PPP4R1L chr20 59399011 59399011 chr20 59624451 59624451 TCGA-HC-A6AP DUP 16 6 * PHACTR3 chr20 62017982 62017982 chr20 62400347 62400347 TCGA-HC-A6AP DUP 33 14 TAF4 CABLES2 chr20 62190153 62190153 chr20 62190221 62190221 TCGA-HC-A6AP INV 49 37 MTG2 MTG2 chr21 35930482 35930482 chr21 36297558 36297558 TCGA-HC-A6AP DUP 16 32 RUNX1 * chr21 38445838 38445838 chr21 41498683 41498690 TCGA-HC-A6AP DEL 4 25 ERG TMPRSS2 chr21 38461749 38461749 chr21 41497567 41497567 TCGA-HC-A6AP DEL 49 31 ERG TMPRSS2 chr21 41381262 41381262 chr21 41731896 41731896 TCGA-HC-A6AP DUP 21 11 MX2 * chr21 43499726 43499726 chr21 43500898 43500898 TCGA-HC-A6AP INV 27 13 * * chr22 26357641 26357641 chr22 26651623 26651623 TCGA-HC-A6AP DUP 43 31 SEZ6L MIAT chr22 27498983 27498983 chr22 28033274 28033274 TCGA-HC-A6AP DUP 44 36 * TTC28 chr22 28051068 28051068 chr22 29044047 29044047 TCGA-HC-A6AP DEL 8 12 TTC28 ZNRF3 chr22 39610905 39610905 chr22 39820449 39820449 TCGA-HC-A6AP DUP 8 43 CACNA1I ENTHD1 chr2 120248845 120248845 chr2 120517301 120517301 TCGA-HC-A6AP DUP 41 24 RALB * chr2 14792531 14792531 chr2 14982732 14982732 TCGA-HC-A6AP DUP 40 40 * * chr2 150607063 150607063 chr2 153962561 153962561 TCGA-HC-A6AP DUP 26 4 AC104777.1 GALNT13 chr2 190758013 190758013 chr2 190856498 190856498 TCGA-HC-A6AP DUP 43 24 * * chr2 201479313 201479313 chr2 201755892 201755892 TCGA-HC-A6AP DEL 25 33 STRADB ALS2 chr2 231004772 231004772 chr20 63443202 63443202 TCGA-HC-A6AP BND 13 1 SPATA3 KCNQ2 chr2 238475284 238475284 chr2 238485445 238485445 TCGA-HC-A6AP INV 40 10 * * chr2 241037740 241037740 chr2 241041939 241041939 TCGA-HC-A6AP INV 31 20 SNED1 SNED1 chr2 41015924 41015924 chr2 41184359 41184359 TCGA-HC-A6AP DUP 8 14 * * chr2 5015713 5015713 chr2 5058275 5058275 TCGA-HC-A6AP DUP 12 35 * * chr2 5017653 5017653 chr2 5058275 5058275 TCGA-HC-A6AP DUP 23 6 * * chr2 5058899 5058899 chr2 5196838 5196838 TCGA-HC-A6AP DUP 42 39 * * chr2 59454528 59454528 chr18 63198671 63198671 TCGA-HC-A6AP BND 25 48 AC007100.1 BCL2 chr2 61181184 61181184 chr17 60838181 60838181 TCGA-HC-A6AP BND 36 1 AHSA2P BCAS3 chr2 74561071 74561071 chr8 132673770 132673770 TCGA-HC-A6AP BND 47 26 M1AP LRRC6 chr2 76366031 76366031 chr5 3067509 3067509 TCGA-HC-A6AP BND 33 41 * * chr2 8415309 8415309 chr2 11622896 11622896 TCGA-HC-A6AP DUP 10 36 * GREB1 chr2 85383990 85383990 chr2 85742242 85742242 TCGA-HC-A6AP DUP 5 39 ELMOD3 * chr2 86525915 86525915 chr2 86709828 86709828 TCGA-HC-A6AP DUP 34 16 CHMP3 RNF103-CHMP3 chr2 98471069 98471069 chr2 101303918 101303918 TCGA-HC-A6AP DUP 11 18 INPP4A RNF149 chr3 105411412 105411412 chr3 105698343 105698343 TCGA-HC-A6AP DUP 34 44 ALCAM CBLB chr3 130044501 130044501 chr3 130087940 130087940 TCGA-HC-A6AP DEL 15 50 * ALG1L2 chr3 130849111 130849111 chr3 185177562 185177562 TCGA-HC-A6AP INS 40 49 ATP2C1 EHHADH-AS1 chr3 135372141 135372141 chr3 179352021 179352021 TCGA-HC-A6AP DUP 18 18 AC092969.1 MFN1 chr3 140517383 140517383 chr3 176003299 176003299 TCGA-HC-A6AP DEL 32 1 CLSTN2 * chr3 146176004 146176004 chr3 146226618 146226618 TCGA-HC-A6AP DUP 11 16 * PLSCR4 chr3 146184176 146184176 chr3 151024594 151024594 TCGA-HC-A6AP DUP 44 28 * CLRN1-AS1 chr3 153821758 153821758 chr3 154382306 154382306 TCGA-HC-A6AP DUP 29 47 LINC02006 GPR149 chr3 157606925 157606925 chr3 185177986 185177986 TCGA-HC-A6AP DEL 39 5 SLC66A1L EHHADH-AS1 chr3 173730935 173730935 chr3 174506759 174506759 TCGA-HC-A6AP DUP 22 7 NLGN1 NAALADL2 chr3 188354849 188354849 chr11 23803093 23803093 TCGA-HC-A6AP BND 12 21 LPP AC100768.1 chr3 188852805 188852805 chr3 189035054 189035054 TCGA-HC-A6AP DUP 33 17 LPP TPRG1 chr3 193688633 193688633 chr3 193848619 193848619 TCGA-HC-A6AP DUP 4 42 OPA1 * chr3 195390148 195390148 chr3 195741463 195741463 TCGA-HC-A6AP DUP 17 17 ACAP2 * chr3 30147880 30147880 chr3 30586464 30586464 TCGA-HC-A6AP DUP 39 7 * * chr3 54947484 54947484 chr3 59516665 59516665 TCGA-HC-A6AP DUP 47 25 CACNA2D3 * chr3 55716469 55716469 chr3 55899282 55899282 TCGA-HC-A6AP DUP 45 22 ERC2 ERC2 chr3 57768170 57768170 chr3 58239946 58239946 TCGA-HC-A6AP DUP 23 39 SLMAP ABHD6 chr3 63842061 63842061 chr3 67165690 67165690 TCGA-HC-A6AP DUP 37 13 C3orf49 * chr3 70423985 70423985 chr3 73613478 73613478 TCGA-HC-A6AP DUP 8 3 SAMMSON PDZRN3 chr3 71510039 71510039 chr3 72111050 72111050 TCGA-HC-A6AP DUP 17 13 FOXP1 LINC00877 chr3 82136076 82136076 chr3 85686808 85686808 TCGA-HC-A6AP DUP 13 8 LINC02008 CADM2 chr3 82568293 82568293 chr3 83457057 83457057 TCGA-HC-A6AP DUP 18 32 * * chr4 140319178 140319178 chr4 152925964 152925964 TCGA-HC-A6AP DEL 24 48 SCOC FAM192BP chr4 149228061 149228061 chr4 151484391 151484391 TCGA-HC-A6AP DUP 43 30 LINC02355 FAM160A1 chr4 150523065 150523065 chr4 150710313 150710313 TCGA-HC-A6AP DUP 20 49 LRBA LRBA chr4 159282980 159282980 chr4 159669840 159669840 TCGA-HC-A6AP DUP 16 46 RAPGEF2 LINC02233 chr4 160906076 160906076 chr4 162440114 162440114 TCGA-HC-A6AP DUP 40 14 * * chr4 171701498 171701498 chr4 174036253 174036253 TCGA-HC-A6AP DUP 11 23 * * chr4 29062849 29062849 chr4 29311934 29311934 TCGA-HC-A6AP DUP 31 17 * * chr4 3541303 3541303 chr9 41757203 41757203 TCGA-HC-A6AP BND 31 2 * * chr4 3569441 3569441 chr9 61991926 61991926 TCGA-HC-A6AP BND 9 27 * * chr4 41233722 41233722 chr4 41633639 41633639 TCGA-HC-A6AP DUP 3 3 UCHL1-AS1 LIMCH1 chr4 53666249 53666249 chr4 56618693 56618693 TCGA-HC-A6AP DUP 17 23 LNX1 * chr4 56277324 56277324 chr4 56800752 56800752 TCGA-HC-A6AP DUP 43 24 CRACD * chr4 58103707 58103707 chr4 59360692 59360692 TCGA-HC-A6AP DUP 24 8 * * chr4 70913300 70913300 chr4 71113946 71113946 TCGA-HC-A6AP DUP 32 13 MOB1B SLC4A4 chr4 71302655 71302655 chr4 71623274 71623274 TCGA-HC-A6AP DUP 21 2 SLC4A4 * chr4 71523955 71523955 chr4 71856383 71856383 TCGA-HC-A6AP DUP 2 24 SLC4A4 * chr4 71623064 71623064 chr4 71633869 71633869 TCGA-HC-A6AP DUP 34 8 * * chr4 72417132 72417132 chr4 72768483 72768483 TCGA-HC-A6AP DUP 32 11 ADAMTS3 * chr4 74536761 74536761 chr4 76520073 76520073 TCGA-HC-A6AP DUP 35 14 * SHROOM3 chr4 75719810 75719810 chr4 75822808 75822808 TCGA-HC-A6AP DEL 24 47 G3BP2 * chr4 77006135 77006135 chr4 77323054 77323054 TCGA-HC-A6AP DUP 36 12 SEPTIN11 CCNG2 chr4 91273893 91273893 chr4 91441670 91441670 TCGA-HC-A6AP DUP 46 3 CCSER1 CCSER1 chr4 91390945 91390945 chr4 91615415 91615415 TCGA-HC-A6AP DUP 1 9 CCSER1 * chr5 121910375 121910375 chr5 122472991 122472991 TCGA-HC-A6AP DUP 43 3 * MGC32805 chr5 136165995 136165995 chr5 136377881 136377881 TCGA-HC-A6AP DUP 25 49 SMAD5 AC063980.1 chr5 144301785 144301785 chr5 144449506 144449506 TCGA-HC-A6AP DUP 14 27 KCTD16 KCTD16 chr5 157013468 157013468 chr13 37279734 37279734 TCGA-HC-A6AP BND 16 24 * * chr5 159784151 159784151 chr5 162577081 162577081 TCGA-HC-A6AP INV 14 23 AC008691.1 AC113414.1 chr5 166705096 166705096 chr5 168722123 168722123 TCGA-HC-A6AP DUP 10 22 * SLIT3 chr5 6555608 6555608 chr5 7041522 7041522 TCGA-HC-A6AP DUP 1 47 * LINC02196 chr5 74789099 74789099 chr5 75199141 75199141 TCGA-HC-A6AP DUP 27 3 FAM169A ANKRD31 chr5 74999355 74999355 chr5 76503919 76503919 TCGA-HC-A6AP DUP 15 23 AC116337.3 IQGAP2 chr5 84295725 84295725 chr5 84390989 84390989 TCGA-HC-A6AP DUP 37 3 EDIL3 EDIL3-DT chr5 85059469 85059469 chr5 85209048 85209048 TCGA-HC-A6AP DUP 9 22 * * chr5 86388257 86388257 chr5 86424861 86424861 TCGA-HC-A6AP DUP 13 27 * * chr5 95786097 95786097 chr5 96129115 96129115 TCGA-HC-A6AP DUP 19 43 RHOBTB3 AC104123.1 chr6 104801203 104801203 chr6 105414200 105414200 TCGA-HC-A6AP DUP 43 30 HACE1 * chr6 127250684 127250684 chr6 127417315 127417315 TCGA-HC-A6AP DUP 40 28 * AL590002.1 chr6 18361540 18361540 chr6 18797650 18797650 TCGA-HC-A6AP DUP 29 11 * * chr6 26971733 26971733 chr6 27177280 27177280 TCGA-HC-A6AP DUP 3 21 LINC00240 * chr6 47629292 47629292 chr10 87870175 87870175 TCGA-HC-A6AP BND 40 37 * PTEN chr6 57429536 57429536 chr10 51809336 51809336 TCGA-HC-A6AP BND 35 49 PRIM2 PRKG1 chr6 70976286 70976286 chr6 70999804 70999804 TCGA-HC-A6AP DEL 24 34 * * chr6 92689447 92689447 chr6 93665827 93665827 TCGA-HC-A6AP DUP 50 9 * * chr7 105437593 105437593 chr7 105798522 105798522 TCGA-HC-A6AP DUP 20 44 * ATXN7L1 chr7 106546023 106546023 chr7 106611060 106611060 TCGA-HC-A6AP DUP 37 21 AC004917.1 AC004917.1 chr7 11107518 11107518 chr7 11107548 11107548 TCGA-HC-A6AP INV 45 31 PHF14 PHF14 chr7 111096319 111096319 chr7 113031243 113031243 TCGA-HC-A6AP DUP 40 16 IMMP2L * chr7 111113383 111113383 chr7 111113627 111113627 TCGA-HC-A6AP INV 26 15 IMMP2L IMMP2L chr7 111460172 111460172 chr7 111460350 111460350 TCGA-HC-A6AP INV 44 34 IMMP2L IMMP2L chr7 115976847 115976847 chr7 116423584 116423584 TCGA-HC-A6AP DUP 6 3 TFEC AC002066.1 chr7 115978421 115978421 chr7 116007408 116007408 TCGA-HC-A6AP DUP 14 43 TFEC TFEC chr7 115978501 115978501 chr7 116001492 116001492 TCGA-HC-A6AP DEL 1 41 TFEC TFEC chr7 11643609 11643609 chr12 11270853 11270853 TCGA-HC-A6AP BND 17 36 THSD7A PRB3 chr7 126472609 126472609 chr7 126529554 126529554 TCGA-HC-A6AP DUP 15 31 GRM8 GRM8 chr7 14008738 14008738 chr14 37591115 37591115 TCGA-HC-A6AP BND 18 17 * FOXA1 chr7 142749876 142749876 chr7 142749977 142749977 TCGA-HC-A6AP INV 48 41 PRSS1 PRSS1 chr7 142942619 142942619 chr7 145051205 145051205 TCGA-HC-A6AP DUP 40 2 KEL * chr7 146211465 146211465 chr7 146369256 146369256 TCGA-HC-A6AP DUP 47 27 CNTNAP2 CNTNAP2 chr7 151274958 151274958 chr7 151718840 151718840 TCGA-HC-A6AP DUP 45 4 SMARCD3 PRKAG2 chr7 157192542 157192542 chr7 157485306 157485306 TCGA-HC-A6AP DUP 8 17 UBE3C AC006372.3 chr7 23787328 23787328 chr7 46252543 46252543 TCGA-HC-A6AP INS 31 21 STK31 * chr7 24795069 24795069 chr7 25170959 25170959 TCGA-HC-A6AP DUP 4 7 * C7orf31 chr7 28764847 28764847 chr7 31823705 31823705 TCGA-HC-A6AP DUP 10 47 CREB5 PDE1C chr7 29975151 29975151 chr7 30567169 30567169 TCGA-HC-A6AP DUP 41 17 SCRN1 GARS1-DT chr7 41652719 41652719 chr7 100464648 100464648 TCGA-HC-A6AP INS 20 25 * C7orf61 chr7 42959054 42959054 chr7 43608414 43608414 TCGA-HC-A6AP DUP 38 32 AC005537.1 STK17A chr7 43184697 43184697 chr7 43184894 43184894 TCGA-HC-A6AP INV 32 8 HECW1 HECW1 chr7 43473183 43473183 chr7 43473321 43473321 TCGA-HC-A6AP INV 49 24 HECW1 HECW1 chr7 45742903 45742903 chr7 47732378 47732378 TCGA-HC-A6AP DEL 16 36 SEPTIN7P2 * chr7 6829771 6829771 chr7 7026946 7026946 TCGA-HC-A6AP DUP 27 2 * * chr7 78952496 78952496 chr7 79196392 79196392 TCGA-HC-A6AP DUP 47 34 MAGI2 MAGI2 chr7 83913197 83913197 chr7 83945413 83945413 TCGA-HC-A6AP DUP 46 50 * * chr7 90338746 90338746 chr7 94731258 94731258 TCGA-HC-A6AP DUP 22 9 GTPBP10 * chr7 9113655 9113655 chr7 9314623 9314623 TCGA-HC-A6AP DUP 30 28 AC004852.2 * chr7 91151428 91151428 chr7 91151597 91151597 TCGA-HC-A6AP INV 28 8 CDK14 CDK14 chr7 91535813 91535813 chr7 91735531 91735531 TCGA-HC-A6AP DUP 34 3 AC079760.1 MTERF1 chr7 91721030 91721030 chr7 91721482 91721482 TCGA-HC-A6AP INV 11 46 MTERF1 MTERF1 chr7 91728887 91728887 chr7 91729095 91729095 TCGA-HC-A6AP INV 30 37 MTERF1 MTERF1 chr7 93274991 93274991 chr7 93275274 93275274 TCGA-HC-A6AP INV 10 39 VPS50 VPS50 chr7 93985553 93985553 chr7 93985799 93985799 TCGA-HC-A6AP INV 35 16 BET1 BET1 chr7 95122649 95122649 chr7 95163582 95163582 TCGA-HC-A6AP DUP 24 12 PPP1R9A PPP1R9A chr7 97308181 97308181 chr7 97328727 97328727 TCGA-HC-A6AP DUP 25 33 * * chr7 98948779 98948779 chr7 101117477 101117477 TCGA-HC-A6AP DUP 28 6 TRRAP * chr8 108098077 108098077 chrX 142942102 142942102 TCGA-HC-A6AP BND 39 24 * * chr8 109125867 109125867 chr8 113436478 113436478 TCGA-HC-A6AP DUP 17 11 * CSMD3 chr8 117643727 117643727 chr8 117827457 117827457 TCGA-HC-A6AP DEL 22 22 * EXT1 chr8 120490715 120490715 chr8 120822949 120822949 TCGA-HC-A6AP DUP 8 31 MTBP * chr8 127475163 127475163 chr8 127749534 127749534 TCGA-HC-A6AP DUP 7 2 CASC8 * chr8 132322600 132322600 chr8 132616865 132616865 TCGA-HC-A6AP DUP 12 47 KCNQ3 LRRC6 chr8 141311032 141311032 chr8 144544579 144544579 TCGA-HC-A6AP DUP 7 44 * ARHGAP39 chr8 142229063 142229063 chr8 142230771 142230771 TCGA-HC-A6AP INV 2 19 TSNARE1 TSNARE1 chr8 16616802 16616802 chr8 109297498 109297498 TCGA-HC-A6AP INV 16 44 AC011586.2 NUDCD1 chr8 22496735 22496735 chr8 24489793 24489793 TCGA-HC-A6AP DUP 39 1 PPP3CC AC120193.1 chr8 27064121 27064121 chr8 27064245 27064245 TCGA-HC-A6AP DEL 35 26 AC067904.2 AC067904.2 chr8 3711303 3711303 chr8 3933681 3933681 TCGA-HC-A6AP DEL 15 8 CSMD1 CSMD1 chr8 41466320 41466320 chr8 41804209 41804209 TCGA-HC-A6AP DUP 38 20 * ANK1 chr8 59688359 59688359 chr8 125081280 125081280 TCGA-HC-A6AP DUP 25 42 * WASHC5 chr8 60768564 60768564 chr8 61205166 61205166 TCGA-HC-A6AP DUP 48 28 CHD7 CLVS1 chr8 69662843 69662843 chr8 69852760 69852760 TCGA-HC-A6AP DUP 29 4 * Metazoa_SRP chr8 73595244 73595244 chr8 73878317 73878317 TCGA-HC-A6AP DUP 8 10 STAU2 UBE2W chr8 74675450 74675450 chr8 75202541 75202541 TCGA-HC-A6AP DUP 6 42 MIR2052HG * chr8 79568757 79568757 chr12 97950710 97950710 TCGA-HC-A6AP BND 37 49 * * chr8 80359069 80359069 chr8 80664164 80664164 TCGA-HC-A6AP DUP 29 14 AC034114.2 ZNF704 chr8 91805034 91805034 chr8 91822949 91822949 TCGA-HC-A6AP DEL 44 18 AC103409.1 AC103409.1 chr8 96426033 96426033 chr8 96568529 96568529 TCGA-HC-A6AP DUP 35 17 * SDC2 chr9 110347960 110347960 chr9 110515991 110515991 TCGA-HC-A6AP DUP 15 2 * SVEP1 chr9 136533072 136533072 chr9 136533344 136533344 TCGA-HC-A6AP DEL 13 45 NOTCH1 NOTCH1 chr9 17990629 17990629 chr14 68608832 68608832 TCGA-HC-A6AP BND 7 10 ADAMTSL1 RAD51B chr9 38239144 38239144 chr10 87868120 87868120 TCGA-HC-A6AP BND 45 47 * PTEN chr9 41758230 41758230 chr9 61970332 61970332 TCGA-HC-A6AP INV 42 50 * * chr9 73429769 73429769 chr9 73434460 73434460 TCGA-HC-A6AP INV 36 10 * * chr9 97614579 97614579 chrX 52604946 52604946 TCGA-HC-A6AP BND 47 19 TSTD2 * chrX 113454936 113454936 chrX 113648044 113648044 TCGA-HC-A6AP DUP 41 3 * XACT chrX 136755202 136755202 chrX 137100079 137100079 TCGA-HC-A6AP DUP 38 40 ARHGEF6 * chrX 52026706 52026706 chrX 86561514 86561514 TCGA-HC-A6AP DEL 20 12 * DACH2 chrX 64110151 64110151 chrX 64225024 64225024 TCGA-HC-A6AP DUP 32 35 * ASB12 chrX 64332656 64332656 chrX 66334452 66334452 TCGA-HC-A6AP INV 38 2 MTMR8 * chrX 66681486 66681486 chrX 68095031 68095031 TCGA-HC-A6AP INV 28 2 * OPHN1 chrX 66794980 66794980 chrX 66795127 66795127 TCGA-HC-A6AP INV 25 23 * * chrX 66817727 66817727 chrX 66818665 66818665 TCGA-HC-A6AP INV 32 31 * * chrX 66826970 66826970 chrX 66827313 66827313 TCGA-HC-A6AP INV 38 7 * * chrX 66873011 66873011 chrX 66873392 66873392 TCGA-HC-A6AP INV 35 4 * * chrX 66884533 66884533 chrX 66884606 66884606 TCGA-HC-A6AP INV 34 39 * * chrX 66919784 66919784 chrX 66919903 66919903 TCGA-HC-A6AP INV 3 35 * * chrX 67049267 67049267 chrX 67171618 67171618 TCGA-HC-A6AP DEL 42 2 * * chrX 67246344 67246344 chrX 67246487 67246487 TCGA-HC-A6AP INV 21 49 * * chrX 67538709 67538709 chrX 67538835 67538835 TCGA-HC-A6AP INV 9 22 * * chrX 67544701 67544701 chrX 67544885 67544885 TCGA-HC-A6AP INV 14 46 AR AR chrX 67546264 67546264 chrX 67546514 67546514 TCGA-HC-A6AP INV 1 44 AR AR chrX 67569450 67569450 chrX 67569489 67569489 TCGA-HC-A6AP INV 49 15 AR AR chrX 67621307 67621307 chrX 68464775 68464775 TCGA-HC-A6AP INV 47 6 AR * chrX 67692545 67692545 chrX 67692614 67692614 TCGA-HC-A6AP INV 36 44 AR AR chrX 67701498 67701498 chrX 67701528 67701528 TCGA-HC-A6AP INV 49 18 AR AR chrX 67757809 67757809 chrX 69062882 69062882 TCGA-HC-A6AP INV 35 8 * * chrX 67766897 67766897 chrX 67766934 67766934 TCGA-HC-A6AP INV 24 3 * * chrX 67774891 67774891 chrX 67774958 67774958 TCGA-HC-A6AP INV 26 35 * * chrX 67872875 67872875 chrX 67873097 67873097 TCGA-HC-A6AP INV 47 17 * * chrX 67912791 67912791 chrX 67912842 67912842 TCGA-HC-A6AP INV 36 28 * * chrX 68021789 68021789 chrX 68381990 68381990 TCGA-HC-A6AP INV 16 23 * OPHN1 chrX 68156504 68156504 chrX 68156581 68156581 TCGA-HC-A6AP INV 37 46 OPHN1 OPHN1 chrX 68156684 68156684 chrX 68156756 68156756 TCGA-HC-A6AP INV 21 17 OPHN1 OPHN1 chrX 68164584 68164584 chrX 68692578 68692578 TCGA-HC-A6AP DUP 11 27 OPHN1 STARD8 chrX 68514212 68514212 chrX 68514607 68514607 TCGA-HC-A6AP INV 40 16 YIPF6 YIPF6 chrX 68803422 68803422 chrX 68803668 68803668 TCGA-HC-A6AP INV 22 37 * * chrX 69280892 69280892 chrX 69281209 69281209 TCGA-HC-A6AP INV 41 17 * * chrX 69430837 69430837 chrX 69430936 69430936 TCGA-HC-A6AP INV 7 11 * * chrX 69580504 69580504 chrX 70348819 70348819 TCGA-HC-A6AP DEL 7 11 * KIF4A chrX 69675131 69675131 chrX 71658518 71658518 TCGA-HC-A6AP INV 37 31 EDA * chrX 70587774 70587774 chrX 71244596 71244596 TCGA-HC-A6AP DEL 12 8 TEX11 ZMYM3 chrX 85188527 85188527 chrX 87687051 87687051 TCGA-HC-A6AP DUP 44 8 SATL1 * chrX 88498804 88498804 chrX 88602853 88602853 TCGA-HC-A6AP DUP 18 39 * * chr10 50816126 50816126 chr10 52630030 52630030 TCGA-YL-A8S9 DEL 34 20 ASAH2B LNCAROD chr10 50964288 50964288 chr10 51914444 51914444 TCGA-YL-A8S9 DEL 47 28 CCDC58P2 PRKG1 chr11 21429273 21429273 chr11 36558393 36558393 TCGA-YL-A8S9 DEL 45 5 NELL1 RAG1 chr11 27864654 27864654 chr11 29936692 29936692 TCGA-YL-A8S9 INS 5 25 AC103796.1 * chr11 30657166 30657166 chr11 32149761 32149761 TCGA-YL-A8S9 INS 8 19 * THEM7P chr11 31025932 31025932 chr11 31030858 31030858 TCGA-YL-A8S9 DEL 40 37 DCDC1 DCDC1 chr11 31981221 31981221 chr11 31999666 31999666 TCGA-YL-A8S9 DEL 50 31 PAUPAR PAUPAR chr12 125032734 125032734 chr4 127192284 127192284 TCGA-YL-A8S9 BND 42 7 * AC093772.1 chr12 72533868 72533868 chr12 125334759 125334759 TCGA-YL-A8S9 DEL 41 36 TRHDE TMEM132B chr12 75494289 75494289 chr12 127367595 127367595 TCGA-YL-A8S9 INS 43 19 GLIPR1 * chr12 9701881 9701881 chr12 9726679 9726679 TCGA-YL-A8S9 DEL 41 13 * CLECL1 chr13 80285386 80285386 chr13 80796915 80796915 TCGA-YL-A8S9 INS 19 5 * * chr18 61623375 61623375 chr18 75866080 75866080 TCGA-YL-A8S9 DEL 46 50 AC105094.2 AC021506.1 chr1 191466863 191466863 chr1 194431678 194431678 TCGA-YL-A8S9 INS 39 36 * * chr1 194846465 194846465 chr1 213188141 213188141 TCGA-YL-A8S9 DEL 15 16 AL353072.2 RPS6KC1 chr1 213138470 213138470 chr1 214135302 214135302 TCGA-YL-A8S9 DEL 14 26 RPS6KC1 LINC02775 chr2 103612924 103612924 chr2 103780520 103780520 TCGA-YL-A8S9 DEL 33 40 * * chr2 140941426 140941426 chr2 164428678 164428678 TCGA-YL-A8S9 INS 2 29 LRP1B * chr2 145258104 145258104 chr2 145265325 145265325 TCGA-YL-A8S9 DEL 29 38 TEX41 * chr3 158494525 158494525 chr3 158710646 158710646 TCGA-YL-A8S9 DEL 40 15 RSRC1 RARRES1 chr3 175298155 175298155 chr3 175982842 175982842 TCGA-YL-A8S9 INS 29 35 NAALADL2 * chr3 99765675 99765675 chr3 99801059 99801059 TCGA-YL-A8S9 DEL 33 42 COL8A1 * chr4 126649021 126649021 chr4 127396439 127396439 TCGA-YL-A8S9 DEL 45 34 * AC093772.1 chr4 173063115 173063115 chr4 174036936 174036936 TCGA-YL-A8S9 DEL 31 4 * * chr4 181290194 181290194 chr4 181381487 181381487 TCGA-YL-A8S9 DEL 35 42 * * chr4 41806063 41806063 chr4 42141844 42141844 TCGA-YL-A8S9 DEL 16 16 PHOX2B-AS1 BEND4 chr4 42169454 42169454 chr4 44077974 44077974 TCGA-YL-A8S9 INS 33 19 AC111006.1 * chr4 43358489 43358489 chr4 43396960 43396960 TCGA-YL-A8S9 DEL 23 37 * * chr5 164583083 164583083 chr5 165965021 165965021 TCGA-YL-A8S9 INS 1 27 AC109466.1 * chr5 45803395 45803395 chr5 85746168 85746168 TCGA-YL-A8S9 INS 29 38 * * chr6 100187713 100187713 chr6 126451819 126451819 TCGA-YL-A8S9 DEL 18 29 * * chr6 122866885 122866885 chr6 122869382 122869382 TCGA-YL-A8S9 DEL 6 5 * * chr10 124735798 124735798 chr10 125001412 125001412 TCGA-FC-A4JI DUP 2 9 FAM53B CTBP2 chr10 124749453 124749454 chr10 125684983 125684990 TCGA-FC-A4JI INV 38 37 AC068896.1 AL158835.1 chr10 133427616 133427616 chr10 133571973 133571973 TCGA-FC-A4JI DEL 2 50 * * chr10 46443070 46443070 chr10 62139777 62139777 TCGA-FC-A4JI DUP 46 6 AC244230.2 * chr10 56742787 56742787 chr14 47444905 47444905 TCGA-FC-A4JI BND 28 10 * MDGA2 chr10 87858924 87858924 chr10 128267116 128267116 TCGA-FC-A4JI INV 17 28 * LINC01163 chr10 89213704 89213704 chr10 132775125 132775125 TCGA-FC-A4JI INV 45 38 LIPA INPP5A chr11 100703179 100703179 chr11 100712785 100712785 TCGA-FC-A4JI DEL 11 31 ARHGAP42 ARHGAP42 chr11 101963249 101963249 chr11 132976133 132976133 TCGA-FC-A4JI DEL 43 49 CEP126 OPCML chr11 109350951 109350952 chr9 12118452 12118453 TCGA-FC-A4JI BND 11 16 * AL589678.1 chr11 47534999 47534999 chr11 47797196 47797196 TCGA-FC-A4JI INV 15 2 CELF1 NUP160 chr11 54910368 54910368 chr12 109955814 109955814 TCGA-FC-A4JI BND 12 20 * TCHP chr11 59418304 59418304 chr11 59522150 59522150 TCGA-FC-A4JI INS 3 12 OR5A2 * chr11 69969261 69969261 chr11 69992565 69992565 TCGA-FC-A4JI DEL 18 15 * AP003555.2 chr11 92201947 92201947 chr11 92202579 92202579 TCGA-FC-A4JI DEL 37 39 * * chr12 11068767 11068767 chr12 11098150 11098166 TCGA-FC-A4JI DEL 1 23 PRH1 PRH1 chr12 15412024 15412024 chr12 79499030 79499032 TCGA-FC-A4JI DEL 34 31 PTPRO AC027288.3 chr12 16961488 16961488 chr12 83784443 83784443 TCGA-FC-A4JI DEL 31 21 * * chr12 16966143 16966146 chr1 170394695 170394698 TCGA-FC-A4JI BND 20 48 * * chr12 17028535 17028535 chr12 83978064 83978064 TCGA-FC-A4JI INS 21 14 * * chr12 18725914 18725914 chr11 108243518 108243518 TCGA-FC-A4JI BND 7 46 PLCZ1 ATM chr12 21149708 21149708 chr12 79809828 79809828 TCGA-FC-A4JI INS 14 43 SLCO1B1 PPP1R12A chr12 39192095 39192095 chr3 79489482 79489482 TCGA-FC-A4JI BND 17 35 * ROBO1 chr12 39198923 39198923 chr12 41175872 41175872 TCGA-FC-A4JI INS 35 17 * * chr12 39210041 39210041 chr12 39693646 39693646 TCGA-FC-A4JI DEL 29 31 * C12orf40 chr12 39218519 39218519 chr12 39241740 39241740 TCGA-FC-A4JI DEL 44 29 * * chr12 39680574 39680574 chr3 82419646 82419646 TCGA-FC-A4JI BND 44 47 C12orf40 LINC02008 chr12 45716839 45716839 chr12 45735804 45735804 TCGA-FC-A4JI DEL 13 7 * ARID2 chr12 72874879 72874879 chr3 79470641 79470641 TCGA-FC-A4JI BND 21 7 * ROBO1 chr12 72874879 72874879 chr4 5818091 5818091 TCGA-FC-A4JI BND 17 18 * CRMP1 chr12 73561034 73561034 chr12 73720925 73720925 TCGA-FC-A4JI DEL 20 11 * * chr12 78867535 78867535 chr12 114646969 114646969 TCGA-FC-A4JI DUP 13 24 SYT1 * chr12 80431613 80431613 chr12 81702705 81702705 TCGA-FC-A4JI DEL 29 3 PTPRQ PPFIA2 chr12 81661465 81661465 chr12 86902995 86902995 TCGA-FC-A4JI INV 16 34 PPFIA2 * chr12 84104726 84104726 chr12 85501025 85501025 TCGA-FC-A4JI DEL 11 3 * * chr12 86541323 86541323 chr12 87125397 87125397 TCGA-FC-A4JI DUP 10 35 MGAT4C * chr13 101809087 101809087 chr13 107805719 107805719 TCGA-FC-A4JI INV 15 45 FGF14 FAM155A chr13 107079354 107079354 chr13 108035180 108035180 TCGA-FC-A4JI DEL 39 27 * * chr13 107135744 107135744 chr13 108506510 108506510 TCGA-FC-A4JI INS 24 36 * * chr13 37209583 37209583 chr11 93428404 93428404 TCGA-FC-A4JI BND 44 12 * DEUP1 chr13 47689032 47689032 chr13 58571342 58571342 TCGA-FC-A4JI DEL 23 34 * * chr13 48359253 48359253 chr8 71811058 71811058 TCGA-FC-A4JI BND 33 30 RB1 * chr13 58878962 58878962 chr13 95978675 95978675 TCGA-FC-A4JI DUP 30 19 * UGGT2 chr13 59201184 59201184 chr13 59771826 59771826 TCGA-FC-A4JI INS 38 20 * DIAPH3 chr13 59771569 59771569 chr2 208143720 208143720 TCGA-FC-A4JI BND 7 26 DIAPH3 CRYGB chr13 88046342 88046342 chr13 88052502 88052502 TCGA-FC-A4JI DEL 30 35 * * chr14 105568937 105568981 chr14 105683362 105683362 TCGA-FC-A4JI INV 18 46 * * chr14 105568937 105568981 chr14 105689282 105689282 TCGA-FC-A4JI DUP 17 50 * * chr14 105569062 105569062 chr14 105687611 105687611 TCGA-FC-A4JI INV 49 31 * * chr14 105569118 105569144 chr14 105691425 105691425 TCGA-FC-A4JI DUP 12 11 * * chr14 105569217 105569223 chr14 105690357 105690357 TCGA-FC-A4JI DUP 46 20 * * chr14 105569370 105569370 chr14 105683117 105683117 TCGA-FC-A4JI INV 27 18 * * chr14 105569607 105569622 chr14 105689632 105689637 TCGA-FC-A4JI DEL 44 8 * * chr14 37713692 37713692 chr14 38872439 38872439 TCGA-FC-A4JI INS 45 39 TTC6 LINC00639 chr14 45214998 45214998 chr14 45489106 45489106 TCGA-FC-A4JI INS 15 25 MIS18BP1 * chr14 88344599 88344599 chr14 88463501 88463501 TCGA-FC-A4JI DEL 38 15 * SPATA7 chr14 89361629 89361629 chr14 99927921 99927921 TCGA-FC-A4JI INV 23 13 FOXN3 EML1 chr14 92952868 92952868 chr14 93908293 93908293 TCGA-FC-A4JI INV 25 14 ITPK1 FAM181A-AS1 chr15 38047247 38047247 chr15 57247789 57247789 TCGA-FC-A4JI DEL 48 27 LINC02345 TCF12 chr15 45515692 45515692 chr7 13938878 13938878 TCGA-FC-A4JI BND 9 45 SLC30A4 ETV1 chr15 50588449 50588449 chr17 17212794 17212794 TCGA-FC-A4JI BND 49 3 TRPM7 MPRIP chr15 55161295 55161295 chr15 94739692 94739692 TCGA-FC-A4JI DEL 47 45 * * chr15 97160368 97160368 chr15 97160610 97160610 TCGA-FC-A4JI INS 36 46 * * chr15 97161957 97161957 chr15 97162543 97162543 TCGA-FC-A4JI INS 4 41 * * chr16 27139030 27139030 chr16 87221707 87221707 TCGA-FC-A4JI INV 9 4 * C16orf95 chr16 32317727 32317739 chr20 53862646 53862664 TCGA-FC-A4JI BND 31 43 * * chr16 72526205 72526205 chr16 73174079 73174079 TCGA-FC-A4JI DEL 13 36 LINC01572 ZFHX3 chr16 86419194 86419200 chrX 3524602 3524602 TCGA-FC-A4JI BND 40 41 * * chr17 16051561 16051561 chr17 16580233 16580233 TCGA-FC-A4JI DEL 24 11 NCOR1 * chr17 17035071 17035071 chr21 34661134 34661134 TCGA-FC-A4JI BND 27 21 * * chr17 21412184 21412184 chr17 21661751 21661751 TCGA-FC-A4JI INV 6 25 KCNJ12 * chr17 21626938 21626938 chr17 21655166 21655166 TCGA-FC-A4JI INV 35 41 AC233702.1 * chr17 37678362 37678362 chr17 37678414 37678414 TCGA-FC-A4JI DEL 44 49 AC243571.2 AC243571.2 chr17 41849053 41849053 chr17 44512421 44512421 TCGA-FC-A4JI DEL 46 9 AC125257.1 * chr17 54934808 54934808 chr17 54934907 54934907 TCGA-FC-A4JI DEL 31 35 TOM1L1 TOM1L1 chr17 6066158 6066158 chr17 8057946 8057946 TCGA-FC-A4JI DEL 26 28 WSCD1 AC129492.2 chr17 71284066 71284066 chr22 47810085 47810098 TCGA-FC-A4JI BND 5 32 * AL117329.1 chr17 72747715 72747715 chr17 73174871 73174871 TCGA-FC-A4JI DEL 26 15 SLC39A11 SSTR2 chr17 7684646 7684648 chr17 8124905 8124905 TCGA-FC-A4JI DEL 2 48 TP53 HES7 chr17 8121580 8121580 chr17 8172644 8172644 TCGA-FC-A4JI INV 29 17 HES7 * chr18 13908078 13908078 chr18 14012588 14012588 TCGA-FC-A4JI INV 13 13 MC2R * chr18 33270507 33270507 chr18 33284631 33284631 TCGA-FC-A4JI DUP 49 28 CCDC178 CCDC178 chr19 20654307 20654307 chr19 20688449 20688449 TCGA-FC-A4JI DEL 50 49 AC010636.2 AC010329.5 chr19 42241509 42241509 chr19 42347146 42347146 TCGA-FC-A4JI DEL 50 22 GSK3A MEGF8 chr19 55530440 55530440 chr19 55530777 55530777 TCGA-FC-A4JI DEL 45 12 SBK2 SBK2 chr19 5638095 5638095 chr19 5841889 5841889 TCGA-FC-A4JI DUP 17 18 SAFB * chr19 5674488 5674488 chr19 9504611 9504611 TCGA-FC-A4JI INV 17 24 RPL36 AC008567.2 chr1 115658518 115658518 chr4 153380084 153380084 TCGA-FC-A4JI BND 45 14 VANGL1 MND1 chr1 121364324 121364324 chr1 145023098 145023098 TCGA-FC-A4JI DUP 11 11 SRGAP2C SRGAP2B chr1 143497378 143497378 chr1 143539523 143539523 TCGA-FC-A4JI INV 44 2 AC239859.4 * chr1 145454745 145454745 chr9 137891295 137891295 TCGA-FC-A4JI BND 13 38 * CACNA1B chr1 159420482 159420482 chr8 75851217 75851217 TCGA-FC-A4JI BND 38 22 AL513323.1 * chr1 16562524 16562524 chr11 85483986 85483986 TCGA-FC-A4JI BND 40 27 NBPF1 DLG2 chr1 205637721 205637721 chr1 205651318 205651318 TCGA-FC-A4JI DEL 25 27 * * chr1 233729393 233729393 chr1 233729725 233729725 TCGA-FC-A4JI DEL 2 38 * * chr1 237511635 237511635 chr1 237515504 237515504 TCGA-FC-A4JI DEL 23 14 RYR2 RYR2 chr1 32788366 32788366 chr17 16110642 16110642 TCGA-FC-A4JI BND 15 47 YARS1 NCOR1 chr1 32791121 32791121 chr17 5062689 5062689 TCGA-FC-A4JI BND 49 25 YARS1 * chr1 45314954 45314954 chr6 22643082 22643082 TCGA-FC-A4JI BND 19 13 * * chr1 8322339 8322339 chr4 7695516 7695535 TCGA-FC-A4JI BND 3 50 SLC45A1 SORCS2 chr1 9135578 9135578 chr1 64046797 64046797 TCGA-FC-A4JI DEL 22 4 * ROR1 chr1 95050705 95050705 chr1 96056007 96056007 TCGA-FC-A4JI INV 8 15 ALG14 * chr1 95052066 95052066 chr1 97397380 97397380 TCGA-FC-A4JI DUP 36 25 ALG14 DPYD chr1 95060098 95060098 chr1 96054397 96054397 TCGA-FC-A4JI DEL 21 28 ALG14 * chr1 95061566 95061566 chr1 98625539 98625539 TCGA-FC-A4JI INV 31 7 ALG14 * chr1 95741520 95741520 chr1 97336784 97336784 TCGA-FC-A4JI DEL 48 32 LINC02607 DPYD chr1 96092988 96092988 chr1 98599726 98599726 TCGA-FC-A4JI DEL 32 21 * * chr1 96093285 96093285 chr13 107795291 107795291 TCGA-FC-A4JI BND 24 7 * FAM155A chr1 98599530 98599530 chr13 107804949 107804950 TCGA-FC-A4JI BND 34 3 * FAM155A chr20 13486971 13486971 chr20 14373130 14373130 TCGA-FC-A4JI INS 45 40 TASP1 MACROD2 chr20 25783302 25783302 chr20 25845168 25845168 TCGA-FC-A4JI DEL 50 32 FAM182B FAM182B chr20 30274391 30274391 chr20 30318892 30318892 TCGA-FC-A4JI DEL 33 33 * * chr21 10427019 10427019 chr21 31784913 31784938 TCGA-FC-A4JI DUP 21 37 BAGE2 * chr21 10427747 10427747 chr21 31784744 31784750 TCGA-FC-A4JI INV 16 30 BAGE2 * chr21 31784913 31784938 chr21 43335990 43335990 TCGA-FC-A4JI DEL 15 41 * * chr21 33269576 33269576 chr21 38500665 38500665 TCGA-FC-A4JI DEL 20 35 AP000295.1 ERG chr21 36141538 36141538 chr21 41500082 41500082 TCGA-FC-A4JI DUP 44 27 CBR3-AS1 TMPRSS2 chr21 38458711 38458711 chr21 41503112 41503112 TCGA-FC-A4JI DEL 48 23 ERG TMPRSS2 chr21 38510013 38510013 chr21 41495245 41495245 TCGA-FC-A4JI DEL 32 2 ERG TMPRSS2 chr21 41806066 41806066 chr21 43336765 43336765 TCGA-FC-A4JI DUP 20 26 PRDM15 * chr22 18429829 18429829 chr22 20346918 20346918 TCGA-FC-A4JI DEL 26 36 FAM230A FAM230G chr22 19649102 19649102 chr7 126465366 126465366 TCGA-FC-A4JI BND 18 48 * GRM8 chr22 22830654 22830654 chr22 36455248 36455248 TCGA-FC-A4JI INV 25 18 * AL022313.2 chr22 26724849 26724850 chr9 73568370 73568371 TCGA-FC-A4JI BND 7 29 MIATNB * chr22 26724963 26724963 chr9 104846274 104846274 TCGA-FC-A4JI BND 50 21 MIATNB ABCA1 chr22 38409156 38409156 chr22 47418840 47418841 TCGA-FC-A4JI DEL 49 8 * * chr22 42039647 42039647 chr22 45254727 45254727 TCGA-FC-A4JI DEL 26 19 WBP2NL * chr2 121494742 121494742 chr2 121710836 121710836 TCGA-FC-A4JI INS 23 16 CLASP1 NIFK-AS1 chr2 128341047 128341047 chr21 10426485 10426485 TCGA-FC-A4JI BND 37 26 * BAGE2 chr2 1388078 1388078 chr2 1427981 1427981 TCGA-FC-A4JI DUP 26 15 TPO TPO chr2 154293159 154293159 chr2 182373853 182373853 TCGA-FC-A4JI DEL 23 40 GALNT13 PDE1A chr2 165472771 165472771 chrX 74420899 74420899 TCGA-FC-A4JI BND 24 6 CSRNP3 SLC16A2 chr2 241990267 241990267 chr22 49477248 49477248 TCGA-FC-A4JI BND 36 47 LINC01237 C22orf34 chr2 25722408 25722408 chr2 25969773 25969773 TCGA-FC-A4JI DEL 19 43 * KIF3C chr2 37321641 37321641 chr2 37990416 37990416 TCGA-FC-A4JI DEL 49 36 PRKD3 RMDN2 chr2 37895140 37895140 chr2 37896760 37896760 TCGA-FC-A4JI DEL 30 45 * * chr2 39381340 39381340 chr10 87883413 87883413 TCGA-FC-A4JI BND 7 33 MAP4K3 PTEN chr2 75677822 75677825 chr4 159418029 159418030 TCGA-FC-A4JI BND 16 38 MRPL19 * chr2 77895400 77895400 chr8 110768926 110768926 TCGA-FC-A4JI BND 24 25 * AP005357.1 chr2 77896961 77896961 chr8 110777331 110777331 TCGA-FC-A4JI BND 28 8 * * chr3 101333868 101333869 chr3 112806097 112806098 TCGA-FC-A4JI INV 24 19 SENP7 CD200R1L-AS1 chr3 12561662 12561662 chr3 12561923 12561923 TCGA-FC-A4JI INS 35 40 MKRN2 MKRN2 chr3 157707921 157707921 chr3 191691129 191691129 TCGA-FC-A4JI DUP 2 41 * * chr3 162401438 162401438 chr3 162428270 162428270 TCGA-FC-A4JI DEL 20 1 * * chr3 184313456 184313456 chr3 184877629 184877629 TCGA-FC-A4JI DEL 8 41 EIF4G1 VPS8 chr3 22277115 22277115 chr3 22284948 22284948 TCGA-FC-A4JI INV 28 7 ZNF385D ZNF385D chr3 47057516 47057516 chr3 47383303 47383303 TCGA-FC-A4JI DEL 38 44 SETD2 PTPN23 chr3 69254886 69254886 chr3 73453768 73453768 TCGA-FC-A4JI DEL 38 26 FRMD4B PDZRN3 chr3 69256065 69256065 chr3 73495770 73495770 TCGA-FC-A4JI INV 2 4 FRMD4B PDZRN3 chr3 82817135 82817135 chr3 82820626 82820626 TCGA-FC-A4JI DEL 30 20 * * chr3 83749614 83749617 chrX 129504286 129504289 TCGA-FC-A4JI BND 42 7 * SMARCA1 chr3 86977612 86977612 chr3 88107858 88107858 TCGA-FC-A4JI DEL 7 25 VGLL3 CGGBP1 chr4 101328309 101328322 chr4 112737103 112737103 TCGA-FC-A4JI INV 21 15 PPP3CA * chr4 111101573 111101573 chr4 111103935 111103935 TCGA-FC-A4JI DEL 21 20 * * chr4 112963750 112963750 chr20 55438994 55438994 TCGA-FC-A4JI BND 34 13 ANK2 LINC01440 chr4 117082533 117082533 chrX 67652287 67652287 TCGA-FC-A4JI BND 43 25 * AR chr4 117197382 117197382 chrX 66706647 66706647 TCGA-FC-A4JI BND 43 16 * * chr4 123265317 123265317 chr4 123288475 123288475 TCGA-FC-A4JI DEL 24 16 SPATA5 SPATA5 chr4 123377215 123377215 chrX 64987911 64987911 TCGA-FC-A4JI BND 30 8 * ZC4H2 chr4 126311442 126311442 chr4 126370249 126370249 TCGA-FC-A4JI DEL 19 3 * * chr4 130322960 130322960 chr4 132928066 132928066 TCGA-FC-A4JI DEL 38 29 * AC115622.1 chr4 134504136 134504136 chr4 134505755 134505755 TCGA-FC-A4JI DEL 24 42 * * chr4 143133038 143133038 chr4 143133516 143133516 TCGA-FC-A4JI DEL 31 21 AC104596.1 AC104596.1 chr4 144665729 144665729 chr4 144666774 144666774 TCGA-FC-A4JI DEL 27 10 AC098588.3 AC098588.3 chr4 151029136 151029136 chr4 151421500 151421500 TCGA-FC-A4JI DUP 30 21 * FAM160A1 chr4 161980927 161980927 chr4 161981240 161981240 TCGA-FC-A4JI DEL 39 31 FSTL5 FSTL5 chr4 162802243 162802243 chr4 162802391 162802391 TCGA-FC-A4JI DEL 48 23 * * chr4 16720629 16720629 chr4 17262058 17262058 TCGA-FC-A4JI DEL 43 25 LDB2 * chr4 172193695 172193695 chr4 172196457 172196457 TCGA-FC-A4JI DEL 29 22 GALNTL6 GALNTL6 chr4 189691960 189691960 chr4 189734895 189734895 TCGA-FC-A4JI INV 7 8 * * chr4 19832107 19832107 chr4 19832455 19832455 TCGA-FC-A4JI DEL 24 35 AC024230.1 AC024230.1 chr4 4107300 4107300 chr4 4157521 4157521 TCGA-FC-A4JI DEL 50 16 AC116562.3 OR7E99P chr4 49486987 49486987 chr4 49568656 49568656 TCGA-FC-A4JI INV 10 2 AC119751.3 * chr4 60602105 60602105 chr4 112737138 112737138 TCGA-FC-A4JI INV 10 41 * * chr4 63388220 63388220 chr4 113389845 113389845 TCGA-FC-A4JI DUP 19 40 * * chr4 63673737 63673737 chr4 63701338 63701338 TCGA-FC-A4JI DEL 36 17 * * chr4 65478502 65478502 chr4 116608231 116608231 TCGA-FC-A4JI INV 24 46 EPHA5 * chr4 65494132 65494132 chr4 122132274 122132274 TCGA-FC-A4JI DUP 28 5 EPHA5 * chr4 66972696 66972696 chr4 66972729 66972729 TCGA-FC-A4JI INV 41 34 * * chr4 67309959 67309959 chr4 67321365 67321365 TCGA-FC-A4JI INV 20 3 * * chr4 68826 68826 chr4 190106089 190106089 TCGA-FC-A4JI DEL 37 34 ZNF595 * chr4 69191608 69191608 chr7 136292544 136292544 TCGA-FC-A4JI BND 48 14 AC111000.4 AC078845.1 chr4 69261283 69261283 chr7 136228891 136228891 TCGA-FC-A4JI BND 4 44 * AC078845.1 chr4 72914766 72914766 chr4 113319943 113319943 TCGA-FC-A4JI INV 23 18 * ANK2 chr4 72978201 72978201 chr4 116945758 116945758 TCGA-FC-A4JI INV 12 5 * * chr4 74281763 74281763 chr4 74282064 74282064 TCGA-FC-A4JI INV 20 34 MTHFD2L MTHFD2L chr4 74480796 74480796 chr4 74480863 74480863 TCGA-FC-A4JI INV 44 42 * * chr4 74818647 74818647 chr4 116638006 116638006 TCGA-FC-A4JI INV 25 50 * * chr4 76959069 76959069 chr7 136119439 136119439 TCGA-FC-A4JI BND 43 45 SEPTIN11 AC078845.1 chr4 81504136 81504141 chr12 2720921 2720921 TCGA-FC-A4JI BND 21 13 RASGEF1B ITFG2-AS1 chr4 91604661 91604661 chr4 91604877 91604877 TCGA-FC-A4JI DEL 27 40 AC110774.1 AC110774.1 chr4 93153289 93153289 chr4 93260657 93260657 TCGA-FC-A4JI DEL 19 11 GRID2 GRID2 chr5 100878011 100878011 chr5 100888964 100888964 TCGA-FC-A4JI DEL 7 14 ST8SIA4 ST8SIA4 chr5 103434110 103434110 chr6 73955543 73955543 TCGA-FC-A4JI BND 40 40 PDZPH1P * chr5 161977547 161977547 chr5 162165306 162165306 TCGA-FC-A4JI DEL 7 22 LINC01202 * chr5 178358350 178358363 chr5 180670565 180670565 TCGA-FC-A4JI DUP 14 13 COL23A1 * chr5 178358350 178358363 chr5 180670243 180670243 TCGA-FC-A4JI DEL 16 34 COL23A1 * chr5 27139707 27139707 chr5 27140551 27140551 TCGA-FC-A4JI DEL 28 25 * * chr5 41283539 41283539 chr5 41541479 41541479 TCGA-FC-A4JI DEL 41 4 * * chr5 41691203 41691204 chr5 42875573 42875573 TCGA-FC-A4JI DEL 25 33 * SELENOP chr5 53097305 53097305 chr5 61590333 61590333 TCGA-FC-A4JI DEL 12 11 MOCS2 * chr5 55797342 55797342 chr6 45802455 45802455 TCGA-FC-A4JI BND 23 3 DDX4 * chr5 55801435 55801435 chr6 48886852 48886852 TCGA-FC-A4JI BND 3 40 DDX4 * chr5 58026529 58026529 chr5 58038009 58038009 TCGA-FC-A4JI DEL 38 17 * * chr5 64435139 64435139 chr3 15774864 15774864 TCGA-FC-A4JI BND 9 40 AC091862.1 ANKRD28 chr5 99914045 99914045 chr5 100139139 100139139 TCGA-FC-A4JI DEL 38 19 * * chr6 101295938 101295938 chr6 101301514 101301514 TCGA-FC-A4JI DEL 40 6 GRIK2 GRIK2 chr6 10437574 10437574 chr6 129405821 129405821 TCGA-FC-A4JI INV 2 26 MIR5689HG LAMA2 chr6 142394008 142394008 chr6 143431638 143431638 TCGA-FC-A4JI DEL 30 27 ADGRG6 ADAT2 chr6 160456919 160456919 chr6 160535406 160535406 TCGA-FC-A4JI DEL 41 50 LPAL2 LPA chr6 22610645 22610646 chr1 45314842 45314843 TCGA-FC-A4JI BND 15 34 * * chr6 382463 382464 chr16 33625820 33625820 TCGA-FC-A4JI BND 27 24 * * chr6 76236277 76236277 chr6 77412667 77412667 TCGA-FC-A4JI DEL 7 38 * * chr6 76240337 76240337 chr6 78627339 78627339 TCGA-FC-A4JI DUP 28 20 * * chr6 76245069 76245069 chr13 65568743 65568743 TCGA-FC-A4JI BND 12 29 * * chr6 77483671 77483671 chr6 77500138 77500138 TCGA-FC-A4JI INV 39 17 * * chr6 77517076 77517076 chr6 78422149 78422149 TCGA-FC-A4JI INV 27 49 * * chr6 9371641 9371641 chr14 92782266 92782266 TCGA-FC-A4JI BND 24 9 * * chr6 9571261 9571262 chr6 127742034 127742035 TCGA-FC-A4JI INV 39 44 * THEMIS chr7 101309979 101309979 chr19 1594870 1594870 TCGA-FC-A4JI BND 47 21 EMSLR AC005943.1 chr7 101531406 101531406 chr19 1397909 1397909 TCGA-FC-A4JI BND 41 4 COL26A1 GAMT chr7 120487674 120487674 chr10 62936910 62936910 TCGA-FC-A4JI BND 12 14 KCND2 * chr7 126311446 126311446 chr7 127421355 127421355 TCGA-FC-A4JI DEL 27 21 * ZNF800 chr7 134087820 134087820 chrX 67889878 67889878 TCGA-FC-A4JI BND 34 31 * * chr7 135980540 135980540 chr7 135980801 135980801 TCGA-FC-A4JI INV 47 21 * * chr7 136952306 136952306 chr7 136971001 136971001 TCGA-FC-A4JI INV 3 39 AC009264.1 AC009264.1 chr7 141337198 141337198 chr11 36309762 36309762 TCGA-FC-A4JI BND 6 17 TMEM178B PRR5L chr7 146133430 146133430 chr7 146234491 146234491 TCGA-FC-A4JI DUP 40 49 CNTNAP2 CNTNAP2 chr7 150003969 150003969 chr7 154093383 154093383 TCGA-FC-A4JI DEL 45 28 AC092681.2 DPP6 chr7 19605393 19605393 chr7 53681988 53681988 TCGA-FC-A4JI INV 47 50 * LINC01446 chr7 26193696 26193696 chr7 26195848 26195848 TCGA-FC-A4JI DEL 6 13 HNRNPA2B1 HNRNPA2B1 chr7 34572500 34572500 chr7 34573843 34573843 TCGA-FC-A4JI DEL 22 8 NPSR1-AS1 NPSR1-AS1 chr7 39015205 39015205 chr7 39227125 39227125 TCGA-FC-A4JI DEL 48 21 POU6F2 POU6F2 chr7 39492363 39492363 chr7 144586207 144586207 TCGA-FC-A4JI INV 16 8 POU6F2 TPK1 chr7 44292449 44292449 chr8 77121622 77121622 TCGA-FC-A4JI BND 8 24 CAMK2B * chr7 54340429 54340429 chr7 134900456 134900456 TCGA-FC-A4JI DEL 19 17 LINC01445 CALD1 chr7 66081906 66081906 chr7 149627082 149627083 TCGA-FC-A4JI INV 41 15 ASL * chr7 90190163 90190163 chr9 94809056 94809056 TCGA-FC-A4JI BND 49 38 STEAP2-AS1 AOPEP chr7 90342777 90342777 chr9 95072343 95072343 TCGA-FC-A4JI BND 45 35 GTPBP10 AOPEP chr8 100706997 100706997 chr8 100709133 100709133 TCGA-FC-A4JI DEL 44 47 PABPC1 PABPC1 chr8 133242282 133242282 chr8 133266373 133266373 TCGA-FC-A4JI DEL 46 28 NDRG1 NDRG1 chr8 138150972 138150972 chr8 138151140 138151140 TCGA-FC-A4JI DEL 18 38 FAM135B FAM135B chr8 140658170 140658170 chr16 50847548 50847548 TCGA-FC-A4JI BND 15 31 PTK2 LINC02128 chr8 16389506 16389506 chr8 25572869 25572869 TCGA-FC-A4JI DEL 21 31 MSR1 * chr8 19696368 19696368 chr8 24319737 24319737 TCGA-FC-A4JI DUP 22 42 CSGALNACT1 ADAM28 chr8 19696594 19696594 chr19 36220346 36220346 TCGA-FC-A4JI BND 9 46 CSGALNACT1 ZNF565 chr8 21444291 21444291 chr8 24323441 24323441 TCGA-FC-A4JI INV 16 45 * ADAM28 chr8 21446632 21446632 chr8 28105322 28105322 TCGA-FC-A4JI DEL 29 6 * ELP3 chr8 21446663 21446663 chr16 54346854 54346854 TCGA-FC-A4JI BND 5 28 * * chr8 24237498 24237498 chr8 67030519 67030519 TCGA-FC-A4JI INV 18 42 * PPP1R42 chr8 24342879 24342879 chr8 24405336 24405336 TCGA-FC-A4JI DEL 41 29 ADAM28 ADAMDEC1 chr8 24399411 24399411 chr8 67230148 67230148 TCGA-FC-A4JI DEL 6 23 ADAMDEC1 ARFGEF1 chr8 25033006 25033006 chr8 25034396 25034396 TCGA-FC-A4JI DEL 2 13 * * chr8 27779286 27779286 chr16 50847692 50847692 TCGA-FC-A4JI BND 3 2 ESCO2 LINC02128 chr8 28044127 28044127 chr16 54474609 54474609 TCGA-FC-A4JI BND 50 29 NUGGC * chr8 66810023 66810023 chr16 53340574 53340574 TCGA-FC-A4JI BND 46 17 SGK3 * chr8 67035764 67035764 chr8 67226172 67226172 TCGA-FC-A4JI DEL 39 16 PPP1R42 ARFGEF1 chr8 87312161 87312161 chr8 89434303 89434303 TCGA-FC-A4JI DEL 37 41 CNBD1 * chr9 104846274 104846274 chr22 26724963 26724963 TCGA-FC-A4JI BND 48 31 ABCA1 MIATNB chr9 104846303 104846303 chr9 113311792 113311792 TCGA-FC-A4JI INS 22 30 ABCA1 * chr9 106686676 106686676 chr9 106686762 106686762 TCGA-FC-A4JI INS 11 1 LINC01505 LINC01505 chr9 109010482 109010482 chr9 111776072 111776072 TCGA-FC-A4JI DEL 10 46 CTNNAL1 SHOC1 chr9 12118452 12118453 chr11 109350951 109350952 TCGA-FC-A4JI BND 37 35 AL589678.1 * chr9 27771270 27771270 chr9 29561368 29561377 TCGA-FC-A4JI INV 22 38 * * chr9 27771270 27771270 chr9 31314703 31314703 TCGA-FC-A4JI INV 31 8 * * chr9 28038086 28038086 chr9 32405651 32405651 TCGA-FC-A4JI DEL 6 23 LINGO2 ACO1 chr9 28038152 28038153 chr9 31688945 31688945 TCGA-FC-A4JI DEL 40 22 LINGO2 * chr9 29561368 29561377 chr9 31317861 31317861 TCGA-FC-A4JI DUP 28 10 * * chr9 31055117 31055117 chr9 33402213 33402213 TCGA-FC-A4JI INV 3 15 * AQP7 chr9 31128871 31128871 chr9 31155622 31155622 TCGA-FC-A4JI INV 6 13 * * chr9 31436599 31436600 chr9 37782706 37782707 TCGA-FC-A4JI INV 33 49 * AL138752.2 chr9 31690528 31690528 chr9 32405608 32405608 TCGA-FC-A4JI DEL 12 2 * ACO1 chr9 39077812 39077812 chr9 67289597 67289597 TCGA-FC-A4JI DUP 8 23 CNTNAP3 CNTNAP3P2 chr9 41747101 41747101 chr9 41754823 41754823 TCGA-FC-A4JI DEL 40 10 * * chr9 61533035 61533035 chr9 61992066 61992074 TCGA-FC-A4JI INV 12 10 * * chr9 61534512 61534520 chr9 61993869 61993869 TCGA-FC-A4JI INV 11 12 * * chr9 70057004 70057004 chr9 70584888 70584888 TCGA-FC-A4JI DEL 17 50 MAMDC2 TRPM3 chr9 71409665 71409665 chr9 72680523 72680523 TCGA-FC-A4JI INS 23 13 TRPM3 TMC1 chr9 71970823 71970823 chr9 112221931 112221931 TCGA-FC-A4JI DEL 9 22 C9orf85 PTBP3 chr9 71971921 71971921 chr9 109372751 109372751 TCGA-FC-A4JI INS 34 17 C9orf85 * chr9 72680638 72680638 chr9 112901996 112901996 TCGA-FC-A4JI INS 40 7 TMC1 * chr9 73246462 73246462 chr9 76758032 76758032 TCGA-FC-A4JI INV 29 33 * PRUNE2 chr9 73568242 73568242 chr9 112901870 112901870 TCGA-FC-A4JI DEL 38 13 * * chr9 73568370 73568371 chr22 26724849 26724850 TCGA-FC-A4JI BND 12 3 * MIATNB chrX 113957077 113957077 chrX 113957557 113957557 TCGA-FC-A4JI DEL 27 10 XACT XACT chrX 120875857 120875857 chrX 120986759 120986759 TCGA-FC-A4JI DEL 13 21 CT47B1 CT47A1 chrX 128519637 128519637 chr3 83521329 83521329 TCGA-FC-A4JI BND 19 30 AL008633.1 * chrX 129504286 129504289 chr3 83749614 83749617 TCGA-FC-A4JI BND 5 46 SMARCA1 * chrX 23810747 23810747 chrX 23811047 23811047 TCGA-FC-A4JI DEL 48 18 * * chrX 89327869 89327869 chrX 89330645 89330645 TCGA-FC-A4JI DEL 41 11 * * chr10 10544224 10544224 chr10 10616310 10616310 TCGA-KC-A7F3 DUP 30 2 * * chr10 110115140 110115157 chr4 104636528 104636531 TCGA-KC-A7F3 BND 11 44 ADD3 CXXC4-AS1 chr10 1369073 1369073 chr10 100981643 100981643 TCGA-KC-A7F3 INV 47 28 ADARB2 MRPL43 chr10 17932130 17932130 chr10 17933477 17933477 TCGA-KC-A7F3 INV 29 17 * * chr10 46525591 46525591 chr10 46527322 46527322 TCGA-KC-A7F3 INV 48 8 AC244230.2 AC244230.2 chr10 65547098 65547098 chr10 65555549 65555549 TCGA-KC-A7F3 INS 36 49 * * chr10 86466805 86466805 chr10 86663129 86663129 TCGA-KC-A7F3 INV 46 35 WAPL OPN4 chr10 86745997 86745997 chr10 87870236 87870236 TCGA-KC-A7F3 DEL 8 38 * PTEN chr10 974780 974780 chr10 1125887 1125887 TCGA-KC-A7F3 DUP 36 16 AL359878.1 WDR37 chr11 131687921 131687921 chr11 131888838 131888838 TCGA-KC-A7F3 DUP 32 49 NTM NTM chr11 15018529 15018529 chr11 15049023 15049023 TCGA-KC-A7F3 DUP 50 42 CALCB CALCB chr11 49714394 49714394 chr11 49728472 49728472 TCGA-KC-A7F3 INV 42 19 AC136759.1 AC136759.1 chr11 5406347 5406347 chr11 5437785 5437785 TCGA-KC-A7F3 DUP 30 8 HBG2 HBG2 chr11 57427762 57427762 chr11 57460572 57460572 TCGA-KC-A7F3 DUP 37 37 SLC43A3 RTN4RL2 chr11 87646100 87646100 chr22 36053442 36053442 TCGA-KC-A7F3 BND 22 30 * * chr12 110693451 110693451 chr12 111130457 111130457 TCGA-KC-A7F3 DUP 29 31 HVCN1 CUX2 chr12 124093169 124093169 chr12 132464298 132464308 TCGA-KC-A7F3 INV 28 31 RFLNA * chr12 124093438 124093438 chr12 131396423 131396423 TCGA-KC-A7F3 DUP 22 38 RFLNA * chr12 126281324 126281324 chr12 126317993 126317993 TCGA-KC-A7F3 DUP 47 36 AC007368.1 AC007368.1 chr12 99534793 99534793 chr12 99540486 99540486 TCGA-KC-A7F3 INV 37 15 ANKS1B ANKS1B chr13 60915619 60915619 chr13 68900258 68900258 TCGA-KC-A7F3 DUP 34 7 LINC01442 * chr13 64485808 64485808 chr13 64981916 64981916 TCGA-KC-A7F3 INV 20 4 * * chr13 64538103 64538103 chr13 65236474 65236474 TCGA-KC-A7F3 INV 34 29 * * chr13 66242788 66242788 chr13 66254318 66254318 TCGA-KC-A7F3 DEL 9 50 * * chr13 67533832 67533832 chr13 67533987 67533987 TCGA-KC-A7F3 INV 21 43 * * chr13 79934765 79934765 chr13 79968159 79968159 TCGA-KC-A7F3 DEL 50 48 * AL158064.1 chr13 94246886 94246886 chr13 94338427 94338427 TCGA-KC-A7F3 DEL 3 19 GPC6 GPC6 chr14 100664107 100664107 chr14 100665565 100665565 TCGA-KC-A7F3 INV 19 15 LINC00523 LINC00523 chr14 33667408 33667408 chr8 110142639 110142639 TCGA-KC-A7F3 BND 25 24 NPAS3 * chr14 40140576 40140576 chr14 40148777 40148777 TCGA-KC-A7F3 INS 14 48 * * chr14 94595693 94595693 chr14 94595827 94595827 TCGA-KC-A7F3 INV 23 49 AL049839.2 AL049839.2 chr14 97844576 97844576 chr14 97844809 97844809 TCGA-KC-A7F3 INV 13 9 * * chr14 99663754 99663754 chr14 99664076 99664076 TCGA-KC-A7F3 INV 14 2 HHIPL1 HHIPL1 chr15 20534416 20534416 chr15 28559938 28559938 TCGA-KC-A7F3 INV 6 31 GOLGA6L6 AC138749.1 chr15 20534774 20534774 chr15 22466055 22466055 TCGA-KC-A7F3 DUP 21 37 GOLGA6L6 GOLGA6L22 chr15 20534892 20534892 chr15 22466563 22466563 TCGA-KC-A7F3 DEL 45 15 GOLGA6L6 GOLGA6L22 chr15 20535448 20535448 chr15 28561333 28561336 TCGA-KC-A7F3 INV 25 11 GOLGA6L6 AC138749.1 chr15 70530251 70530251 chr15 70558885 70558885 TCGA-KC-A7F3 DUP 25 29 * * chr15 84522534 84522534 chr15 84632216 84632216 TCGA-KC-A7F3 DUP 3 42 AC048382.2 AC048382.5 chr16 29197262 29197262 chr16 88164607 88164607 TCGA-KC-A7F3 DUP 29 39 AC009093.8 * chr16 3720871 3720871 chr16 3721021 3721021 TCGA-KC-A7F3 INV 42 1 * * chr16 48450254 48450254 chr16 48600033 48600033 TCGA-KC-A7F3 DUP 22 33 * N4BP1 chr16 72583064 72583064 chr16 72690182 72690182 TCGA-KC-A7F3 DEL 34 6 LINC01572 AC004943.2 chr16 86587969 86587969 chr16 87210552 87210552 TCGA-KC-A7F3 INV 15 46 * C16orf95 chr16 86852081 86852081 chr17 17460380 17460380 TCGA-KC-A7F3 BND 16 45 * Y_RNA chr16 88193145 88193145 chrX 3524786 3524786 TCGA-KC-A7F3 BND 19 13 AC134312.6 * chr17 40282721 40282721 chr17 43538379 43538379 TCGA-KC-A7F3 DEL 20 16 WIPF2 DHX8 chr17 45449967 45449967 chr17 64796167 64796167 TCGA-KC-A7F3 DEL 30 22 PLEKHM1 PLEKHM1P1 chr17 63331250 63331250 chr17 63362033 63362033 TCGA-KC-A7F3 DUP 34 15 TANC2 TANC2 chr17 7673470 7673470 chr17 7677231 7677231 TCGA-KC-A7F3 DEL 8 12 TP53 TP53 chr18 35768310 35768310 chr18 35777738 35777738 TCGA-KC-A7F3 INS 18 46 * * chr18 41531284 41531284 chr18 41668160 41668161 TCGA-KC-A7F3 INV 32 47 KC6 * chr18 43847027 43847027 chr18 44210071 44210071 TCGA-KC-A7F3 DUP 19 19 * * chr19 51668350 51668350 chr19 51792550 51792550 TCGA-KC-A7F3 DUP 28 2 * FPR1 chr1 100537093 100537093 chr1 100568413 100568413 TCGA-KC-A7F3 DUP 43 41 GPR88 * chr1 121616382 121616382 chr1 121741488 121741488 TCGA-KC-A7F3 DEL 14 1 * * chr1 1227325 1227325 chr1 1227500 1227500 TCGA-KC-A7F3 DEL 22 29 SDF4 SDF4 chr1 152437999 152437999 chr1 152672748 152672748 TCGA-KC-A7F3 INV 14 5 FLG-AS1 * chr1 196618766 196618766 chr13 39017103 39017103 TCGA-KC-A7F3 BND 46 22 * PROSER1 chr1 203463046 203463046 chr1 203495361 203495361 TCGA-KC-A7F3 DUP 49 6 * OPTC chr1 205668322 205668322 chr21 38506305 38506305 TCGA-KC-A7F3 BND 16 20 SLC45A3 ERG chr1 210184828 210184828 chr13 47563823 47563823 TCGA-KC-A7F3 BND 44 36 * * chr1 210240045 210240045 chr13 38977635 38977635 TCGA-KC-A7F3 BND 10 31 SERTAD4 STOML3 chr1 243656787 243656787 chr1 244409820 244409820 TCGA-KC-A7F3 DUP 46 48 AKT3 AL645465.1 chr1 243787509 243787509 chr1 243933245 243933245 TCGA-KC-A7F3 DUP 23 25 AKT3 LINC02774 chr1 80920514 80920514 chr1 80953420 80953420 TCGA-KC-A7F3 DUP 33 31 * * chr20 14457875 14457875 chr20 15032880 15032880 TCGA-KC-A7F3 DEL 3 45 MACROD2 MACROD2 chr20 33585047 33585047 chr20 51975397 51975397 TCGA-KC-A7F3 INV 47 17 CBFA2T2 * chr20 36181094 36181094 chr20 36211510 36211510 TCGA-KC-A7F3 DUP 50 28 EPB41L1 EPB41L1 chr20 37304427 37304427 chr20 50523989 50523989 TCGA-KC-A7F3 INV 27 42 MANBAL PTPN1 chr20 683226 683226 chr20 713901 713901 TCGA-KC-A7F3 DUP 34 35 * * chr21 38506613 38506613 chr21 41502983 41502983 TCGA-KC-A7F3 DEL 30 18 ERG TMPRSS2 chr2 102460652 102460652 chr2 102494730 102494730 TCGA-KC-A7F3 DUP 28 37 * SLC9A4 chr2 123493949 123493949 chr2 126847384 126847384 TCGA-KC-A7F3 DUP 27 18 * * chr2 125685535 125685535 chr2 125694304 125694304 TCGA-KC-A7F3 INS 32 28 * * chr2 155671649 155671649 chr14 104514898 104514898 TCGA-KC-A7F3 BND 26 34 * TMEM179 chr2 167254692 167254692 chr2 167317580 167317580 TCGA-KC-A7F3 DEL 11 2 XIRP2 AC073050.1 chr2 167275691 167275691 chr2 167507713 167507713 TCGA-KC-A7F3 INV 9 42 * AC073050.1 chr2 187011921 187011921 chr18 41668160 41668161 TCGA-KC-A7F3 BND 44 5 AC007319.1 * chr2 187036776 187036776 chr18 41529594 41529594 TCGA-KC-A7F3 BND 36 21 AC007319.1 KC6 chr2 21369869 21369869 chr2 21371546 21371546 TCGA-KC-A7F3 INV 24 22 AC018742.1 AC018742.1 chr2 25741887 25741887 chr2 26154882 26154882 TCGA-KC-A7F3 DEL 14 10 ASXL2 * chr2 26655104 26655118 chr10 105091140 105091140 TCGA-KC-A7F3 BND 35 2 * SORCS3 chr2 49606037 49606037 chr2 49640654 49640654 TCGA-KC-A7F3 DUP 33 10 * * chr2 52323712 52323712 chr2 79522262 79522262 TCGA-KC-A7F3 INS 35 45 AC007402.1 CTNNA2 chr2 53337285 53337285 chr2 53344531 53344531 TCGA-KC-A7F3 DEL 42 14 * * chr2 78625933 78625933 chr2 79918638 79918638 TCGA-KC-A7F3 DEL 43 2 * CTNNA2 chr2 78934257 78934257 chr2 78934705 78934705 TCGA-KC-A7F3 DEL 22 25 * * chr3 129172654 129172654 chr3 129221265 129221265 TCGA-KC-A7F3 INV 25 30 CNBP * chr3 132335040 132335040 chr8 127726760 127726760 TCGA-KC-A7F3 BND 33 24 ACP3 CASC11 chr3 169486336 169486336 chr3 169523162 169523162 TCGA-KC-A7F3 DUP 34 31 MECOM MECOM chr3 198139557 198139557 chr7 76737 76737 TCGA-KC-A7F3 BND 37 48 * AC093627.1 chr3 79811168 79811168 chr18 6464319 6464319 TCGA-KC-A7F3 BND 8 11 * RPL6P27 chr4 103814134 103814134 chr5 123364560 123364560 TCGA-KC-A7F3 BND 18 48 * CEP120 chr4 104636528 104636531 chr10 110115140 110115157 TCGA-KC-A7F3 BND 13 26 CXXC4-AS1 ADD3 chr4 128792141 128792141 chr4 130656958 130656958 TCGA-KC-A7F3 DEL 1 24 * * chr4 130942380 130942380 chr4 130946027 130946027 TCGA-KC-A7F3 DEL 5 3 * * chr4 132512675 132512675 chr4 132522550 132522550 TCGA-KC-A7F3 DEL 38 31 * * chr4 144224147 144224147 chr4 144225118 144225118 TCGA-KC-A7F3 DEL 41 5 AC098588.3 AC098588.3 chr4 145998424 145998424 chr4 146006588 146006588 TCGA-KC-A7F3 INS 37 38 * * chr4 29803348 29803348 chr4 29807531 29807531 TCGA-KC-A7F3 DEL 47 3 * * chr4 38733695 38733695 chr19 8543637 8543637 TCGA-KC-A7F3 BND 6 21 * MYO1F chr4 43445688 43445688 chr4 43477269 43477269 TCGA-KC-A7F3 DUP 31 5 * LINC02383 chr4 49110724 49110724 chr4 49655930 49655930 TCGA-KC-A7F3 INV 25 17 * * chr4 7181840 7181840 chr14 99228979 99228979 TCGA-KC-A7F3 BND 37 42 * BCL11B chr4 95666596 95666596 chr7 6259922 6259922 TCGA-KC-A7F3 BND 24 11 * CYTH3 chr5 137671236 137671236 chr5 137705313 137705313 TCGA-KC-A7F3 DUP 8 12 KLHL3 KLHL3 chr5 23908936 23908936 chr5 23943681 23943681 TCGA-KC-A7F3 DUP 3 44 * * chr5 25606294 25606294 chr5 26324705 26324705 TCGA-KC-A7F3 DEL 16 9 * * chr5 2571825 2571825 chr5 2572218 2572218 TCGA-KC-A7F3 INV 23 38 * * chr5 26386047 26386047 chr13 80413050 80413050 TCGA-KC-A7F3 BND 22 20 AC025475.1 * chr5 28744099 28744099 chr13 80423611 80423611 TCGA-KC-A7F3 BND 4 22 * * chr5 34520127 34520127 chr5 36776844 36776844 TCGA-KC-A7F3 DUP 50 21 * * chr5 60520524 60520524 chr5 60522025 60522025 TCGA-KC-A7F3 DEL 4 30 PDE4D PDE4D chr5 98564384 98564384 chr11 93427151 93427151 TCGA-KC-A7F3 BND 46 4 * DEUP1 chr5 98837961 98837961 chr5 109236289 109236289 TCGA-KC-A7F3 DEL 12 28 * * chr6 102544339 102544339 chr6 102552706 102552706 TCGA-KC-A7F3 DEL 39 1 * * chr6 127534643 127534643 chr6 127551528 127551528 TCGA-KC-A7F3 DEL 21 13 C6orf58 C6orf58 chr6 128986347 128986347 chr6 129031049 129031049 TCGA-KC-A7F3 DUP 5 5 LAMA2 LAMA2 chr6 159665205 159665205 chr6 159667638 159667638 TCGA-KC-A7F3 DEL 11 26 * * chr6 1761828 1761828 chr6 1761989 1761989 TCGA-KC-A7F3 DEL 44 49 GMDS GMDS chr6 29864378 29864378 chr6 29907711 29907711 TCGA-KC-A7F3 DUP 13 9 AL645929.2 * chr6 32482938 32482982 chr6 32590581 32590598 TCGA-KC-A7F3 DUP 1 28 * HLA-DRB1 chr6 39735712 39735712 chr10 99790821 99790821 TCGA-KC-A7F3 BND 30 50 * ABCC2 chr6 44631574 44631574 chr6 56526332 56526332 TCGA-KC-A7F3 DUP 2 13 * DST chr6 49463304 49463304 chr6 49569180 49569180 TCGA-KC-A7F3 DUP 6 1 MMUT CYP2AC1P chr6 64876447 64876447 chr6 124573331 124573331 TCGA-KC-A7F3 DEL 1 31 EYS NKAIN2 chr6 68885464 68885464 chr6 71740881 71740881 TCGA-KC-A7F3 DEL 9 21 ADGRB3 * chr6 71853496 71853496 chr6 71855445 71855445 TCGA-KC-A7F3 DEL 42 27 * * chr7 105733500 105733500 chr13 99463067 99463067 TCGA-KC-A7F3 BND 45 17 ATXN7L1 TM9SF2 chr7 118158770 118158770 chr7 118158880 118158880 TCGA-KC-A7F3 DEL 42 19 * * chr7 122441218 122441218 chr18 6364745 6364745 TCGA-KC-A7F3 BND 6 7 CADPS2 L3MBTL4 chr7 122441380 122441380 chr7 152206182 152206182 TCGA-KC-A7F3 DEL 50 1 CADPS2 KMT2C chr7 152206124 152206124 chr6 142339473 142339473 TCGA-KC-A7F3 BND 13 21 KMT2C ADGRG6 chr7 66564041 66564041 chr7 66813990 66813990 TCGA-KC-A7F3 DUP 47 5 AC006001.3 GTF2IRD1P1 chr7 71004396 71004396 chr7 71061151 71061151 TCGA-KC-A7F3 DUP 41 23 * * chr7 99020709 99020709 chr7 99221457 99221469 TCGA-KC-A7F3 DEL 39 44 TRRAP * chr7 99020761 99020761 chrX 118181471 118181471 TCGA-KC-A7F3 BND 9 29 TRRAP * chr7 99221457 99221469 chr6 108530504 108530504 TCGA-KC-A7F3 BND 41 40 * * chr8 123557430 123557430 chr11 90693095 90693095 TCGA-KC-A7F3 BND 46 32 * DISC1FP1 chr8 13132324 13132324 chr8 35497285 35497285 TCGA-KC-A7F3 DEL 20 28 DLC1 UNC5D chr8 144378810 144378810 chr8 144379060 144379060 TCGA-KC-A7F3 INV 26 24 ADCK5 ADCK5 chr8 3740478 3740478 chr8 4059519 4059519 TCGA-KC-A7F3 DEL 19 38 CSMD1 CSMD1 chr8 47302007 47302007 chr8 47318552 47318552 TCGA-KC-A7F3 INV 29 33 SPIDR SPIDR chr8 72400521 72400521 chr8 72413460 72413460 TCGA-KC-A7F3 DEL 20 25 * * chr8 88962018 88962018 chr8 89037170 89037170 TCGA-KC-A7F3 INV 40 50 * * chr9 101952565 101952565 chr9 101962206 101962206 TCGA-KC-A7F3 INS 16 50 * * chr9 17461001 17461001 chr9 29188321 29188321 TCGA-KC-A7F3 DUP 41 32 CNTLN * chr9 61534862 61534862 chr9 61991898 61991898 TCGA-KC-A7F3 DEL 9 47 * * chr9 61970388 61970388 chr9 67619227 67619227 TCGA-KC-A7F3 INV 42 6 * * chr9 78196124 78196124 chr9 78333845 78333845 TCGA-KC-A7F3 DUP 24 7 * * chr9 87571597 87571597 chr18 37283865 37283865 TCGA-KC-A7F3 BND 2 42 DAPK1 CELF4 chrX 118180059 118180059 chr6 142377547 142377547 TCGA-KC-A7F3 BND 14 42 * ADGRG6 chrX 118181471 118181471 chr7 99020761 99020761 TCGA-KC-A7F3 BND 36 30 * TRRAP chrX 142454585 142454585 chrX 142471279 142471279 TCGA-KC-A7F3 DEL 40 9 * * chrX 27799093 27799093 chrX 28701470 28701470 TCGA-KC-A7F3 DUP 15 13 * IL1RAPL1 chrX 47174207 47174207 chrX 56252418 56252418 TCGA-KC-A7F3 INV 25 10 RBM10 KLF8 chrX 47181227 47181227 chrX 53039747 53039747 TCGA-KC-A7F3 DEL 38 4 RBM10 * chrX 48585929 48585929 chrX 53099288 53099288 TCGA-KC-A7F3 DUP 36 44 * KANTR chrX 48587544 48587544 chrX 58406225 58406225 TCGA-KC-A7F3 DEL 28 14 * * chrX 49997455 49997455 chrX 56253273 56253273 TCGA-KC-A7F3 DUP 33 38 CLCN5 KLF8 chrX 50058108 50058108 chrX 58406373 58406373 TCGA-KC-A7F3 INV 22 41 CLCN5 * chrX 50193705 50193705 chrX 50193741 50193741 TCGA-KC-A7F3 INV 19 14 AKAP4 AKAP4 chrX 508693 508693 chr10 87868175 87868175 TCGA-KC-A7F3 BND 27 4 * PTEN chrX 50888556 50888556 chrX 50888580 50888580 TCGA-KC-A7F3 INV 21 37 * * chrX 51232123 51232123 chrX 55919223 55919223 TCGA-KC-A7F3 INV 15 43 * AL050309.1 chrX 51579644 51579644 chrX 55319949 55319949 TCGA-KC-A7F3 INV 21 37 * * chrX 51917033 51917033 chrX 69005336 69005336 TCGA-KC-A7F3 INV 45 38 * * chrX 53171771 53171771 chrX 54257027 54257027 TCGA-KC-A7F3 DEL 7 46 * WNK3 chrX 54587531 54587531 chrX 55322098 55322098 TCGA-KC-A7F3 INV 29 16 * * chrX 55675947 55675947 chrX 55683539 55683539 TCGA-KC-A7F3 INS 6 24 * * chrX 56255149 56255149 chrX 63268083 63268083 TCGA-KC-A7F3 DUP 26 41 KLF8 * chrX 57940234 57940234 chrX 57940360 57940360 TCGA-KC-A7F3 INV 11 5 * * chrX 58362962 58362962 chrX 58372229 58372229 TCGA-KC-A7F3 INV 19 4 * * chrX 58363061 58363061 chrX 58371985 58371985 TCGA-KC-A7F3 INV 43 7 * * chrX 58363503 58363503 chrX 64978274 64978274 TCGA-KC-A7F3 DEL 35 44 * ZC4H2 chrX 64247891 64247891 chrX 64248388 64248388 TCGA-KC-A7F3 INV 11 29 * * chrX 64940059 64940059 chrX 66129373 66129373 TCGA-KC-A7F3 DEL 38 6 ZC4H2 * chrX 67714879 67714879 chrX 67714933 67714933 TCGA-KC-A7F3 INV 45 21 AR AR chr11 102311680 102311680 chr11 102316269 102316269 TCGA-EJ-7330 DEL 19 48 * BIRC3 chr11 49913473 49913473 chr2 17609120 17609120 TCGA-EJ-7330 BND 3 23 * VSNL1 chr11 88546360 88546360 chr11 104593583 104593583 TCGA-EJ-7330 INS 9 8 GRM5 LINC02552 chr12 97035895 97035895 chr12 97326103 97326103 TCGA-EJ-7330 DEL 21 32 AC007656.2 * chr13 28368554 28368554 chr13 66853248 66853248 TCGA-EJ-7330 DEL 13 7 FLT1 PCDH9 chr13 52985118 52985118 chr13 84047572 84047572 TCGA-EJ-7330 DEL 38 43 * * chr13 53528468 53528468 chr13 54519059 54519059 TCGA-EJ-7330 INS 26 5 * * chr13 53569286 53569286 chr13 56825457 56825457 TCGA-EJ-7330 DEL 23 44 * * chr13 54688080 54688080 chr13 83935951 83935951 TCGA-EJ-7330 INS 7 22 * * chr13 55610747 55610747 chr13 56583941 56583941 TCGA-EJ-7330 DEL 24 15 * * chr13 55611993 55611993 chr13 78756245 78756245 TCGA-EJ-7330 INS 24 40 * * chr13 56660280 56660280 chr13 78402765 78402765 TCGA-EJ-7330 DEL 10 36 * OBI1-AS1 chr13 56826309 56826309 chr2 207947079 207947079 TCGA-EJ-7330 BND 9 48 * PLEKHM3 chr13 57665730 57665730 chr13 60422830 60422830 TCGA-EJ-7330 INS 38 27 PCDH17 TDRD3 chr13 58669840 58669840 chr13 58724153 58724153 TCGA-EJ-7330 DEL 9 4 * * chr13 60223303 60223303 chr13 60263110 60263110 TCGA-EJ-7330 DEL 49 33 * * chr13 78408172 78408172 chr13 78882716 78882716 TCGA-EJ-7330 INS 6 7 OBI1-AS1 * chr13 81971536 81971536 chr13 81971731 81971731 TCGA-EJ-7330 DEL 45 12 * * chr13 84657108 84657108 chr4 43789256 43789256 TCGA-EJ-7330 BND 34 11 * * chr13 84782375 84782375 chr13 84783862 84783862 TCGA-EJ-7330 DEL 47 7 * * chr13 86329359 86329359 chr13 86620157 86620157 TCGA-EJ-7330 DEL 23 49 * * chr16 48412767 48412767 chr16 48425625 48425625 TCGA-EJ-7330 DEL 45 7 SIAH1 SIAH1 chr16 58759178 58759178 chr16 59252850 59252850 TCGA-EJ-7330 INS 32 33 AC106793.1 * chr18 33170562 33170562 chr18 33182635 33182635 TCGA-EJ-7330 DEL 30 24 CCDC178 CCDC178 chr18 50013373 50013373 chr18 74340026 74340026 TCGA-EJ-7330 DEL 13 1 MYO5B C18orf63 chr18 66866304 66866304 chr18 78828099 78828099 TCGA-EJ-7330 DEL 9 41 * * chr1 106029428 106029428 chr1 107278287 107278287 TCGA-EJ-7330 DEL 43 50 LINC01677 NTNG1 chr1 238624909 238624909 chr1 238629870 238629870 TCGA-EJ-7330 DEL 10 30 * * chr1 92045416 92045416 chr1 92047727 92047727 TCGA-EJ-7330 DEL 22 2 EPHX4 EPHX4 chr21 13233602 13233602 chr21 20020392 20020392 TCGA-EJ-7330 DEL 42 21 * * chr2 121713975 121713975 chr2 123953414 123953414 TCGA-EJ-7330 DEL 27 23 NIFK-AS1 * chr2 133088045 133088045 chr2 164375193 164375193 TCGA-EJ-7330 INS 18 20 NCKAP5 * chr2 146246762 146246762 chr2 146323259 146323259 TCGA-EJ-7330 DEL 1 10 * * chr2 166445674 166445674 chr2 166468899 166468899 TCGA-EJ-7330 DEL 31 44 SCN7A SCN7A chr2 182883756 182883756 chr2 184392881 184392881 TCGA-EJ-7330 DEL 21 28 * * chr2 19263582 19263582 chr2 31026492 31026492 TCGA-EJ-7330 INS 3 23 LINC01376 GALNT14 chr2 198140327 198140327 chr2 199003255 199003255 TCGA-EJ-7330 DEL 27 36 PLCL1 AC020718.1 chr2 20005657 20005657 chr2 21754670 21754670 TCGA-EJ-7330 DEL 8 44 MATN3 AC018742.1 chr2 207946783 207946783 chr13 83531138 83531138 TCGA-EJ-7330 BND 29 34 PLEKHM3 * chr2 32145757 32145757 chr2 38031910 38031910 TCGA-EJ-7330 DEL 31 3 SPAST RMDN2 chr2 32816151 32816151 chr2 32825176 32825176 TCGA-EJ-7330 DEL 47 8 TTC27 LINC00486 chr2 75980848 75980848 chr2 76027561 76027561 TCGA-EJ-7330 DEL 26 49 * * chr2 78632360 78632360 chr2 78662546 78662546 TCGA-EJ-7330 DEL 41 5 * * chr3 104041688 104041688 chr3 108625574 108625574 TCGA-EJ-7330 DEL 50 38 * DZIP3 chr3 104303289 104303289 chr3 112325768 112325768 TCGA-EJ-7330 INS 33 22 * AC112487.1 chr3 143198525 143198525 chr3 143209454 143209454 TCGA-EJ-7330 DEL 31 46 * * chr3 145023712 145023712 chr3 145182334 145182334 TCGA-EJ-7330 DEL 16 47 * * chr3 163973706 163973706 chr3 163987170 163987170 TCGA-EJ-7330 DEL 46 33 * * chr3 77542151 77542151 chr3 77553623 77553623 TCGA-EJ-7330 DEL 50 7 ROBO2 ROBO2 chr3 85212716 85212716 chr3 85574545 85574545 TCGA-EJ-7330 INS 28 20 CADM2 CADM2 chr3 95101038 95101038 chr3 95412800 95412800 TCGA-EJ-7330 INS 42 23 LINC00879 * chr4 10325338 10325338 chr4 12011237 12011237 TCGA-EJ-7330 INS 25 39 * * chr4 118226735 118226735 chr4 181601067 181601067 TCGA-EJ-7330 DEL 36 22 NDST3 * chr4 123688228 123688228 chr4 123688410 123688410 TCGA-EJ-7330 DEL 36 29 LINC01091 LINC01091 chr4 124603333 124603333 chr4 127844914 127844914 TCGA-EJ-7330 DEL 18 48 * AC093591.2 chr4 130941648 130941648 chr4 130949777 130949777 TCGA-EJ-7330 DEL 47 27 * * chr4 131102147 131102147 chr4 133226663 133226663 TCGA-EJ-7330 DEL 50 50 * * chr4 132362493 132362493 chr12 85443761 85443761 TCGA-EJ-7330 BND 3 18 * * chr4 132970477 132970477 chr4 133308440 133308440 TCGA-EJ-7330 DEL 48 48 AC115622.1 * chr4 135041586 135041586 chr4 135042865 135042865 TCGA-EJ-7330 DEL 33 4 * * chr4 136969326 136969326 chr4 182643228 182643228 TCGA-EJ-7330 INS 37 4 LINC02511 TENM3 chr4 137061480 137061480 chr4 137063093 137063093 TCGA-EJ-7330 DEL 7 48 LINC02511 LINC02511 chr4 163334727 163334727 chr4 163353767 163353767 TCGA-EJ-7330 DEL 23 21 NPY1R * chr4 164899098 164899098 chr4 166857385 166857385 TCGA-EJ-7330 INS 50 35 * SPOCK3 chr4 165796337 165796337 chr4 167568241 167568241 TCGA-EJ-7330 INS 50 23 * * chr4 172083782 172083782 chr4 172091462 172091462 TCGA-EJ-7330 DEL 34 9 GALNTL6 GALNTL6 chr4 175044900 175044900 chr4 175888103 175888103 TCGA-EJ-7330 DEL 4 25 * GPM6A chr4 177076554 177076554 chr4 179828865 179828865 TCGA-EJ-7330 INS 36 16 * * chr4 182071865 182071865 chr4 182644058 182644058 TCGA-EJ-7330 DEL 21 19 TENM3-AS1 TENM3 chr4 26393325 26393325 chr4 42382577 42382577 TCGA-EJ-7330 DEL 26 45 RBPJ AC024022.1 chr4 33927631 33927631 chr4 35818919 35818919 TCGA-EJ-7330 DEL 47 5 AC016687.3 * chr5 105337109 105337109 chr5 105997317 105997317 TCGA-EJ-7330 INS 48 37 AC099520.1 * chr5 106863808 106863808 chr5 106866472 106866472 TCGA-EJ-7330 DEL 18 20 LINC01950 LINC01950 chr5 115713068 115713068 chr5 123747175 123747175 TCGA-EJ-7330 DEL 8 17 * * chr5 160382583 160382583 chr5 163455407 163455407 TCGA-EJ-7330 DEL 31 15 * NUDCD2 chr5 19584078 19584078 chr5 102603554 102603554 TCGA-EJ-7330 DEL 27 39 CDH18 LINC00492 chr5 20904355 20904355 chr5 103483176 103483176 TCGA-EJ-7330 DEL 4 35 LINC02241 PDZPH1P chr5 21337726 21337726 chr5 21950219 21950219 TCGA-EJ-7330 INS 17 33 AC093274.1 CDH12 chr5 21639052 21639052 chr5 21645258 21645258 TCGA-EJ-7330 DEL 25 5 AC091946.1 AC091946.1 chr5 22291104 22291104 chr5 22319090 22319090 TCGA-EJ-7330 DEL 44 49 CDH12 CDH12 chr5 82729386 82729386 chr5 82751498 82751498 TCGA-EJ-7330 DEL 41 31 * * chr5 86353722 86353722 chr5 93888220 93888220 TCGA-EJ-7330 INS 6 7 AC016550.2 FAM172A chr6 100074501 100074501 chr6 114764798 114764798 TCGA-EJ-7330 DEL 30 49 MCHR2-AS1 * chr6 102876393 102876393 chr6 105372700 105372700 TCGA-EJ-7330 DEL 9 4 * PREP chr6 106195630 106195630 chr6 106565241 106565241 TCGA-EJ-7330 DEL 25 1 ATG5 CRYBG1 chr6 125218229 125218229 chr6 152683208 152683208 TCGA-EJ-7330 DEL 49 12 TPD52L1 * chr6 128077425 128077425 chr6 128088128 128088128 TCGA-EJ-7330 DEL 18 45 PTPRK PTPRK chr6 98351409 98351409 chr6 105301868 105301868 TCGA-EJ-7330 INS 29 37 AL589740.1 PREP chr7 8470608 8470608 chr7 10947535 10947535 TCGA-EJ-7330 DEL 50 6 NXPH1 * chr8 105520997 105520997 chr13 59056391 59056391 TCGA-EJ-7330 BND 6 46 ZFPM2 * chr8 110866981 110866981 chr8 111805899 111805899 TCGA-EJ-7330 INS 19 5 * * chr8 121731132 121731132 chr8 122080597 122080597 TCGA-EJ-7330 DEL 12 27 HAS2-AS1 AC037486.1 chr8 13801559 13801559 chr8 13802871 13802871 TCGA-EJ-7330 DEL 44 6 * * chr8 56399134 56399134 chr8 56400864 56400864 TCGA-EJ-7330 DEL 30 48 * * chr9 10117795 10117795 chr9 11800549 11800549 TCGA-EJ-7330 DEL 15 20 PTPRD AL353595.1 chr9 17850918 17850918 chr9 17852539 17852539 TCGA-EJ-7330 DEL 5 6 * * chr9 28101924 28101924 chr9 28109238 28109238 TCGA-EJ-7330 DEL 44 45 LINGO2 LINGO2 chr9 77383960 77383960 chr9 77394472 77394472 TCGA-EJ-7330 DEL 28 19 VPS13A VPS13A chr9 9751163 9751163 chr9 11227784 11227784 TCGA-EJ-7330 DEL 7 14 PTPRD * chr10 117305089 117305089 chr10 117305238 117305238 TCGA-YL-A9WI DEL 30 26 PDZD8 PDZD8 chr10 125779906 125779906 chr10 125781354 125781354 TCGA-YL-A9WI INS 6 32 * * chr10 125780596 125780596 chr10 125781386 125781386 TCGA-YL-A9WI DEL 47 14 * * chr10 18941097 18941097 chrX 85672101 85672101 TCGA-YL-A9WI BND 44 6 * * chr10 27162650 27162650 chr10 27162813 27162813 TCGA-YL-A9WI DEL 17 29 MASTL MASTL chr10 49891480 49891480 chr18 63736043 63736043 TCGA-YL-A9WI BND 14 7 PARG * chr10 55196943 55196943 chr10 55197379 55197379 TCGA-YL-A9WI DEL 36 18 PCDH15 PCDH15 chr11 106787599 106787599 chr1 188194218 188194218 TCGA-YL-A9WI BND 8 16 GUCY1A2 * chr11 127399664 127399664 chr11 130023245 130023245 TCGA-YL-A9WI DEL 35 2 * * chr11 43833231 43833231 chr11 43833627 43833627 TCGA-YL-A9WI DEL 8 50 AC068205.2 AC068205.2 chr11 46564288 46564288 chr11 46564654 46564654 TCGA-YL-A9WI DEL 13 50 AMBRA1 AMBRA1 chr11 66438544 66438544 chr11 66438690 66438690 TCGA-YL-A9WI DEL 7 28 MRPL11 MRPL11 chr11 98679816 98679816 chr11 98680663 98680663 TCGA-YL-A9WI DEL 42 19 AP003715.1 AP003715.1 chr12 38228547 38228547 chr12 38234841 38234841 TCGA-YL-A9WI DEL 31 31 * * chr12 97033556 97033556 chr12 97034218 97034218 TCGA-YL-A9WI DEL 24 49 AC007656.2 AC007656.2 chr13 113871117 113871117 chr13 113871615 113871615 TCGA-YL-A9WI DEL 30 8 * * chr13 32037925 32037925 chr2 159998996 159998996 TCGA-YL-A9WI BND 26 6 FRY PLA2R1 chr13 32587890 32587892 chr2 159992931 159992933 TCGA-YL-A9WI BND 37 21 PDS5B PLA2R1 chr13 32626794 32626794 chr1 54108344 54108344 TCGA-YL-A9WI BND 12 21 PDS5B TCEANC2 chr13 83652308 83652310 chr13 83652568 83652568 TCGA-YL-A9WI DEL 23 49 * * chr13 98958864 98958867 chr1 55058232 55058235 TCGA-YL-A9WI BND 50 9 DOCK9 PCSK9 chr14 57884460 57884460 chr14 57903856 57903856 TCGA-YL-A9WI DEL 23 10 SLC35F4 SLC35F4 chr14 59571948 59571948 chr14 59572707 59572707 TCGA-YL-A9WI DEL 19 29 CCDC175 CCDC175 chr15 41043840 41043840 chr15 41044044 41044044 TCGA-YL-A9WI INS 43 18 INO80 INO80 chr15 48066107 48066107 chr15 48107982 48107982 TCGA-YL-A9WI INS 16 32 * * chr15 51385487 51385487 chr15 51386310 51386310 TCGA-YL-A9WI DEL 21 46 GLDN GLDN chr16 13115968 13115988 chr9 107116407 107116408 TCGA-YL-A9WI BND 16 17 SHISA9 AL807761.2 chr16 13485639 13485639 chr12 129074094 129074094 TCGA-YL-A9WI BND 20 5 U91319.1 TMEM132D chr16 70362179 70362179 chr16 70362417 70362417 TCGA-YL-A9WI DEL 44 33 AC012184.2 AC012184.2 chr17 1226766 1226766 chr6 46787485 46787485 TCGA-YL-A9WI BND 10 10 ABR * chr17 12416300 12416300 chr17 12416922 12416922 TCGA-YL-A9WI DEL 6 48 * * chr17 17452850 17452850 chr17 17534542 17534542 TCGA-YL-A9WI DEL 36 37 * PEMT chr17 27878371 27878371 chr17 27878516 27878516 TCGA-YL-A9WI DEL 37 2 LYRM9 LYRM9 chr17 3127300 3127300 chr16 70929683 70929683 TCGA-YL-A9WI BND 28 6 OR1G1 HYDIN chr17 44320857 44320857 chr5 127169218 127169218 TCGA-YL-A9WI BND 12 5 SLC25A39 * chr17 49819857 49819857 chr17 49820174 49820174 TCGA-YL-A9WI DEL 6 2 KAT7 KAT7 chr17 50673675 50673675 chr17 50674198 50674198 TCGA-YL-A9WI DEL 33 14 ABCC3 ABCC3 chr17 56132011 56132011 chr17 56132334 56132334 TCGA-YL-A9WI DEL 9 46 ANKFN1 ANKFN1 chr17 7568780 7568780 chr17 7900424 7900424 TCGA-YL-A9WI DEL 34 18 SENP3 CHD3 chr17 78343809 78343809 chr17 78344543 78344543 TCGA-YL-A9WI DEL 27 34 AC087645.2 AC087645.2 chr18 32928142 32928142 chr18 32928956 32928956 TCGA-YL-A9WI DEL 30 13 AC090371.2 AC090371.2 chr18 64376281 64376281 chr8 102104159 102104159 TCGA-YL-A9WI BND 41 33 LINC01924 NCALD chr18 7678350 7678350 chr18 7679194 7679194 TCGA-YL-A9WI DEL 6 7 PTPRM PTPRM chr19 2090847 2090847 chr19 2093020 2093020 TCGA-YL-A9WI DEL 18 26 MOB3A MOB3A chr19 9664511 9664511 chr2 9775722 9775722 TCGA-YL-A9WI BND 40 30 ZNF562 * chr1 114636491 114636491 chr1 115488754 115488754 TCGA-YL-A9WI DEL 26 42 DENND2C * chr1 117296865 117296865 chr2 215938024 215938024 TCGA-YL-A9WI BND 6 44 LINC01525 * chr1 117296908 117296909 chr2 215938246 215938247 TCGA-YL-A9WI BND 4 39 LINC01525 * chr1 147482529 147482529 chr1 147482669 147482669 TCGA-YL-A9WI DEL 11 36 LINC00624 LINC00624 chr1 153749704 153749705 chr1 153749844 153749844 TCGA-YL-A9WI DEL 41 11 INTS3 INTS3 chr1 225591438 225591438 chr1 225592263 225592263 TCGA-YL-A9WI DEL 32 20 ENAH ENAH chr1 28851256 28851256 chr1 28851408 28851408 TCGA-YL-A9WI DEL 32 25 OPRD1 OPRD1 chr1 3463733 3463733 chr1 3463930 3463930 TCGA-YL-A9WI DEL 24 47 ARHGEF16 ARHGEF16 chr1 4450021 4450021 chr1 4458005 4458005 TCGA-YL-A9WI DEL 40 5 * * chr1 54108344 54108344 chr13 32626794 32626794 TCGA-YL-A9WI BND 39 44 TCEANC2 PDS5B chr1 55058232 55058235 chr13 98958864 98958867 TCGA-YL-A9WI BND 38 11 PCSK9 DOCK9 chr1 85901859 85901859 chr1 85902291 85902291 TCGA-YL-A9WI DEL 1 6 COL24A1 COL24A1 chr1 86092218 86092218 chr1 86092434 86092434 TCGA-YL-A9WI DEL 21 21 COL24A1 COL24A1 chr20 1843307 1843307 chr11 72664726 72664726 TCGA-YL-A9WI BND 2 35 * PDE2A chr20 41025079 41025079 chr20 41029790 41029790 TCGA-YL-A9WI DEL 36 45 * TOP1 chr20 41752319 41752319 chr20 41752484 41752484 TCGA-YL-A9WI DEL 28 2 * * chr20 53702193 53702193 chr20 54344704 54344704 TCGA-YL-A9WI INS 27 1 * * chr21 20740300 20740300 chr4 56218770 56218777 TCGA-YL-A9WI BND 8 16 * CRACD chr21 28393481 28393481 chr21 28395335 28395335 TCGA-YL-A9WI DEL 22 42 * * chr21 34543060 34543060 chr21 34543281 34543281 TCGA-YL-A9WI DEL 44 50 RCAN1 RCAN1 chr21 43850220 43850225 chr21 43857246 43857255 TCGA-YL-A9WI INV 45 35 * MYL6P1 chr22 24503957 24503957 chr22 24556892 24556892 TCGA-YL-A9WI INS 24 44 UPB1 GUCD1 chr22 24531281 24531281 chr22 24532550 24532550 TCGA-YL-A9WI DEL 20 20 * * chr2 106544355 106544355 chr2 106544561 106544561 TCGA-YL-A9WI DEL 50 34 * * chr2 12080900 12080900 chr17 43550476 43550476 TCGA-YL-A9WI BND 21 24 MIR3681HG DHX8 chr2 127661706 127661706 chr2 127662155 127662155 TCGA-YL-A9WI DEL 43 43 LIMS2 LIMS2 chr2 131993557 131993557 chr2 136609979 136609979 TCGA-YL-A9WI INV 31 7 LINC01945 * chr2 159992931 159992933 chr13 32587890 32587892 TCGA-YL-A9WI BND 27 21 PLA2R1 PDS5B chr2 159993018 159993018 chr2 161243439 161243439 TCGA-YL-A9WI DEL 41 44 PLA2R1 AC009299.2 chr2 159998996 159998996 chr13 32037925 32037925 TCGA-YL-A9WI BND 28 39 PLA2R1 FRY chr2 160970511 160970511 chr13 32842401 32842401 TCGA-YL-A9WI BND 48 5 * * chr2 161243541 161243541 chr13 98083569 98083569 TCGA-YL-A9WI BND 2 24 AC009299.2 * chr2 213234855 213234860 chr2 213235163 213235163 TCGA-YL-A9WI DEL 15 49 * * chr2 215938246 215938247 chr1 117296908 117296909 TCGA-YL-A9WI BND 39 20 * LINC01525 chr2 41381275 41381275 chr2 41381652 41381652 TCGA-YL-A9WI DEL 1 23 * * chr2 8138837 8138837 chr2 14803768 14803768 TCGA-YL-A9WI INS 14 39 LINC00298 * chr2 9775489 9775489 chr19 9664541 9664541 TCGA-YL-A9WI BND 3 12 * ZNF562 chr2 97895191 97895191 chr2 97896206 97896206 TCGA-YL-A9WI DEL 42 16 TMEM131 TMEM131 chr3 175879273 175879273 chr3 175879642 175879642 TCGA-YL-A9WI DEL 24 48 * * chr3 197734195 197734195 chr3 197736092 197736092 TCGA-YL-A9WI DEL 10 17 RUBCN RUBCN chr3 35046304 35046304 chr3 35046977 35046979 TCGA-YL-A9WI DEL 15 13 * * chr3 35510728 35510728 chr3 35511380 35511380 TCGA-YL-A9WI DEL 40 3 * * chr3 44892820 44892820 chr3 44918734 44918734 TCGA-YL-A9WI DEL 36 6 TGM4 ZDHHC3 chr3 44907480 44907480 chrX 67199092 67199092 TCGA-YL-A9WI BND 22 35 TGM4 * chr3 44914341 44914341 chr3 153014222 153014222 TCGA-YL-A9WI INS 20 11 TGM4 * chr3 44915639 44915643 chr6 20285521 20285525 TCGA-YL-A9WI BND 13 1 ZDHHC3 AL158198.1 chr4 16438194 16438194 chr4 16438599 16438599 TCGA-YL-A9WI DEL 23 20 AC097515.1 AC097515.1 chr4 173330989 173330989 chr4 173331394 173331394 TCGA-YL-A9WI DEL 25 33 AC097534.1 * chr4 179662013 179662013 chr4 179664742 179664742 TCGA-YL-A9WI DEL 11 48 * * chr4 33485362 33485362 chr3 35046977 35046979 TCGA-YL-A9WI BND 16 44 * * chr4 44797942 44797942 chr4 44799307 44799307 TCGA-YL-A9WI DEL 28 50 * * chr4 48406516 48406516 chr3 184301991 184301991 TCGA-YL-A9WI BND 48 42 SLAIN2 PSMD2 chr4 56218770 56218777 chr21 20740140 20740140 TCGA-YL-A9WI BND 49 28 CRACD * chr4 68090470 68090470 chr4 68090638 68090638 TCGA-YL-A9WI DEL 25 17 TMPRSS11F TMPRSS11F chr4 7329332 7329332 chr4 7329774 7329774 TCGA-YL-A9WI DEL 28 32 SORCS2 SORCS2 chr4 85841837 85841837 chr4 100486507 100486507 TCGA-YL-A9WI DEL 5 42 ARHGAP24 EMCN chr4 87328292 87328292 chr4 87328512 87328512 TCGA-YL-A9WI DEL 45 27 AC108516.2 AC108516.2 chr5 111405960 111405960 chr5 111410154 111410154 TCGA-YL-A9WI DEL 42 5 CAMK4 CAMK4 chr5 24267412 24267412 chr5 24270250 24270266 TCGA-YL-A9WI INS 46 37 * * chr5 24267579 24267579 chr5 24270250 24270266 TCGA-YL-A9WI DEL 14 4 * * chr5 53254082 53254082 chr5 80409879 80409879 TCGA-YL-A9WI DEL 17 28 * ZFYVE16 chr5 88572920 88572920 chr5 130135633 130135633 TCGA-YL-A9WI INS 38 39 LINC00461 CHSY3 chr5 91830887 91830887 chr5 91845499 91845499 TCGA-YL-A9WI DEL 7 42 * PCBP2P3 chr6 117157336 117157336 chr6 117158152 117158152 TCGA-YL-A9WI DEL 30 11 * * chr6 130584861 130584861 chr6 130585064 130585064 TCGA-YL-A9WI DEL 2 47 * * chr6 132897082 132897082 chr6 132899607 132899607 TCGA-YL-A9WI DEL 4 23 * * chr6 20285018 20285018 chrX 68811510 68811510 TCGA-YL-A9WI BND 36 42 AL158198.1 * chr6 20285521 20285525 chr3 44915639 44915643 TCGA-YL-A9WI BND 23 28 AL158198.1 ZDHHC3 chr6 26756689 26756689 chr6 26757955 26757955 TCGA-YL-A9WI DEL 37 45 * * chr6 43821401 43821401 chrX 138040274 138040281 TCGA-YL-A9WI BND 19 48 AL157371.2 * chr6 61590054 61590054 chr6 61612030 61612030 TCGA-YL-A9WI DEL 37 10 * * chr6 81698208 81698208 chr6 103239618 103239618 TCGA-YL-A9WI DEL 8 44 TENT5A * chr7 142266043 142266043 chr7 142267457 142267457 TCGA-YL-A9WI DEL 6 7 TRY2P TRY2P chr7 41567183 41567183 chr7 41602523 41602523 TCGA-YL-A9WI DEL 4 5 * * chr8 113894778 113894778 chr8 113897732 113897732 TCGA-YL-A9WI DEL 11 14 * * chr8 114247469 114247469 chr8 114248311 114248311 TCGA-YL-A9WI DEL 37 46 * * chr8 133494578 133494578 chr8 133495118 133495118 TCGA-YL-A9WI DEL 26 14 ST3GAL1 ST3GAL1 chr8 133630759 133630759 chr9 82098695 82098695 TCGA-YL-A9WI BND 22 24 * AL162726.3 chr8 3110058 3110071 chr8 29702115 29702115 TCGA-YL-A9WI INS 24 40 CSMD1 LINC00589 chr8 3110058 3110071 chr8 3110506 3110506 TCGA-YL-A9WI DEL 26 44 CSMD1 CSMD1 chr8 49689079 49689079 chr8 49689979 49689979 TCGA-YL-A9WI DEL 28 2 * * chr8 57688798 57688798 chr8 74088718 74088718 TCGA-YL-A9WI INS 47 17 AC104051.1 AC087672.2 chr8 90745890 90745890 chr2 97896206 97896206 TCGA-YL-A9WI BND 45 38 TMEM64 TMEM131 chr8 95752561 95752561 chr8 95752870 95752870 TCGA-YL-A9WI DEL 9 27 C8orf37-AS1 C8orf37-AS1 chr9 107116407 107116408 chr16 13115968 13115988 TCGA-YL-A9WI BND 9 7 AL807761.2 SHISA9 chr9 118898727 118898727 chr9 118899554 118899554 TCGA-YL-A9WI DEL 35 21 * * chr9 13493759 13493759 chr9 13495514 13495514 TCGA-YL-A9WI DEL 27 5 * * chr9 15122893 15122893 chr9 15123039 15123039 TCGA-YL-A9WI DEL 22 4 CLCN3P1 CLCN3P1 chr9 30683169 30683169 chr9 30683352 30683352 TCGA-YL-A9WI DEL 24 32 * * chr9 96947563 96947563 chr16 13115968 13115988 TCGA-YL-A9WI BND 37 13 MFSD14C SHISA9 chrX 135161643 135161643 chrX 135162122 135162122 TCGA-YL-A9WI DEL 25 31 CT55 CT55 chrX 138040274 138040281 chr6 43821459 43821459 TCGA-YL-A9WI BND 17 20 * AL157371.2 chrX 32518102 32518102 chrX 32518236 32518236 TCGA-YL-A9WI DEL 33 16 DMD DMD chrX 68811510 68811510 chr6 20285018 20285018 TCGA-YL-A9WI BND 26 10 * AL158198.1 chrX 88514719 88514719 chrX 88515038 88515038 TCGA-YL-A9WI DEL 28 42 * * chr14 89702382 89702382 chr14 89755352 89755352 TCGA-ZG-A9ND INS 31 23 AL137230.2 AL137230.2 chr15 37038788 37038788 chr15 37040605 37040605 TCGA-ZG-A9ND DEL 49 1 MEIS2 MEIS2 chr16 53197964 53197964 chr17 28061163 28061163 TCGA-ZG-A9ND BND 45 43 CHD9 NLK chr17 28014841 28014841 chr17 28124600 28124600 TCGA-ZG-A9ND DEL 3 44 * NLK chr17 28078716 28078716 chr16 53453266 53453266 TCGA-ZG-A9ND BND 9 38 NLK RBL2 chr1 156643668 156643668 chr11 23719356 23719356 TCGA-ZG-A9ND BND 35 8 BCAN * chr21 38487936 38487936 chr21 41511525 41511525 TCGA-ZG-A9ND DEL 28 47 ERG TMPRSS2 chr21 41484300 41484300 chr21 41484500 41484500 TCGA-ZG-A9ND DEL 13 6 TMPRSS2 TMPRSS2 chr3 59575864 59575864 chr3 59576701 59576701 TCGA-ZG-A9ND DEL 36 2 * * chr5 154655226 154655226 chr5 154655487 154655487 TCGA-ZG-A9ND INS 6 26 * * chr6 64957141 64957141 chr6 68775597 68775597 TCGA-ZG-A9ND DEL 14 14 EYS ADGRB3 chr6 85065980 85065980 chr6 85096709 85096709 TCGA-ZG-A9ND DEL 39 37 * * chr6 87014414 87014414 chr6 87283459 87283459 TCGA-ZG-A9ND DEL 12 1 HTR1E GJB7 chr7 131224166 131224166 chr7 131224310 131224310 TCGA-ZG-A9ND INS 28 32 MKLN1 MKLN1 chr8 75743070 75743070 chr8 76880908 76880908 TCGA-ZG-A9ND INS 45 32 * * chr10 103684732 103684740 chr21 39648827 39648831 TCGA-EJ-A65E BND 40 6 SH3PXD2A B3GALT5 chr10 98833956 98833956 chr10 99986046 99986046 TCGA-EJ-A65E DEL 36 44 HPSE2 DNMBP chr12 112782652 112782652 chr12 118163461 118163461 TCGA-EJ-A65E INS 26 47 RPH3A TAOK3 chr12 118058861 118058861 chr4 146737485 146737485 TCGA-EJ-A65E BND 37 48 WSB2 TTC29 chr12 118308385 118308385 chr15 48512864 48512864 TCGA-EJ-A65E BND 32 40 TAOK3 FBN1 chr12 71610674 71610674 chr19 44544526 44544526 TCGA-EJ-A65E BND 33 34 ZFC3H1 CEACAM22P chr13 37072591 37072591 chr13 80958654 80958654 TCGA-EJ-A65E DEL 3 35 * * chr13 63697257 63697257 chr13 84041897 84041897 TCGA-EJ-A65E DEL 21 47 LINC00395 * chr14 29244810 29244810 chr10 6229150 6229150 TCGA-EJ-A65E BND 4 40 * PFKFB3 chr15 56645243 56645243 chr15 57149754 57149754 TCGA-EJ-A65E DEL 23 27 ZNF280D TCF12 chr15 57100646 57100646 chr4 7985571 7985571 TCGA-EJ-A65E BND 28 15 TCF12 ABLIM2 chr15 63781139 63781139 chr15 101731808 101731808 TCGA-EJ-A65E DEL 42 20 HERC1 * chr15 63804000 63804000 chr12 118125070 118125070 TCGA-EJ-A65E BND 13 25 HERC1 VSIG10 chr16 3758116 3758116 chr16 48813240 48813240 TCGA-EJ-A65E INS 11 17 CREBBP * chr19 44526994 44526994 chr12 79397439 79397439 TCGA-EJ-A65E BND 16 33 CEACAM20 SYT1 chr1 185114071 185114071 chr10 75389405 75389405 TCGA-EJ-A65E BND 33 44 * AC010997.3 chr1 209568054 209568054 chr1 211233376 211233376 TCGA-EJ-A65E DEL 47 3 AL023754.1 * chr1 228137062 228137062 chr10 76042859 76042859 TCGA-EJ-A65E BND 25 5 * LRMDA chr1 47135408 47135412 chr21 37009265 37009269 TCGA-EJ-A65E BND 22 37 CYP4A22-AS1 RIPPLY3 chr21 37009186 37009186 chr1 48866118 48866118 TCGA-EJ-A65E BND 17 3 RIPPLY3 AGBL4 chr21 37016586 37016586 chr1 87186696 87186696 TCGA-EJ-A65E BND 38 45 RIPPLY3 * chr21 39635235 39635235 chr1 230616312 230616312 TCGA-EJ-A65E BND 48 8 B3GALT5 * chr21 39775515 39775520 chr10 103684732 103684740 TCGA-EJ-A65E BND 8 43 IGSF5 SH3PXD2A chr21 41489704 41489706 chr2 9577161 9577163 TCGA-EJ-A65E BND 3 47 TMPRSS2 * chr21 41489704 41489706 chr3 53293009 53293009 TCGA-EJ-A65E BND 25 22 TMPRSS2 DCP1A chr2 119664206 119664206 chr2 119930725 119930725 TCGA-EJ-A65E DEL 15 12 * PTPN4 chr2 169127427 169127427 chr21 37016856 37016856 TCGA-EJ-A65E BND 38 45 LRP2 RIPPLY3 chr2 28552752 28552752 chr8 28848174 28848174 TCGA-EJ-A65E BND 23 21 PLB1 INTS9 chr2 9577161 9577163 chr2 28552456 28552456 TCGA-EJ-A65E DEL 30 15 * PLB1 chr3 112801089 112801089 chr3 112885818 112885818 TCGA-EJ-A65E DEL 41 35 CD200R1L-AS1 * chr3 174805965 174805965 chr3 181530076 181530076 TCGA-EJ-A65E DEL 43 7 NAALADL2 SOX2-OT chr3 47243924 47243924 chr3 48737589 48737589 TCGA-EJ-A65E DEL 42 50 KIF9 IP6K2 chr3 53293083 53293083 chr2 100046646 100046646 TCGA-EJ-A65E BND 33 30 DCP1A AFF3 chr4 146705683 146705683 chr15 63938520 63938520 TCGA-EJ-A65E BND 28 50 * DAPK2 chr4 146745570 146745570 chr15 50902614 50902614 TCGA-EJ-A65E BND 23 26 TTC29 AC021752.1 chr4 77949925 77949925 chr4 146746650 146746650 TCGA-EJ-A65E DEL 42 3 MRPL1 TTC29 chr4 77975549 77975549 chr15 50956466 50956466 TCGA-EJ-A65E BND 25 41 * AP4E1 chr4 78049653 78049653 chr15 50918660 50918660 TCGA-EJ-A65E BND 22 36 * AP4E1 chr4 78076613 78076613 chr4 146736870 146736870 TCGA-EJ-A65E INS 26 19 FRAS1 TTC29 chr4 7985799 7985799 chr15 48512918 48512918 TCGA-EJ-A65E BND 33 4 ABLIM2 FBN1 chr4 7991425 7991425 chr15 41120231 41120231 TCGA-EJ-A65E BND 36 49 ABLIM2 * chr4 8007502 8007502 chr4 8008201 8008201 TCGA-EJ-A65E INS 23 26 ABLIM2 ABLIM2 chr4 80780514 80780514 chr7 105650191 105650191 TCGA-EJ-A65E BND 9 6 CFAP299 ATXN7L1 chr6 121296469 121296469 chr6 121297489 121297489 TCGA-EJ-A65E DEL 32 27 TBC1D32 TBC1D32 chr6 97456180 97456180 chr6 101386307 101386307 TCGA-EJ-A65E DEL 46 43 AL589740.1 GRIK2 chr7 100620305 100620305 chr4 37758606 37758606 TCGA-EJ-A65E BND 39 6 * * chr7 114681232 114681232 chr7 114681842 114681842 TCGA-EJ-A65E DEL 48 34 FOXP2 FOXP2 chr8 19904247 19904247 chr3 49913199 49913199 TCGA-EJ-A65E BND 37 28 LPL MON1A chr9 4653215 4653215 chr9 6943959 6943959 TCGA-EJ-A65E DEL 45 20 SPATA6L KDM4C chr10 60671822 60671822 chr10 62801789 62801789 TCGA-CH-5748 INS 49 12 ANK3 AC067751.1 chr10 7077281 7077281 chr10 7430836 7430836 TCGA-CH-5748 INS 15 29 * * chr11 109927426 109927426 chr11 110261245 110261245 TCGA-CH-5748 INS 3 44 RDX RDX chr11 31076767 31076767 chr11 35511213 35511213 TCGA-CH-5748 INS 14 22 DCDC1 PAMR1 chr11 5497966 5497966 chr11 7605342 7605342 TCGA-CH-5748 INS 25 36 HBG2 PPFIBP2 chr11 64989731 64989731 chr11 71418890 71418890 TCGA-CH-5748 INS 38 34 BATF2 ACTE1P chr11 6827815 6827815 chr11 10656087 10656087 TCGA-CH-5748 INS 9 34 AC087280.2 IRAG1 chr11 76959155 76959155 chr11 81250588 81250588 TCGA-CH-5748 INS 34 11 ACER3 * chr12 116126416 116126416 chr12 116389818 116389818 TCGA-CH-5748 INS 18 31 MED13L * chr12 132156128 132156128 chr12 133138126 133138126 TCGA-CH-5748 DEL 43 3 * ZNF10 chr13 78506012 78506012 chr13 78775096 78775096 TCGA-CH-5748 DEL 30 35 OBI1-AS1 * chr14 29354674 29354674 chr14 31109640 31109640 TCGA-CH-5748 INS 39 10 AL133166.1 HECTD1 chr14 29879896 29879896 chr14 30181371 30181371 TCGA-CH-5748 INS 31 35 PRKD1 PRKD1 chr14 75074407 75074407 chr14 75329700 75329700 TCGA-CH-5748 INS 42 8 ZC2HC1C * chr15 37845931 37845931 chr15 38062546 38062546 TCGA-CH-5748 INS 12 23 * * chr15 49679029 49679029 chr15 52646041 52646041 TCGA-CH-5748 INS 37 36 * FAM214A chr15 87777838 87777838 chr15 87780976 87780976 TCGA-CH-5748 INS 6 39 * * chr15 98059179 98059179 chr15 98776819 98776819 TCGA-CH-5748 INS 22 41 LINC02251 IGF1R chr16 76658728 76658728 chr16 76872382 76872382 TCGA-CH-5748 INS 44 46 * AC106729.1 chr16 84188211 84188211 chr16 84188654 84188654 TCGA-CH-5748 DEL 2 20 TAF1C * chr17 31187036 31187036 chr17 43651310 43651310 TCGA-CH-5748 DEL 1 32 NF1 MEOX1 chr17 59075996 59075996 chr17 62840518 62840518 TCGA-CH-5748 INS 2 4 TRIM37 PRELID3BP3 chr17 7337542 7337542 chr17 7678801 7678801 TCGA-CH-5748 INS 39 15 ACAP1 TP53 chr18 52760203 52760203 chr18 55707611 55707611 TCGA-CH-5748 INS 11 2 DCC * chr19 10183121 10183121 chr11 97260805 97260805 TCGA-CH-5748 BND 10 14 DNMT1 LINC02553 chr19 48411995 48411995 chr19 52188311 52188311 TCGA-CH-5748 INS 37 39 GRIN2D * chr1 151741346 151741346 chr1 155200220 155200220 TCGA-CH-5748 INS 35 25 * THBS3-AS1 chr1 160495524 160495524 chr1 161290362 161290362 TCGA-CH-5748 INS 14 14 SLAMF6 * chr1 168726365 168726365 chr1 173427306 173427306 TCGA-CH-5748 INS 8 3 DPT PRDX6-AS1 chr1 171835744 171835744 chr1 171836073 171836073 TCGA-CH-5748 INS 5 50 * * chr1 174087752 174087752 chr5 133406174 133406174 TCGA-CH-5748 BND 41 15 * FSTL4 chr1 188960305 188960305 chr1 189345164 189345164 TCGA-CH-5748 INS 32 3 LINC01035 * chr1 204363546 204363546 chr1 204661356 204661356 TCGA-CH-5748 INS 37 4 PLEKHA6 LRRN2 chr1 20438890 20438890 chr1 20913436 20913436 TCGA-CH-5748 INS 1 37 * EIF4G3 chr1 20784117 20784117 chr1 25903008 25903008 TCGA-CH-5748 INS 23 36 HP1BP3 STMN1 chr20 57769324 57769324 chr20 58083806 58083806 TCGA-CH-5748 INS 39 47 * * chr21 22117811 22117811 chr21 22538914 22538914 TCGA-CH-5748 INS 32 32 * * chr21 36162810 36162810 chr21 36581958 36581958 TCGA-CH-5748 INS 33 38 CBR3-AS1 * chr22 40272919 40272919 chr22 42217236 42217236 TCGA-CH-5748 INS 2 45 TNRC6B TCF20 chr2 129067168 129067168 chr2 129288091 129288091 TCGA-CH-5748 INS 25 18 AC068483.1 * chr2 146559951 146559951 chr2 146560014 146560014 TCGA-CH-5748 DEL 9 18 * * chr2 147602184 147602193 chr2 150136248 150136248 TCGA-CH-5748 DEL 21 5 * * chr2 15930049 15930049 chr2 16521556 16521556 TCGA-CH-5748 INS 35 2 MYCNUT * chr2 200674677 200674677 chr2 200997346 200997346 TCGA-CH-5748 INS 14 20 AOX1 FAM126B chr2 203915720 203915720 chr2 204834364 204834364 TCGA-CH-5748 INS 47 7 * PARD3B chr2 42625458 42625458 chr2 46743177 46743177 TCGA-CH-5748 DEL 17 7 MTA3 SOCS5 chr3 128303884 128303884 chr3 129038310 129038310 TCGA-CH-5748 INS 36 34 EEFSEC EFCC1 chr3 170730585 170730585 chr3 173592746 173592746 TCGA-CH-5748 INS 32 6 AC026316.4 NLGN1 chr3 175780074 175780074 chr3 176332131 176332131 TCGA-CH-5748 INS 35 9 NAALADL2 * chr3 23059642 23059642 chr3 23891042 23891042 TCGA-CH-5748 INS 13 14 * UBE2E1 chr3 25653706 25653706 chr3 26028982 26028982 TCGA-CH-5748 INS 18 28 TOP2B * chr3 68801464 68801464 chr3 69661575 69661575 TCGA-CH-5748 INS 50 33 TAFA4 * chr4 10333830 10333830 chr4 15197587 15197587 TCGA-CH-5748 INS 11 22 * C1QTNF7-AS1 chr4 132075791 132075791 chr4 132477299 132477299 TCGA-CH-5748 INS 36 5 AC093916.1 * chr4 134262384 134262384 chr4 136188936 136188936 TCGA-CH-5748 INS 4 15 AC015631.1 AC018680.1 chr4 152541240 152541240 chr4 152651345 152651345 TCGA-CH-5748 DEL 23 38 * TMEM154 chr4 57453874 57453874 chr4 59605659 59605659 TCGA-CH-5748 INS 44 47 LINC02380 AC096588.1 chr4 70274143 70274143 chr4 73753635 73753636 TCGA-CH-5748 INS 44 8 * * chr4 96612378 96612378 chr4 96875531 96875531 TCGA-CH-5748 INS 13 20 LINC02267 * chr5 168040042 168040042 chr5 169246514 169246516 TCGA-CH-5748 INS 25 16 TENM2 SLIT3 chr5 22568149 22568149 chr5 22687361 22687361 TCGA-CH-5748 INS 29 14 CDH12 CDH12 chr5 33770991 33770991 chr5 37333704 37333704 TCGA-CH-5748 INS 31 23 ADAMTS12 NUP155 chr5 50572915 50572915 chr5 50865767 50865767 TCGA-CH-5748 INS 4 38 * * chr7 12022869 12022869 chr7 12024154 12024154 TCGA-CH-5748 DEL 1 28 * * chr7 126661972 126661972 chr7 131342404 131342404 TCGA-CH-5748 INS 50 46 GRM8 MKLN1 chr7 149005552 149005552 chr7 149277277 149277277 TCGA-CH-5748 INS 13 20 PDIA4 ZNF783 chr7 72817253 72817253 chr7 73565662 73565662 TCGA-CH-5748 INS 30 20 TYW1B * chr7 81790966 81790966 chr7 83073530 83073530 TCGA-CH-5748 INS 19 36 * PCLO chr8 105972328 105972328 chr8 106222010 106222010 TCGA-CH-5748 INS 4 41 ZFPM2-AS1 * chr8 127902902 127902902 chr8 128044226 128044226 TCGA-CH-5748 INS 25 24 PVT1 PVT1 chr8 129387697 129387697 chr8 130887528 130887528 TCGA-CH-5748 INS 8 47 CCDC26 ADCY8 chr8 137263350 137263351 chr8 137288412 137288412 TCGA-CH-5748 INS 23 20 * * chr8 15221167 15221167 chr8 16963942 16963942 TCGA-CH-5748 INS 2 18 SGCZ * chr8 28582121 28582121 chr8 31736462 31736462 TCGA-CH-5748 INS 46 28 * NRG1 chr8 29818041 29818041 chr8 31695609 31695609 TCGA-CH-5748 INS 7 3 AC131254.1 NRG1 chr8 87321138 87321138 chrX 88233215 88233215 TCGA-CH-5748 BND 6 39 CNBD1 * chr9 11660464 11660464 chr9 11764216 11764216 TCGA-CH-5748 INS 40 17 AL353595.1 AL353595.1 chr9 69230793 69230793 chr9 69811215 69811215 TCGA-CH-5748 INS 16 31 AL358113.1 * chr9 97054306 97054306 chr9 97768124 97768124 TCGA-CH-5748 INS 14 40 * PTCSC2 chrX 138407598 138407598 chrX 140484879 140484879 TCGA-CH-5748 INS 15 48 * * chr10 34957019 34957019 chr10 133469969 133469969 TCGA-KK-A8ID DEL 41 33 * SCART1 chr10 35503061 35503061 chr10 36146611 36146611 TCGA-KK-A8ID DEL 27 35 CCNY * chr10 35638151 35638151 chr10 50037654 50037654 TCGA-KK-A8ID DEL 6 4 * FAM21EP chr10 35814978 35814978 chr10 36425930 36425930 TCGA-KK-A8ID INS 15 7 * * chr10 35889017 35889017 chr10 35906869 35906869 TCGA-KK-A8ID DEL 5 50 * * chr10 36158175 36158175 chr10 53081755 53081755 TCGA-KK-A8ID INS 26 29 * * chr10 36336804 36336804 chr10 93099303 93099303 TCGA-KK-A8ID DEL 29 36 * * chr10 36348328 36348328 chr10 56770923 56770923 TCGA-KK-A8ID INS 28 46 * * chr10 36423379 36423379 chr10 57935569 57935569 TCGA-KK-A8ID INS 44 39 * * chr10 50460775 50460775 chr10 56676275 56676275 TCGA-KK-A8ID INS 14 24 SGMS1 * chr10 50846270 50846270 chr10 53026137 53026137 TCGA-KK-A8ID DEL 20 39 A1CF * chr10 50850687 50850687 chr10 54067854 54067854 TCGA-KK-A8ID INS 41 14 A1CF PCDH15 chr10 51287354 51287354 chr10 54468347 54468347 TCGA-KK-A8ID DEL 49 31 PRKG1 PCDH15 chr10 51290730 51290730 chr10 57424907 57424907 TCGA-KK-A8ID INS 26 4 PRKG1 * chr10 51309783 51309786 chr10 53769480 53769480 TCGA-KK-A8ID INS 26 50 PRKG1 * chr10 52177039 52177039 chr10 53018606 53018606 TCGA-KK-A8ID DEL 19 17 PRKG1 * chr10 53258170 53258170 chr10 57599607 57599607 TCGA-KK-A8ID DEL 43 27 * * chr10 53279510 53279510 chr10 55813749 55813751 TCGA-KK-A8ID INS 26 31 * * chr10 54568207 54568207 chr10 56227903 56227903 TCGA-KK-A8ID INS 36 38 PCDH15 * chr10 55022479 55022479 chr10 55039163 55039163 TCGA-KK-A8ID DEL 37 25 PCDH15 PCDH15 chr10 55053474 55053474 chr10 81311216 81311216 TCGA-KK-A8ID INS 33 50 PCDH15 * chr10 55843543 55843543 chr10 57351383 57351383 TCGA-KK-A8ID INS 6 37 * * chr10 56499426 56499426 chr10 91004980 91004980 TCGA-KK-A8ID DEL 40 7 * AL365434.1 chr10 56789326 56789326 chr10 105266193 105266193 TCGA-KK-A8ID DEL 24 40 * * chr10 56803895 56803895 chr10 105259576 105259576 TCGA-KK-A8ID INS 14 16 * SORCS3 chr10 57343142 57343142 chr10 106147766 106147766 TCGA-KK-A8ID INS 46 47 * LINC02624 chr10 75709381 75709381 chr21 38507945 38507945 TCGA-KK-A8ID BND 21 38 LRMDA ERG chr10 87772705 87772705 chr10 87960471 87960471 TCGA-KK-A8ID DEL 21 36 ATAD1 PTEN chr10 87843354 87843354 chr10 89695525 89695525 TCGA-KK-A8ID DEL 34 20 CFL1P1 AL157400.3 chr10 88500802 88500802 chr10 92030533 92030533 TCGA-KK-A8ID DEL 46 45 RNLS * chr10 88506325 88506325 chr10 89192381 89192381 TCGA-KK-A8ID INS 20 3 RNLS * chr10 88831014 88831015 chr1 100157235 100157236 TCGA-KK-A8ID BND 19 8 ANKRD22 LRRC39 chr10 88844020 88844020 chr10 90978865 90978865 TCGA-KK-A8ID INS 50 28 ANKRD22 * chr10 90968479 90968480 chr1 101457471 101457472 TCGA-KK-A8ID BND 20 50 * * chr10 92027969 92027969 chr1 101872370 101872370 TCGA-KK-A8ID BND 39 18 BTAF1 OLFM3 chr10 92917576 92917576 chr1 101383578 101383578 TCGA-KK-A8ID BND 5 3 EXOC6 LINC01307 chr11 1664532 1664532 chr11 1686312 1686312 TCGA-KK-A8ID INV 19 41 FAM99A FAM99B chr11 1664690 1664690 chr11 1687108 1687108 TCGA-KK-A8ID INV 21 14 FAM99A FAM99B chr11 91540483 91540483 chr11 91604214 91604214 TCGA-KK-A8ID DEL 3 32 * * chr12 116295542 116295542 chr18 79542064 79542064 TCGA-KK-A8ID BND 3 43 * * chr12 126474763 126474763 chr1 71385754 71385754 TCGA-KK-A8ID BND 8 48 * ZRANB2-AS2 chr12 126748097 126748097 chr1 106442680 106442680 TCGA-KK-A8ID BND 36 40 LINC00944 * chr12 126756343 126756345 chr16 71073663 71073665 TCGA-KK-A8ID BND 43 14 LINC00944 HYDIN chr12 127678844 127678846 chr1 147119167 147119169 TCGA-KK-A8ID BND 12 22 * NBPF13P chr12 131303492 131303492 chr12 131656666 131656666 TCGA-KK-A8ID INV 4 22 * * chr12 39718439 39718439 chr12 39726324 39726324 TCGA-KK-A8ID DEL 20 32 C12orf40 C12orf40 chr12 40380835 40380835 chr12 40384201 40384201 TCGA-KK-A8ID DEL 23 12 * * chr12 40875368 40875368 chr12 40914244 40914244 TCGA-KK-A8ID DEL 30 20 CNTN1 CNTN1 chr12 87245192 87245192 chr12 87775609 87775609 TCGA-KK-A8ID INS 4 36 * * chr13 101193164 101193164 chr13 103082808 103082808 TCGA-KK-A8ID INS 32 1 NALCN * chr13 31105355 31105355 chr13 67493504 67493504 TCGA-KK-A8ID DEL 21 28 WDR95P * chr13 48286060 48286060 chr13 48466026 48466026 TCGA-KK-A8ID DEL 29 4 * RB1 chr13 64494613 64494613 chr13 93265136 93265136 TCGA-KK-A8ID DEL 34 37 * GPC6 chr13 82100432 82100432 chr13 82142534 82142534 TCGA-KK-A8ID DEL 39 3 * * chr13 82400791 82400791 chr13 82511391 82511391 TCGA-KK-A8ID DEL 29 41 * * chr13 82846323 82846323 chr13 83913217 83913217 TCGA-KK-A8ID DEL 17 40 * * chr13 93245160 93245161 chr8 65609409 65609410 TCGA-KK-A8ID BND 8 14 GPC6 ARMC1 chr14 105663813 105663813 chr14 105736929 105736929 TCGA-KK-A8ID INV 20 2 * IGHG1 chr14 105740050 105740050 chr14 105767877 105767877 TCGA-KK-A8ID INV 2 48 IGHG1 IGHG3 chr16 24536354 24536354 chr16 75481254 75481254 TCGA-KK-A8ID DUP 23 21 RBBP6 CHST6 chr16 28924847 28924847 chr16 29722602 29722602 TCGA-KK-A8ID INV 16 39 RABEP2 * chr16 31960888 31960888 chr16 33951093 33951093 TCGA-KK-A8ID INV 47 13 AC034105.1 IGHV3OR16-16 chr16 31961254 31961254 chr16 33952263 33952263 TCGA-KK-A8ID INV 10 19 AC034105.1 * chr16 31961536 31961538 chr16 33950990 33950990 TCGA-KK-A8ID DEL 27 5 AC034105.1 IGHV3OR16-16 chr16 31961536 31961538 chr16 32902862 32902862 TCGA-KK-A8ID INV 30 50 AC034105.1 IGHV3OR16-15 chr16 32474067 32474067 chr16 32522232 32522232 TCGA-KK-A8ID INV 26 4 * * chr16 56695230 56695230 chr16 64060387 64060387 TCGA-KK-A8ID INV 49 3 * * chr16 56707281 56707281 chr16 71272148 71272148 TCGA-KK-A8ID DUP 21 28 * * chr16 57704277 57704277 chr16 58186500 58186500 TCGA-KK-A8ID DUP 44 48 DRC7 CSNK2A2 chr16 64237761 64237761 chr16 64258859 64258859 TCGA-KK-A8ID INV 12 16 * AC012322.1 chr16 64238879 64238879 chr16 64738284 64738284 TCGA-KK-A8ID DEL 45 18 * AC009101.1 chr16 64259007 64259007 chr16 67672108 67672108 TCGA-KK-A8ID DUP 23 4 AC012322.1 * chr16 71076099 71076099 chr1 106732390 106732390 TCGA-KK-A8ID BND 44 3 HYDIN * chr16 71363500 71363500 chr16 74516497 74516497 TCGA-KK-A8ID DEL 47 43 CALB2 GLG1 chr17 2816636 2816636 chr11 41604960 41604960 TCGA-KK-A8ID BND 11 25 RAP1GAP2 LINC02741 chr17 61723548 61723548 chr17 61794285 61794285 TCGA-KK-A8ID DEL 28 4 BRIP1 BRIP1 chr17 7674951 7674952 chr17 7674951 7674952 TCGA-KK-A8ID DEL 25 31 TP53 TP53 chr19 54724557 54724557 chr19 54738819 54738819 TCGA-KK-A8ID INV 22 43 KIR3DL3 KIR2DL3 chr19 54724720 54724720 chr19 54850566 54850566 TCGA-KK-A8ID DEL 50 6 KIR3DL3 KIR3DL2 chr1 100156984 100156984 chr1 104025829 104025829 TCGA-KK-A8ID DEL 41 39 LRRC39 * chr1 101385290 101385290 chr1 101853792 101853792 TCGA-KK-A8ID INS 44 12 LINC01307 OLFM3 chr1 101439712 101439712 chr1 102323875 102323875 TCGA-KK-A8ID DEL 15 40 * AC114485.1 chr1 101457471 101457472 chr10 90968479 90968480 TCGA-KK-A8ID BND 37 29 * * chr1 104024224 104024224 chr10 87845126 87845126 TCGA-KK-A8ID BND 11 27 * CFL1P1 chr1 106364041 106364041 chr1 109379010 109379010 TCGA-KK-A8ID DEL 32 13 * SORT1 chr1 106530048 106530048 chr1 106804741 106804741 TCGA-KK-A8ID INS 13 24 * MTATP6P14 chr1 106602361 106602361 chr1 107714516 107714517 TCGA-KK-A8ID DEL 41 33 * VAV3 chr1 106655572 106655572 chr12 126547321 126547321 TCGA-KK-A8ID BND 40 16 * * chr1 107409246 107409246 chr1 108542861 108542861 TCGA-KK-A8ID DEL 19 43 NTNG1 * chr1 107891760 107891760 chr1 109304784 109304786 TCGA-KK-A8ID INS 22 10 VAV3 MYBPHL chr1 116091678 116091678 chr2 239192104 239192104 TCGA-KK-A8ID BND 14 26 * HDAC4 chr1 147119167 147119169 chr12 127678844 127678846 TCGA-KK-A8ID BND 18 34 NBPF13P * chr1 22072233 22072233 chr17 12137550 12137550 TCGA-KK-A8ID BND 35 46 CDC42 MAP2K4 chr1 2325213 2325213 chr4 146742572 146742572 TCGA-KK-A8ID BND 43 17 MORN1 TTC29 chr1 4337447 4337447 chr12 132464246 132464274 TCGA-KK-A8ID BND 46 3 * * chr1 70420031 70420031 chr1 70450461 70450461 TCGA-KK-A8ID DEL 9 22 CTH * chr1 70671421 70671421 chr1 70693248 70693248 TCGA-KK-A8ID DEL 25 5 * * chr1 71385754 71385754 chr12 126474763 126474763 TCGA-KK-A8ID BND 24 18 ZRANB2-AS2 * chr21 38459878 38459878 chr21 41497205 41497205 TCGA-KK-A8ID DEL 8 35 ERG TMPRSS2 chr21 38484237 38484237 chr21 41481333 41481333 TCGA-KK-A8ID DEL 17 33 ERG TMPRSS2 chr2 127043991 127043991 chr11 120122021 120122021 TCGA-KK-A8ID BND 14 14 * TRIM29 chr2 134021962 134021962 chr2 134034488 134034488 TCGA-KK-A8ID DEL 16 28 * * chr2 177939743 177939743 chr2 222440888 222440888 TCGA-KK-A8ID INV 13 14 PDE11A SGPP2 chr2 231826943 231826943 chr2 231841088 231841088 TCGA-KK-A8ID DUP 6 42 * * chr2 237254218 237254218 chr3 46380478 46380478 TCGA-KK-A8ID BND 6 42 * CCR5AS chr2 26655104 26655118 chr11 109841825 109841825 TCGA-KK-A8ID BND 29 3 * * chr2 41677638 41677638 chr4 67251537 67251537 TCGA-KK-A8ID BND 47 48 * * chr2 43753057 43753057 chr2 43756085 43756085 TCGA-KK-A8ID DEL 8 15 PLEKHH2 PLEKHH2 chr2 50594852 50594852 chr2 50597727 50597727 TCGA-KK-A8ID DEL 42 21 NRXN1 NRXN1 chr2 53094089 53094089 chr2 88898516 88898516 TCGA-KK-A8ID DEL 6 33 * * chr2 53109645 53109645 chr2 88918289 88918289 TCGA-KK-A8ID INS 50 50 * * chr2 63697077 63697079 chr2 63950160 63950160 TCGA-KK-A8ID DEL 33 47 WDPCP VPS54 chr2 88879075 88879075 chr2 164218096 164218096 TCGA-KK-A8ID DEL 9 12 * AC016766.1 chr3 141191272 141191272 chr4 7543661 7543661 TCGA-KK-A8ID BND 23 41 * SORCS2 chr3 16785823 16785823 chr3 18929861 18929861 TCGA-KK-A8ID DEL 39 29 * * chr3 16910156 16910156 chr3 17063254 17063254 TCGA-KK-A8ID DEL 39 18 PLCL2 PLCL2 chr3 190693496 190693496 chr4 67247800 67247800 TCGA-KK-A8ID BND 13 39 * * chr3 98172369 98172369 chr3 98218849 98218849 TCGA-KK-A8ID DEL 22 7 * * chr4 129263760 129263760 chr4 129271329 129271329 TCGA-KK-A8ID DEL 47 3 * * chr4 129666219 129666219 chr17 14320008 14320008 TCGA-KK-A8ID BND 25 50 * HS3ST3B1 chr4 135820703 135820703 chr4 178582367 178582367 TCGA-KK-A8ID DEL 33 44 * * chr4 16590856 16590856 chr4 16596747 16596747 TCGA-KK-A8ID DEL 50 10 LDB2 LDB2 chr4 174263792 174263792 chr4 174719738 174719738 TCGA-KK-A8ID DEL 8 45 FBXO8 GLRA3 chr4 174697521 174697521 chr4 178442203 178442203 TCGA-KK-A8ID DEL 38 44 GLRA3 * chr4 179122473 179122473 chr4 179600811 179600811 TCGA-KK-A8ID DEL 4 22 * * chr4 181264208 181264208 chr4 181301482 181301482 TCGA-KK-A8ID DEL 34 38 LINC02500 * chr4 37604505 37604505 chr4 81504065 81504065 TCGA-KK-A8ID INV 42 1 C4orf19 RASGEF1B chr4 37604962 37604962 chr4 81504136 81504141 TCGA-KK-A8ID DEL 21 39 C4orf19 RASGEF1B chr4 49118992 49118992 chr4 49143965 49143965 TCGA-KK-A8ID DUP 31 6 * * chr5 100675945 100675945 chr5 111063791 111063791 TCGA-KK-A8ID INS 39 7 * * chr5 100845309 100845309 chr5 108453619 108453619 TCGA-KK-A8ID DEL 44 48 ST8SIA4 * chr5 101238290 101238290 chr5 111142040 111142040 TCGA-KK-A8ID INS 36 35 * * chr5 101398000 101398000 chr5 103485673 103485673 TCGA-KK-A8ID DEL 49 14 * PDZPH1P chr5 101564581 101564581 chr5 102606784 102606784 TCGA-KK-A8ID DEL 24 33 * LINC00492 chr5 101566892 101566892 chr5 109590923 109590923 TCGA-KK-A8ID INS 26 48 * * chr5 101985186 101985186 chr5 108782456 108782456 TCGA-KK-A8ID INS 13 43 * FER chr5 102108536 102108536 chr5 103363485 103363485 TCGA-KK-A8ID INS 23 42 * * chr5 102847011 102847011 chr5 110108958 110108960 TCGA-KK-A8ID INS 13 18 PAM * chr5 103381046 103381046 chr5 107557591 107557591 TCGA-KK-A8ID INS 2 13 * EFNA5 chr5 103631710 103631710 chr5 107715971 107715971 TCGA-KK-A8ID DEL 35 3 * AC024587.2 chr5 104325200 104325200 chr5 111121255 111121255 TCGA-KK-A8ID DEL 42 24 * WDR36 chr5 107384929 107384929 chr5 107438028 107438028 TCGA-KK-A8ID DEL 39 28 EFNA5 EFNA5 chr5 108358355 108358355 chr8 31635557 31635557 TCGA-KK-A8ID BND 49 29 FBXL17 * chr5 108945336 108945336 chr5 109504203 109504203 TCGA-KK-A8ID INS 36 17 FER * chr5 14152214 14152214 chr5 19239684 19239684 TCGA-KK-A8ID INS 2 36 TRIO * chr5 14819142 14819142 chr5 16906047 16906047 TCGA-KK-A8ID DEL 47 45 ANKH MYO10 chr5 14830967 14830967 chr5 20845976 20845976 TCGA-KK-A8ID INS 27 38 ANKH LINC02241 chr5 15180549 15180549 chr5 18854722 18854722 TCGA-KK-A8ID INS 42 32 * * chr5 169071843 169071843 chr17 50166742 50166742 TCGA-KK-A8ID BND 13 8 SLIT3 SGCA chr5 18888217 18888217 chr5 84363276 84363276 TCGA-KK-A8ID INS 12 15 UBE2V1P12 EDIL3 chr5 21751108 21751108 chr5 21760930 21760930 TCGA-KK-A8ID DEL 23 41 CDH12 CDH12 chr5 691611 691611 chr5 783884 783884 TCGA-KK-A8ID DUP 37 26 TPPP * chr5 83523943 83523943 chr5 83915104 83915104 TCGA-KK-A8ID DEL 7 33 VCAN * chr5 86560081 86560081 chr5 86560250 86560250 TCGA-KK-A8ID DEL 45 39 * * chr5 89975753 89975753 chr5 137238223 137238223 TCGA-KK-A8ID DUP 45 5 * SPOCK1 chr5 98259874 98259874 chr5 104328999 104328999 TCGA-KK-A8ID DEL 19 1 * * chr5 98714686 98714686 chr5 107349061 107349061 TCGA-KK-A8ID DEL 38 14 * * chr5 98997243 98997243 chr5 103234638 103234638 TCGA-KK-A8ID DEL 24 26 * * chr6 157269900 157269900 chr6 157270782 157270782 TCGA-KK-A8ID INV 46 3 * * chr6 165749365 165749365 chr20 61823600 61823600 TCGA-KK-A8ID BND 8 14 PDE10A CDH4 chr6 7211562 7211562 chr9 76326009 76326009 TCGA-KK-A8ID BND 27 8 RREB1 PCSK5 chr7 123387792 123387792 chr7 124334580 124334580 TCGA-KK-A8ID DEL 11 22 * AC006148.1 chr7 124347581 124347581 chr7 125753695 125753695 TCGA-KK-A8ID DEL 48 31 AC006148.1 * chr7 132563073 132563073 chr19 5796388 5796388 TCGA-KK-A8ID BND 28 47 PLXNA4 * chr8 108099287 108099287 chr8 108100268 108100268 TCGA-KK-A8ID DEL 9 4 * * chr8 134512238 134512238 chr8 135417863 135417863 TCGA-KK-A8ID DEL 40 49 ZFAT * chr8 30652893 30652893 chr16 24312777 24312777 TCGA-KK-A8ID BND 12 27 GTF2E2 CACNG3 chr8 32409467 32409467 chr8 32486980 32486980 TCGA-KK-A8ID DEL 38 16 NRG1 NRG1 chr8 32482965 32482965 chr5 109490143 109490143 TCGA-KK-A8ID BND 26 22 NRG1 * chr8 32483160 32483160 chr5 100616905 100616905 TCGA-KK-A8ID BND 50 5 NRG1 * chr8 57536768 57536768 chr8 70852336 70852336 TCGA-KK-A8ID INS 45 43 AC090796.1 AC015687.1 chr8 57998762 57998762 chr8 64471278 64471278 TCGA-KK-A8ID DEL 13 23 FAM110B * chr8 58957600 58957600 chr8 60439571 60439572 TCGA-KK-A8ID DEL 10 3 TOX LINC01301 chr8 58978671 58978671 chr8 64467623 64467623 TCGA-KK-A8ID INS 9 1 TOX * chr8 59492698 59492698 chrX 70459528 70459528 TCGA-KK-A8ID BND 41 4 * DLG3 chr8 60665994 60665994 chr8 70852082 70852082 TCGA-KK-A8ID DEL 33 46 * AC015687.1 chr8 65609409 65609410 chr13 93245160 93245161 TCGA-KK-A8ID BND 33 44 ARMC1 GPC6 chr8 70848310 70848310 chr8 72039253 72039253 TCGA-KK-A8ID DEL 49 40 AC015687.1 MSC-AS1 chr8 71755022 71755022 chr10 133132381 133132381 TCGA-KK-A8ID BND 25 22 * * chr8 91597196 91597196 chr8 91608487 91608487 TCGA-KK-A8ID DEL 14 40 AC103409.1 AC103409.1 chr8 94840659 94840659 chr8 114062800 114062800 TCGA-KK-A8ID INS 5 25 INTS8 * chr9 41758400 41758400 chr9 61556699 61556699 TCGA-KK-A8ID DUP 38 23 * * chr9 41780317 41780317 chr9 61534512 61534520 TCGA-KK-A8ID DEL 15 48 * * chr9 61534825 61534825 chr9 61992066 61992074 TCGA-KK-A8ID DEL 33 38 * * chr9 61556457 61556457 chr9 67618341 67618341 TCGA-KK-A8ID INV 2 35 * * chr9 61557567 61557567 chr9 67619369 67619372 TCGA-KK-A8ID INV 41 8 * * chr9 82899452 82899452 chr9 82899614 82899614 TCGA-KK-A8ID DEL 5 10 * * chrX 85391384 85391384 chrX 87727744 87727744 TCGA-KK-A8ID DEL 15 28 * Z83818.2 chr10 30700154 30700154 chr10 87706391 87706391 TCGA-KK-A59Z DEL 32 15 SVIL2P PAPSS2 chr10 46525938 46525938 chr10 46531456 46531456 TCGA-KK-A59Z INV 50 24 AC244230.2 AC244230.2 chr10 55675733 55675733 chr10 55700058 55700058 TCGA-KK-A59Z DUP 50 49 * * chr10 87951565 87951565 chr10 88323683 88323683 TCGA-KK-A59Z DEL 37 9 PTEN RNLS chr11 101695517 101695517 chr11 101704032 101704032 TCGA-KK-A59Z INS 39 14 TRPC6 TRPC6 chr11 10976317 10976317 chr11 11020407 11020407 TCGA-KK-A59Z DUP 1 50 * LINC02752 chr11 49714163 49714163 chr11 49724065 49724065 TCGA-KK-A59Z INS 21 10 AC136759.1 AC136759.1 chr11 55676539 55676539 chr11 55690279 55690279 TCGA-KK-A59Z INV 28 7 * * chr11 70214230 70214230 chr11 70237685 70237685 TCGA-KK-A59Z INV 45 6 * * chr11 71421888 71421888 chr11 71440716 71440716 TCGA-KK-A59Z DUP 8 46 ACTE1P DHCR7 chr12 132349690 132349690 chr12 132463711 132463711 TCGA-KK-A59Z DUP 45 50 * * chr12 38580814 38580814 chr12 38591573 38591573 TCGA-KK-A59Z DEL 44 29 AC087897.2 * chr12 39469844 39469844 chr12 84381922 84381922 TCGA-KK-A59Z DEL 4 9 * * chr12 39473197 39473197 chr12 42549205 42549205 TCGA-KK-A59Z INS 37 19 * PRICKLE1 chr12 52451920 52451920 chr12 52473728 52473728 TCGA-KK-A59Z INV 30 49 KRT6B KRT6C chr12 84356615 84356615 chr12 85373117 85373117 TCGA-KK-A59Z DEL 36 23 * * chr13 23904232 23904232 chr15 58164825 58164825 TCGA-KK-A59Z BND 47 48 * ALDH1A2 chr13 26820738 26820738 chr17 6550679 6550679 TCGA-KK-A59Z BND 50 22 * PITPNM3 chr13 37932354 37932354 chr13 100800464 100800464 TCGA-KK-A59Z DEL 6 1 * NALCN-AS1 chr13 38311948 38311948 chr13 38324671 38324671 TCGA-KK-A59Z DEL 46 34 * * chr14 105568937 105568981 chr14 105688378 105688378 TCGA-KK-A59Z INV 2 49 * * chr14 105570365 105570365 chr14 105690208 105690226 TCGA-KK-A59Z DEL 32 39 * * chr14 106338413 106338413 chr14 106362503 106362503 TCGA-KK-A59Z DEL 7 40 * * chr14 41889446 41889446 chr14 43230218 43230218 TCGA-KK-A59Z DEL 27 13 LRFN5 * chr14 43198636 43198636 chr5 104591623 104591623 TCGA-KK-A59Z BND 33 24 * AC099520.1 chr14 44415839 44415842 chr5 104995424 104995427 TCGA-KK-A59Z BND 28 47 * AC099520.1 chr15 44928821 44928821 chr15 44961333 44961333 TCGA-KK-A59Z DUP 10 26 AC090888.3 TERB2 chr16 16327284 16327284 chr16 16370696 16370696 TCGA-KK-A59Z DEL 6 30 PKD1P1 PKD1P2 chr16 62406738 62406738 chr16 62417044 62417044 TCGA-KK-A59Z DEL 4 9 * * chr16 62768057 62768064 chr2 133168265 133168272 TCGA-KK-A59Z BND 4 3 * NCKAP5 chr16 62775567 62775572 chr2 133174547 133174552 TCGA-KK-A59Z BND 27 47 * NCKAP5 chr17 67858233 67858233 chr17 68215279 68215279 TCGA-KK-A59Z DUP 7 3 BPTF * chr17 7633702 7633702 chr17 7681701 7681701 TCGA-KK-A59Z DEL 43 36 * TP53 chr18 39778809 39778809 chr18 39780334 39780334 TCGA-KK-A59Z INV 4 16 MIR924HG MIR924HG chr19 12396250 12396250 chr19 12435976 12435976 TCGA-KK-A59Z DUP 21 11 AC008758.4 ZNF443 chr1 103085319 103085319 chr1 103086450 103086450 TCGA-KK-A59Z DEL 30 45 COL11A1 COL11A1 chr1 113972457 113972457 chr10 16098421 16098421 TCGA-KK-A59Z BND 32 6 HIPK1 * chr1 13091746 13091746 chr1 13134364 13134364 TCGA-KK-A59Z INV 39 7 * * chr1 15068434 15068434 chr1 15494130 15494130 TCGA-KK-A59Z INS 3 4 KAZN CASP9 chr1 158154676 158154676 chr1 158156173 158156173 TCGA-KK-A59Z DEL 13 50 * * chr1 16036984 16036984 chr1 16060568 16060568 TCGA-KK-A59Z INV 2 8 AL355994.2 FAM131C chr1 181276731 181276731 chr3 16613102 16613102 TCGA-KK-A59Z BND 4 23 * DAZL chr1 191943114 191943114 chr1 191948218 191948218 TCGA-KK-A59Z DEL 37 16 LINC02770 LINC02770 chr1 192283761 192283762 chr3 86617729 86617730 TCGA-KK-A59Z BND 6 17 AL390957.1 * chr1 192880956 192880958 chr3 21397442 21397444 TCGA-KK-A59Z BND 12 30 AL390957.1 * chr1 196090829 196090829 chr1 197277528 197277528 TCGA-KK-A59Z DEL 38 50 * CRB1 chr1 197246480 197246480 chr3 19674791 19674791 TCGA-KK-A59Z BND 17 15 * * chr1 230812846 230812846 chr10 61536895 61536895 TCGA-KK-A59Z BND 20 21 * * chr1 237015863 237015863 chr1 237077535 237077535 TCGA-KK-A59Z DUP 10 22 * RYR2 chr1 87301387 87301387 chr1 87301970 87301970 TCGA-KK-A59Z DEL 2 29 * * chr20 1580324 1580328 chr20 1613498 1613516 TCGA-KK-A59Z DEL 26 21 SIRPB1 SIRPB1 chr20 23724693 23724693 chr20 23742931 23742931 TCGA-KK-A59Z INV 22 8 * * chr21 38456587 38456587 chr21 41503819 41503819 TCGA-KK-A59Z DEL 32 42 ERG TMPRSS2 chr21 38497394 38497394 chr21 41499244 41499250 TCGA-KK-A59Z DEL 43 21 ERG TMPRSS2 chr21 41483645 41483645 chr3 186137290 186137290 TCGA-KK-A59Z BND 20 47 TMPRSS2 DGKG chr2 115288879 115288879 chr16 62409066 62409066 TCGA-KK-A59Z BND 48 43 DPP10 * chr2 121310981 121310981 chr2 121752605 121752605 TCGA-KK-A59Z DEL 42 42 * TSN chr2 122176521 122176521 chr2 189651218 189651218 TCGA-KK-A59Z DEL 24 5 * * chr2 124625817 124625817 chr6 82786549 82786549 TCGA-KK-A59Z BND 2 33 CNTNAP5 * chr2 125685257 125685257 chr2 125694254 125694273 TCGA-KK-A59Z INS 8 26 * * chr2 133168265 133168272 chr16 62768057 62768064 TCGA-KK-A59Z BND 44 38 NCKAP5 * chr2 133174547 133174552 chr16 62775567 62775572 TCGA-KK-A59Z BND 15 6 NCKAP5 * chr2 148425696 148425696 chr7 562536 562536 TCGA-KK-A59Z BND 4 44 MBD5 PRKAR1B chr2 214057525 214057525 chr2 214057757 214057757 TCGA-KK-A59Z DEL 8 43 SPAG16 SPAG16 chr2 218592175 218592175 chr13 63077580 63077580 TCGA-KK-A59Z BND 36 17 CNOT9 AL354810.1 chr2 25755047 25755047 chr2 62047121 62047121 TCGA-KK-A59Z INV 6 10 ASXL2 COMMD1 chr2 26994267 26994267 chr2 26999877 26999877 TCGA-KK-A59Z INV 1 38 MAPRE3 MAPRE3 chr2 77510336 77510336 chr5 15067628 15067628 TCGA-KK-A59Z BND 48 22 LRRTM4 * chr3 119854933 119854933 chr3 123686973 123686973 TCGA-KK-A59Z DEL 47 4 GSK3B MYLK chr3 16294839 16294839 chr3 16605322 16605322 TCGA-KK-A59Z DEL 40 45 OXNAD1 DAZL chr3 169095145 169095145 chr6 103618412 103618412 TCGA-KK-A59Z BND 21 9 MECOM * chr3 169157589 169157591 chr6 97423639 97423641 TCGA-KK-A59Z BND 6 30 MECOM AL589740.1 chr3 18699111 18699111 chr3 21005738 21005738 TCGA-KK-A59Z INS 18 42 SATB1-AS1 SGO1-AS1 chr3 19530209 19530209 chr3 21006691 21006691 TCGA-KK-A59Z DEL 17 2 KCNH8 SGO1-AS1 chr3 19668866 19668866 chr3 20275040 20275040 TCGA-KK-A59Z DEL 8 46 * SGO1-AS1 chr3 20191345 20191346 chr1 192904082 192904083 TCGA-KK-A59Z BND 39 22 SGO1-AS1 AL390957.1 chr3 21397442 21397444 chr1 192880956 192880958 TCGA-KK-A59Z BND 4 37 * AL390957.1 chr3 86120406 86120406 chr1 193283248 193283248 TCGA-KK-A59Z BND 9 5 * * chr3 86617729 86617730 chr1 192283761 192283762 TCGA-KK-A59Z BND 27 31 * AL390957.1 chr3 94762869 94762869 chr3 94805587 94805587 TCGA-KK-A59Z DEL 33 41 * * chr4 111073955 111073955 chr4 116199164 116199164 TCGA-KK-A59Z DEL 8 38 * AC027613.1 chr4 111075278 111075278 chr4 116183777 116183777 TCGA-KK-A59Z INS 28 50 * AC027613.1 chr4 118032606 118032606 chr4 118035040 118035040 TCGA-KK-A59Z DEL 42 25 NDST3 NDST3 chr4 126026691 126026691 chr4 126030654 126030654 TCGA-KK-A59Z DEL 3 26 * * chr4 126094094 126094094 chr4 126110363 126110363 TCGA-KK-A59Z DEL 28 5 * * chr4 126111345 126111345 chr4 126122599 126122599 TCGA-KK-A59Z DEL 12 34 * * chr4 128789124 128789124 chr4 128801810 128801810 TCGA-KK-A59Z DEL 5 16 * * chr4 132168366 132168366 chr4 132169395 132169395 TCGA-KK-A59Z DEL 25 33 * * chr4 157294284 157294284 chr4 157294928 157294928 TCGA-KK-A59Z DEL 23 22 GRIA2 GRIA2 chr4 164622011 164622011 chr4 164639473 164639473 TCGA-KK-A59Z DEL 46 13 * * chr4 176480163 176480163 chr4 176502513 176502513 TCGA-KK-A59Z DEL 16 19 * * chr4 176533390 176533390 chr4 177358653 177358653 TCGA-KK-A59Z DEL 8 12 * NEIL3 chr4 49118389 49118389 chr4 49147886 49147886 TCGA-KK-A59Z DEL 33 15 * * chr4 85705131 85705131 chr4 85706200 85706200 TCGA-KK-A59Z INV 15 47 ARHGAP24 ARHGAP24 chr5 102226734 102226734 chr5 102230174 102230174 TCGA-KK-A59Z DEL 28 17 * * chr5 103738387 103738387 chr5 103834999 103834999 TCGA-KK-A59Z DEL 37 43 * * chr5 103837178 103837178 chr14 42658576 42658576 TCGA-KK-A59Z BND 34 1 * AL442163.1 chr5 105477933 105477933 chr5 105499858 105499858 TCGA-KK-A59Z DEL 9 4 * * chr5 106724690 106724690 chr10 13396216 13396216 TCGA-KK-A59Z BND 20 30 * * chr5 147255079 147255079 chr6 145170802 145170802 TCGA-KK-A59Z BND 18 33 STK32A * chr5 178839213 178839213 chr5 180673723 180673723 TCGA-KK-A59Z INV 28 31 AC126915.1 AC122714.2 chr5 17959093 17959093 chr5 44610400 44610400 TCGA-KK-A59Z INS 43 17 * * chr5 19267237 19267237 chr5 19549671 19549671 TCGA-KK-A59Z DEL 9 31 * CDH18 chr5 19271241 19271241 chr5 20123321 20123321 TCGA-KK-A59Z INS 40 29 * CDH18 chr5 20088856 20088856 chr5 21002959 21002959 TCGA-KK-A59Z DEL 42 39 CDH18 * chr5 20126266 20126266 chr5 42733587 42733587 TCGA-KK-A59Z INS 25 18 CDH18 * chr5 20141729 20141729 chr5 99025472 99025473 TCGA-KK-A59Z DEL 34 31 CDH18 * chr5 21678177 21678177 chr5 21954600 21954600 TCGA-KK-A59Z DEL 44 14 AC091946.1 CDH12 chr5 21734833 21734833 chr5 98988166 98988166 TCGA-KK-A59Z DEL 25 16 AC091946.1 LINC02062 chr5 24506927 24506927 chr5 57478236 57478236 TCGA-KK-A59Z INS 4 6 CDH10 AC025470.2 chr5 3445707 3445707 chr21 43336828 43336828 TCGA-KK-A59Z BND 1 32 LINC01019 * chr5 44521173 44521173 chr5 44522278 44522278 TCGA-KK-A59Z DEL 42 9 * * chr5 57479699 57479699 chr5 57916664 57916664 TCGA-KK-A59Z INS 47 4 AC025470.2 * chr5 57827636 57827636 chr5 58416204 58416204 TCGA-KK-A59Z DEL 19 2 * * chr5 8916452 8916452 chr5 9138738 9138738 TCGA-KK-A59Z INS 24 41 * SEMA5A chr5 99619062 99619062 chr5 99626940 99626940 TCGA-KK-A59Z DEL 35 29 * * chr6 119890590 119890590 chr6 119896477 119896477 TCGA-KK-A59Z DEL 12 31 * * chr6 123207048 123207048 chr6 123242816 123242816 TCGA-KK-A59Z DEL 19 48 * TRDN chr6 125140884 125140884 chr6 125166700 125166701 TCGA-KK-A59Z DEL 41 32 TPD52L1 TPD52L1 chr6 32482611 32482611 chr6 32570288 32570288 TCGA-KK-A59Z DEL 23 42 * * chr6 40904743 40904743 chr1 222456957 222456957 TCGA-KK-A59Z BND 41 39 * * chr6 73523798 73523798 chr6 73539894 73539894 TCGA-KK-A59Z DEL 50 10 EEF1A1 AL121972.1 chr6 79818382 79818382 chr9 10890624 10890624 TCGA-KK-A59Z BND 11 47 * * chr6 80289220 80289220 chr6 85385940 85385940 TCGA-KK-A59Z INS 49 4 BCKDHB * chr6 81325557 81325557 chr6 85435789 85435789 TCGA-KK-A59Z DEL 23 15 * * chr6 96215823 96215824 chr9 11647892 11647893 TCGA-KK-A59Z BND 22 1 * AL353595.1 chr6 97423639 97423641 chr3 169157589 169157591 TCGA-KK-A59Z BND 21 44 AL589740.1 MECOM chr7 124487123 124487123 chr7 124488320 124488320 TCGA-KK-A59Z DEL 38 44 * * chr7 139865589 139865589 chr20 63049668 63049668 TCGA-KK-A59Z BND 46 29 TBXAS1 LINC01749 chr7 141336608 141336608 chr17 66798960 66798980 TCGA-KK-A59Z BND 39 17 TMEM178B PRKCA chr7 150910544 150910545 chr9 808491 808491 TCGA-KK-A59Z BND 32 28 * * chr7 157776665 157776665 chr14 33898154 33898154 TCGA-KK-A59Z BND 27 46 PTPRN2 * chr7 46471905 46471911 chrX 108105828 108105834 TCGA-KK-A59Z BND 23 50 * ATG4A chr7 57943324 57943324 chr7 57965067 57965067 TCGA-KK-A59Z INV 23 32 * * chr7 86762937 86762937 chr7 86763652 86763652 TCGA-KK-A59Z DEL 12 12 GRM3 GRM3 chr8 111381450 111381450 chr14 37209446 37209446 TCGA-KK-A59Z BND 44 16 LINC02237 MIPOL1 chr8 115768443 115768443 chrX 66077312 66077312 TCGA-KK-A59Z BND 13 7 TRPS1 EIF4BP9 chr8 5286698 5286698 chr8 5287288 5287288 TCGA-KK-A59Z DEL 49 42 * * chr8 88132517 88132517 chr8 88143997 88143997 TCGA-KK-A59Z DEL 5 40 MMP16 MMP16 chr8 89816473 89816473 chrY 7094073 7094073 TCGA-KK-A59Z BND 9 17 * * chr9 10174278 10174278 chr9 11673636 11673636 TCGA-KK-A59Z DEL 22 34 PTPRD AL353595.1 chr9 10201488 10201488 chr9 11250448 11250448 TCGA-KK-A59Z INS 7 16 PTPRD * chr9 11132624 11132624 chr9 12278710 12278710 TCGA-KK-A59Z INS 7 41 * * chr9 11647892 11647893 chr6 96215823 96215824 TCGA-KK-A59Z BND 12 50 AL353595.1 * chr9 11655795 11655795 chr9 17345119 17345119 TCGA-KK-A59Z DEL 34 17 AL353595.1 CNTLN chr9 124090373 124090373 chr9 124101833 124101833 TCGA-KK-A59Z INV 15 50 * * chr9 130971094 130971094 chr9 130972290 130972290 TCGA-KK-A59Z INV 28 4 * * chr9 6117783 6117783 chr9 7149203 7149203 TCGA-KK-A59Z INS 41 3 * KDM4C chr9 8648485 8648485 chr9 11539070 11539070 TCGA-KK-A59Z DEL 9 33 PTPRD * chr9 9117729 9117729 chr9 15502215 15502215 TCGA-KK-A59Z DEL 44 1 PTPRD PSIP1 chrX 136202509 136202509 chrX 145627063 145627063 TCGA-KK-A59Z DEL 33 27 FHL1 * chrX 136378628 136378628 chrX 146630388 146630388 TCGA-KK-A59Z DEL 50 19 ADGRG4 * chrX 136396832 136396832 chrX 147444491 147444491 TCGA-KK-A59Z INS 9 13 ADGRG4 * chrX 137030843 137030843 chrX 137943672 137943672 TCGA-KK-A59Z DEL 21 11 GPR101 Z96074.1 chrX 137571586 137571586 chrX 147443887 147443887 TCGA-KK-A59Z DEL 13 9 ZIC3 * chrX 137970861 137970862 chrX 145625485 145625485 TCGA-KK-A59Z INS 50 16 Z96074.1 * chrX 138270272 138270272 chrX 140944359 140944359 TCGA-KK-A59Z DEL 31 2 * AL451048.1 chrX 145562953 145562953 chrX 145569202 145569202 TCGA-KK-A59Z DEL 15 1 * * chrX 146606176 146606176 chrX 147424568 147424568 TCGA-KK-A59Z DEL 21 24 * * chrX 147064081 147064081 chrX 147076096 147076096 TCGA-KK-A59Z DEL 46 35 * * chrY 7094073 7094073 chr8 89816473 89816473 TCGA-KK-A59Z BND 32 26 * * chr10 103685101 103685101 chr10 106596126 106596126 TCGA-HC-7738 DUP 21 38 SH3PXD2A SORCS1 chr10 107879179 107879179 chr10 108063351 108063351 TCGA-HC-7738 DUP 22 38 LINC01435 LINC01435 chr10 111253681 111253681 chr10 111563427 111563427 TCGA-HC-7738 DUP 44 22 * * chr10 119208910 119208910 chr10 121780283 121780283 TCGA-HC-7738 DUP 34 44 GRK5 ATE1 chr10 119478404 119478404 chr10 121555299 121555299 TCGA-HC-7738 DUP 12 17 * FGFR2 chr10 123404736 123404736 chr10 125328474 125328474 TCGA-HC-7738 DUP 34 36 LINC02641 * chr10 124839191 124839191 chr10 125456554 125456554 TCGA-HC-7738 DUP 37 29 * * chr10 131971242 131971242 chr12 51807295 51807295 TCGA-HC-7738 BND 41 10 BNIP3 SCN8A chr10 13448735 13448735 chr10 14854001 14854001 TCGA-HC-7738 DUP 40 19 BEND7 HSPA14 chr10 16730032 16730032 chr10 18734098 18734098 TCGA-HC-7738 DUP 1 28 RSU1 * chr10 26243257 26243257 chr10 26481319 26481319 TCGA-HC-7738 DUP 44 4 GAD2 APBB1IP chr10 38509010 38509010 chr10 38627124 38627124 TCGA-HC-7738 DUP 47 1 * * chr10 44101548 44101548 chr10 45261483 45261483 TCGA-HC-7738 DUP 7 39 * OR6D1P chr10 49320330 49320330 chr10 49560410 49560410 TCGA-HC-7738 DUP 38 9 C10orf71 * chr10 51076330 51076330 chr10 87926494 87926494 TCGA-HC-7738 DEL 38 35 PRKG1 PTEN chr10 54064728 54064728 chr10 54956504 54956504 TCGA-HC-7738 DUP 18 16 PCDH15 PCDH15 chr10 65015705 65015705 chr10 66155637 66155637 TCGA-HC-7738 DUP 31 40 * CTNNA3 chr10 77481720 77481720 chr10 77815668 77815668 TCGA-HC-7738 DUP 46 44 KCNMA1 DLG5 chr11 101237124 101237124 chr11 102703258 102703258 TCGA-HC-7738 DUP 49 23 * MMP27 chr11 102735039 102735039 chr11 103346857 103346857 TCGA-HC-7738 DUP 23 50 * DYNC2H1 chr11 119783734 119783734 chr11 132606515 132606515 TCGA-HC-7738 DEL 28 30 * OPCML chr11 134422319 134422319 chr11 134647105 134647105 TCGA-HC-7738 DUP 44 11 * * chr11 16578902 16578902 chr22 29005469 29005469 TCGA-HC-7738 BND 2 50 SOX6 ZNRF3 chr11 16610447 16610447 chr11 17817735 17817735 TCGA-HC-7738 DUP 36 36 SOX6 KCNC1 chr11 17609157 17609157 chr11 18436841 18436841 TCGA-HC-7738 DUP 42 40 OTOG LDHC chr11 21583125 21583125 chr11 21879294 21879294 TCGA-HC-7738 DUP 22 42 * ANO5 chr11 31188637 31188637 chr11 31487517 31487517 TCGA-HC-7738 DUP 10 35 DCDC1 IMMP1L chr11 39012694 39012694 chr11 40692758 40692758 TCGA-HC-7738 DUP 43 20 * LRRC4C chr11 42325139 42325139 chr11 42742058 42742058 TCGA-HC-7738 DUP 26 27 * * chr11 44906712 44906712 chr11 44939730 44939730 TCGA-HC-7738 INV 23 34 TSPAN18 TP53I11 chr11 44907192 44907192 chr11 44960762 44960762 TCGA-HC-7738 DUP 3 42 TSPAN18 * chr11 44907241 44907241 chr11 45614628 45614628 TCGA-HC-7738 INV 12 29 TSPAN18 * chr11 44916379 44916379 chr11 44939932 44939932 TCGA-HC-7738 DUP 6 28 TSPAN18 TP53I11 chr11 50331781 50331781 chr11 50723507 50723507 TCGA-HC-7738 DUP 20 3 AC024405.2 * chr11 55104286 55104287 chr4 46333321 46333322 TCGA-HC-7738 BND 5 46 * GABRA2 chr11 55312174 55312174 chr11 55326838 55326838 TCGA-HC-7738 DEL 26 43 * * chr11 55447033 55447033 chr11 56532099 56532099 TCGA-HC-7738 DUP 5 4 * * chr11 60021758 60021758 chr11 62425717 62425717 TCGA-HC-7738 DUP 33 11 OOSP4B AP003064.2 chr11 60092482 60092482 chr11 60902162 60902162 TCGA-HC-7738 DUP 31 42 MS4A2 PRPF19 chr11 65355123 65355123 chr11 65646123 65646123 TCGA-HC-7738 DUP 35 22 TIGD3 SIPA1 chr11 66902728 66902728 chr11 69096733 69096733 TCGA-HC-7738 DUP 12 42 PC TPCN2 chr11 67175420 67175420 chr11 70704857 70704857 TCGA-HC-7738 DUP 14 45 KDM2A SHANK2 chr11 68614734 68614734 chr11 69169514 69169514 TCGA-HC-7738 DUP 18 14 PPP6R3 AP003071.2 chr11 69083592 69083592 chr17 16935449 16935449 TCGA-HC-7738 BND 18 15 TPCN2 TBC1D27P chr11 69169466 69169466 chr19 35433413 35433413 TCGA-HC-7738 BND 28 3 AP003071.2 AC002511.1 chr11 90324711 90324711 chr11 90546980 90546980 TCGA-HC-7738 DUP 36 26 DISC1FP1 DISC1FP1 chr11 95794566 95794566 chr11 99740130 99740130 TCGA-HC-7738 DEL 19 13 CEP57 CNTN5 chr11 9623321 9623321 chr11 10096538 10096538 TCGA-HC-7738 DEL 13 8 * SBF2 chr11 96467806 96467806 chr4 162809186 162809186 TCGA-HC-7738 BND 42 17 JRKL * chr11 96520072 96520072 chr4 162775302 162775302 TCGA-HC-7738 BND 33 50 * * chr11 99734150 99734151 chr12 89504699 89504700 TCGA-HC-7738 BND 41 8 CNTN5 POC1B chr12 100977880 100977880 chr12 101201555 101201555 TCGA-HC-7738 DUP 20 8 ANO4 SLC5A8 chr12 101740487 101740487 chr12 104584249 104584249 TCGA-HC-7738 DUP 33 26 CHPT1 CHST11 chr12 114513490 114513490 chr12 115048438 115048438 TCGA-HC-7738 DUP 29 15 * * chr12 114600200 114600200 chr12 114805736 114805736 TCGA-HC-7738 DUP 29 14 * * chr12 116225129 116225129 chr12 116763710 116763710 TCGA-HC-7738 DUP 19 9 MED13L RNFT2 chr12 120368396 120368396 chr12 120687162 120687162 TCGA-HC-7738 DUP 24 18 MSI1 MLEC chr12 120866580 120866580 chr12 121515421 121515421 TCGA-HC-7738 DUP 14 42 SPPL3 KDM2B chr12 121135993 121135993 chr12 121574836 121574836 TCGA-HC-7738 DUP 7 26 P2RX7 KDM2B chr12 124058540 124058540 chr12 124421821 124421821 TCGA-HC-7738 DUP 7 1 RFLNA NCOR2 chr12 12719081 12719081 chr3 69061155 69061155 TCGA-HC-7738 BND 11 35 CDKN1B UBA3 chr12 19320945 19320945 chr12 19597047 19597047 TCGA-HC-7738 DUP 46 18 PLEKHA5 AEBP2 chr12 22859038 22859038 chr12 23040944 23040944 TCGA-HC-7738 DUP 14 47 AC084816.1 AC084816.1 chr12 38988280 38988280 chr12 39228093 39228093 TCGA-HC-7738 DUP 12 24 * * chr12 39190547 39190547 chr12 39343317 39343317 TCGA-HC-7738 DUP 3 22 * KIF21A chr12 49531634 49531634 chr12 49882737 49882737 TCGA-HC-7738 DUP 2 9 * FAIM2 chr12 51016537 51016537 chr12 51463258 51463258 TCGA-HC-7738 DUP 2 45 SLC11A2 SLC4A8 chr12 51816015 51816015 chr12 53453120 53453120 TCGA-HC-7738 DEL 37 25 TMDD1 PCBP2 chr12 52576692 52576692 chr12 68660223 68660223 TCGA-HC-7738 DEL 47 16 * RAP1B chr12 53450297 53450297 chr1 61774736 61774736 TCGA-HC-7738 BND 13 21 AC023509.1 PATJ chr12 54020493 54020493 chr12 54020647 54020647 TCGA-HC-7738 DEL 8 47 HOXC6 HOXC6 chr12 82320763 82320763 chr12 82666821 82666821 TCGA-HC-7738 DUP 2 49 CCDC59 * chr12 84489159 84489159 chr12 84500584 84500584 TCGA-HC-7738 DEL 12 44 * * chr12 84990246 84990246 chr12 88931528 88931528 TCGA-HC-7738 DEL 36 4 * * chr12 86153216 86153216 chr12 86541780 86541780 TCGA-HC-7738 DUP 17 13 MGAT4C MGAT4C chr12 86544054 86544054 chr11 96482293 96482293 TCGA-HC-7738 BND 13 42 MGAT4C JRKL chr12 86578554 86578554 chr12 86579448 86579448 TCGA-HC-7738 DEL 49 7 MGAT4C MGAT4C chr12 87172278 87172279 chr11 96523433 96523434 TCGA-HC-7738 BND 18 3 * * chr12 87200988 87200990 chr4 162771664 162771666 TCGA-HC-7738 BND 19 42 * * chr12 88930638 88930638 chr11 99414290 99414290 TCGA-HC-7738 BND 37 31 * CNTN5 chr12 89468162 89468162 chr11 99415745 99415745 TCGA-HC-7738 BND 49 46 POC1B CNTN5 chr12 96795224 96795224 chr12 96951384 96951384 TCGA-HC-7738 DUP 21 11 CFAP54 NEDD1 chr12 98545155 98545155 chr12 98664041 98664041 TCGA-HC-7738 DUP 42 6 TMPO APAF1 chr13 104029066 104029066 chr13 104045863 104045863 TCGA-HC-7738 DEL 37 32 * * chr13 105598254 105598254 chr13 105762986 105762986 TCGA-HC-7738 DUP 39 38 * LINC00343 chr13 108740166 108740166 chr8 72322114 72322114 TCGA-HC-7738 BND 17 5 MYO16 * chr13 21140573 21140573 chr13 21435752 21435752 TCGA-HC-7738 DUP 9 28 SAP18 ZDHHC20 chr13 21334732 21334732 chr13 23668851 23668851 TCGA-HC-7738 INV 37 48 LINC00539 TNFRSF19 chr13 26879866 26879866 chr13 27854862 27854862 TCGA-HC-7738 DUP 14 8 * PLUT chr13 31961946 31961946 chr13 32211976 32211976 TCGA-HC-7738 DUP 5 33 FRY FRY chr13 36014224 36014224 chr13 38067448 38067448 TCGA-HC-7738 DUP 50 5 DCLK1 LINC00571 chr13 39042831 39042831 chr13 41361257 41361257 TCGA-HC-7738 DUP 33 11 NHLRC3 NAA16 chr13 39593713 39593713 chr13 39762900 39762900 TCGA-HC-7738 DUP 40 15 LHFPL6 COG6 chr13 43154730 43154730 chr13 43370825 43370825 TCGA-HC-7738 DUP 9 5 * ENOX1 chr13 52392530 52392530 chr13 52424270 52424270 TCGA-HC-7738 DEL 42 43 THSD1 VPS36 chr13 55182789 55182789 chr13 56359413 56359413 TCGA-HC-7738 INV 24 23 * * chr13 58013329 58013329 chr13 58026191 58026191 TCGA-HC-7738 DEL 35 39 * * chr13 63579939 63579939 chr13 63944588 63944588 TCGA-HC-7738 DUP 38 27 * LINC00355 chr13 66309873 66309873 chr13 66577786 66577786 TCGA-HC-7738 DUP 18 12 PCDH9 PCDH9 chr13 67772378 67772378 chr13 68007243 68007243 TCGA-HC-7738 DUP 35 39 * * chr13 74074083 74074083 chr13 74305476 74305476 TCGA-HC-7738 DUP 47 35 * * chr13 74247218 74247218 chr13 75626457 75626457 TCGA-HC-7738 DUP 39 29 LINC00402 LMO7 chr13 74290741 74290741 chr13 75717448 75717448 TCGA-HC-7738 DUP 45 4 * AL137782.1 chr13 93119498 93119498 chr13 95839807 95839807 TCGA-HC-7738 DUP 45 42 * UGGT2 chr13 93413135 93413135 chr13 93552294 93552294 TCGA-HC-7738 DUP 17 9 GPC6 GPC6 chr13 98829982 98829982 chr13 103443554 103443554 TCGA-HC-7738 DUP 29 22 DOCK9 * chr14 100757549 100757549 chr14 102711218 102711218 TCGA-HC-7738 DUP 47 47 * RCOR1 chr14 27939826 27939826 chr14 28006231 28006231 TCGA-HC-7738 DUP 13 18 * * chr14 37169033 37169033 chr14 37601737 37601737 TCGA-HC-7738 DUP 18 50 SLC25A21 TTC6 chr14 45299606 45299606 chr14 45563883 45563883 TCGA-HC-7738 DUP 19 29 * * chr14 47867533 47867533 chr19 18232392 18232392 TCGA-HC-7738 BND 16 48 * PDE4C chr14 54065030 54065030 chr14 54618191 54618191 TCGA-HC-7738 DUP 2 16 * SAMD4A chr14 62909335 62909335 chr14 63218339 63218339 TCGA-HC-7738 DUP 4 48 KCNH5 RHOJ chr14 70369199 70369199 chr14 72136803 72136803 TCGA-HC-7738 DUP 5 41 SYNJ2BP-COX16 RGS6 chr14 87052579 87052579 chr14 87302819 87302819 TCGA-HC-7738 DUP 21 26 * * chr15 22084686 22084686 chr15 22096337 22096337 TCGA-HC-7738 DEL 40 12 AC134980.2 * chr15 23419450 23419450 chr15 23665150 23665150 TCGA-HC-7738 DUP 11 24 * * chr15 25253491 25253491 chr15 25654134 25654134 TCGA-HC-7738 DUP 41 6 SNHG14 * chr15 27457089 27457089 chr15 90001977 90001977 TCGA-HC-7738 DEL 5 31 GABRG3 ZNF710 chr15 42147688 42147688 chr15 42371268 42371268 TCGA-HC-7738 DUP 34 1 PLA2G4F CAPN3 chr15 45003613 45003613 chr15 45503277 45503277 TCGA-HC-7738 DUP 27 25 RNU1-78P SLC30A4 chr15 45392959 45392959 chr15 45766219 45766219 TCGA-HC-7738 DUP 27 13 GATM AC068722.1 chr15 52481882 52481882 chr15 91265700 91265700 TCGA-HC-7738 INV 20 12 MYO5A SV2B chr15 55607777 55607777 chr15 56373708 56373708 TCGA-HC-7738 DUP 3 18 * TEX9 chr15 57440308 57440308 chr15 58775345 58775345 TCGA-HC-7738 DUP 50 24 CGNL1 MINDY2 chr15 70011897 70011897 chr15 70440484 70440484 TCGA-HC-7738 DUP 34 13 * * chr15 76592257 76592257 chr15 76604600 76604600 TCGA-HC-7738 DEL 5 23 SCAPER SCAPER chr15 79587123 79587123 chr15 80527960 80527960 TCGA-HC-7738 DUP 5 22 * ARNT2 chr15 90698363 90698363 chr15 91319220 91319220 TCGA-HC-7738 DUP 26 7 CRTC3-AS1 * chr16 11021785 11021785 chr16 11386942 11386942 TCGA-HC-7738 DUP 28 46 CLEC16A AC099489.1 chr16 32317727 32317739 chr20 53862646 53862664 TCGA-HC-7738 BND 30 4 * * chr16 49335937 49335937 chr16 49339846 49339846 TCGA-HC-7738 INS 47 40 AC007614.1 AC007614.1 chr16 67778782 67778782 chr16 68271683 68271683 TCGA-HC-7738 DUP 2 39 RANBP10 SLC7A6 chr16 67779135 67779135 chr16 68156939 68156939 TCGA-HC-7738 DUP 8 12 RANBP10 NFATC3 chr16 68157228 68157228 chr16 68269958 68269958 TCGA-HC-7738 DEL 19 21 NFATC3 SLC7A6 chr16 72854563 72854563 chr16 73143813 73143813 TCGA-HC-7738 DUP 20 46 ZFHX3 ZFHX3 chr16 80414351 80414351 chr16 81210194 81210194 TCGA-HC-7738 DUP 20 37 AC105411.1 PKD1L2 chr16 88519434 88519434 chr16 88707540 88707540 TCGA-HC-7738 DUP 31 15 ZFPM1 RNF166 chr17 29233106 29233106 chr17 29359929 29359929 TCGA-HC-7738 DUP 6 38 * AC068025.2 chr17 29778641 29778641 chr17 30348972 30348972 TCGA-HC-7738 DEL 14 8 SSH2 * chr17 36739818 36739818 chr17 37164400 37164400 TCGA-HC-7738 DUP 50 13 * ACACA chr17 41264242 41264242 chr17 41275811 41275811 TCGA-HC-7738 DEL 1 15 KRTAP9-6 KRTAP9-7 chr17 4315849 4315849 chr17 5654371 5654371 TCGA-HC-7738 DUP 2 3 UBE2G1 * chr17 55614205 55614205 chr17 56963343 56963343 TCGA-HC-7738 DUP 24 47 * * chr17 56792396 56792401 chr17 66799001 66799010 TCGA-HC-7738 DUP 1 38 C17orf67 PRKCA chr17 56792730 56792746 chr17 66799365 66799383 TCGA-HC-7738 DUP 50 46 C17orf67 PRKCA chr17 56793523 56793523 chr17 66798870 66798909 TCGA-HC-7738 INV 20 47 C17orf67 PRKCA chr17 57278143 57278143 chr17 57580068 57580068 TCGA-HC-7738 DUP 10 40 MSI2 MSI2 chr17 59335009 59335009 chr17 59644931 59644931 TCGA-HC-7738 DUP 50 5 YPEL2 CLTC chr17 64897157 64897157 chr17 65528915 65528915 TCGA-HC-7738 DUP 36 29 LRRC37A3 AXIN2 chr17 65331346 65331346 chr17 65610988 65610988 TCGA-HC-7738 DUP 38 15 * AC004805.1 chr17 66924342 66924342 chr17 67315631 67315631 TCGA-HC-7738 DUP 28 12 * * chr17 71466742 71466742 chr17 72803052 72803052 TCGA-HC-7738 DUP 20 41 * SLC39A11 chr17 72941541 72941541 chr17 73360751 73360751 TCGA-HC-7738 DUP 7 24 SLC39A11 SDK2 chr17 7680222 7680222 chr10 9332703 9332703 TCGA-HC-7738 BND 33 44 TP53 * chr17 774491 774491 chr17 2519224 2519224 TCGA-HC-7738 DUP 35 8 GLOD4 * chr17 78491858 78491858 chr17 81248563 81248563 TCGA-HC-7738 DUP 27 6 DNAH17 SLC38A10 chr17 82582178 82582178 chr17 82837010 82837010 TCGA-HC-7738 DUP 34 2 FOXK2 TBCD chr18 1683829 1683829 chr18 1935238 1935238 TCGA-HC-7738 DUP 24 33 AC019183.1 AP005230.1 chr18 38720185 38720185 chr18 38915193 38915193 TCGA-HC-7738 DUP 11 27 * * chr18 38831810 38831810 chr18 38922502 38922502 TCGA-HC-7738 DUP 47 44 * * chr18 39867042 39867042 chr18 40078940 40078940 TCGA-HC-7738 DUP 39 26 LINC01901 LINC01477 chr18 45162113 45162113 chr18 46224074 46224074 TCGA-HC-7738 DUP 44 16 AC090376.1 C18orf25 chr18 49203705 49203705 chr18 49756336 49756336 TCGA-HC-7738 DUP 30 39 DYM * chr18 53449354 53449354 chr18 53570679 53570679 TCGA-HC-7738 DUP 28 32 DCC LINC01917 chr18 57698384 57698384 chr18 58803327 58803327 TCGA-HC-7738 DUP 8 24 ATP8B1 * chr18 57859589 57859589 chr18 59506220 59506220 TCGA-HC-7738 DUP 27 17 * CCBE1 chr18 58142114 58142114 chr18 61099038 61099038 TCGA-HC-7738 DUP 37 10 NEDD4L * chr18 58180828 58180828 chr18 58749371 58749371 TCGA-HC-7738 DUP 10 17 NEDD4L MALT1 chr18 59882119 59882119 chr18 60537194 60537194 TCGA-HC-7738 DEL 17 46 * AC091576.1 chr18 62769201 62769201 chr18 65474957 65474957 TCGA-HC-7738 DUP 19 26 PHLPP1 * chr18 64505766 64505766 chr18 65043509 65043509 TCGA-HC-7738 DEL 6 43 * * chr18 68901211 68901211 chr18 68919837 68919837 TCGA-HC-7738 DEL 6 49 CCDC102B CCDC102B chr19 10763157 10763157 chr19 11482023 11482023 TCGA-HC-7738 DUP 8 4 DNM2 ELAVL3 chr19 2306508 2306508 chr19 2613947 2613947 TCGA-HC-7738 DUP 38 35 AC005258.1 GNG7 chr19 27380225 27380225 chr19 27399550 27399550 TCGA-HC-7738 INV 43 40 * * chr19 32934753 32934753 chr19 35433169 35433169 TCGA-HC-7738 DUP 11 26 CEP89 AC002511.1 chr19 35600553 35600553 chr19 38088411 38088411 TCGA-HC-7738 DUP 5 31 LINC01766 SIPA1L3 chr19 43727511 43727511 chr19 45188231 45188231 TCGA-HC-7738 DUP 40 11 * MARK4 chr19 44839431 44839431 chr19 47095943 47095943 TCGA-HC-7738 DUP 36 14 * ZC3H4 chr19 56596856 56596856 chr19 57041360 57041360 TCGA-HC-7738 DUP 34 50 ZNF71 * chr19 7832561 7832561 chr19 8999751 8999751 TCGA-HC-7738 DUP 31 45 EVI5L * chr19 8720161 8720173 chr22 46648249 46648249 TCGA-HC-7738 BND 48 40 OR2Z1 GRAMD4 chr1 104441409 104441409 chr1 106339072 106339072 TCGA-HC-7738 DUP 43 42 * * chr1 105518161 105518161 chr1 105755911 105755911 TCGA-HC-7738 DUP 14 16 * * chr1 108311704 108311704 chr1 108349919 108349919 TCGA-HC-7738 DUP 26 5 SLC25A24P1 * chr1 109990756 109990756 chr1 111567690 111567690 TCGA-HC-7738 DUP 49 29 AHCYL1 RAP1A chr1 11056948 11056948 chr1 23427060 23427060 TCGA-HC-7738 INS 42 18 SRM * chr1 11057168 11057168 chr1 23426606 23426606 TCGA-HC-7738 DEL 49 30 SRM * chr1 112547456 112547456 chr1 116576204 116576204 TCGA-HC-7738 DUP 22 18 ST7L IGSF3 chr1 115676379 115676379 chr1 118696339 118696339 TCGA-HC-7738 DUP 36 4 VANGL1 * chr1 117632071 117632071 chr1 119032624 119032624 TCGA-HC-7738 DUP 26 5 * WARS2 chr1 147185103 147185103 chr1 147719159 147719159 TCGA-HC-7738 DUP 10 23 FMO5 * chr1 148977317 148977317 chr1 148990731 148990731 TCGA-HC-7738 DEL 24 4 PDE4DIP PDE4DIP chr1 170232717 170232717 chr1 171649141 171649141 TCGA-HC-7738 DUP 4 44 LINC01681 MYOC chr1 178377705 178377705 chr1 180396605 180396605 TCGA-HC-7738 DUP 37 50 RASAL2 ACBD6 chr1 178980132 178980132 chr1 179256137 179256137 TCGA-HC-7738 DUP 40 22 * * chr1 181985570 181985570 chr1 185737082 185737082 TCGA-HC-7738 DUP 15 30 * HMCN1 chr1 1913563 1913563 chr1 2424479 2424479 TCGA-HC-7738 DUP 2 12 CALML6 * chr1 196151833 196151833 chr1 196231794 196231794 TCGA-HC-7738 DEL 34 49 * KCNT2 chr1 201386177 201386177 chr1 202187717 202187717 TCGA-HC-7738 DUP 39 6 LAD1 PTPRVP chr1 202656407 202656407 chr1 205086017 205086017 TCGA-HC-7738 DUP 21 6 SYT2 * chr1 216230617 216230617 chr1 218091147 218091147 TCGA-HC-7738 DUP 39 29 USH2A * chr1 218326008 218326008 chr1 221142594 221142594 TCGA-HC-7738 DUP 38 47 RRP15 * chr1 227143759 227143759 chr1 227311540 227311540 TCGA-HC-7738 DUP 16 14 CDC42BPA CDC42BPA chr1 231060379 231060379 chr1 231244873 231244873 TCGA-HC-7738 DUP 16 20 * GNPAT chr1 23214635 23214635 chr1 23221112 23221112 TCGA-HC-7738 DEL 25 15 * * chr1 24192603 24192603 chr1 24371298 24371298 TCGA-HC-7738 DUP 12 6 * STPG1 chr1 27952189 27952189 chr1 28188311 28188311 TCGA-HC-7738 DUP 50 43 SMPDL3B PTAFR chr1 34634976 34634976 chr1 34647047 34647047 TCGA-HC-7738 DEL 36 42 * * chr1 3701300 3701300 chr1 3911137 3911137 TCGA-HC-7738 DUP 29 27 TP73 LINC01134 chr1 37735174 37735174 chr11 102678222 102678222 TCGA-HC-7738 BND 18 6 EPHA10 * chr1 39502236 39502236 chr11 101240348 101240348 TCGA-HC-7738 BND 40 41 BMP8A * chr1 39502892 39502892 chr11 102681116 102681116 TCGA-HC-7738 BND 50 39 BMP8A AP000851.2 chr1 40766248 40766248 chr1 41177099 41177099 TCGA-HC-7738 DUP 15 43 NFYC SCMH1 chr1 52383543 52383543 chr1 55362246 55362246 TCGA-HC-7738 DUP 35 7 ORC1 AL603840.1 chr1 54652697 54652697 chr1 55465596 55465596 TCGA-HC-7738 DUP 42 34 MROH7 AL603840.1 chr1 61148130 61148130 chr1 61508376 61508376 TCGA-HC-7738 DUP 24 36 NFIA AC099791.3 chr1 61774783 61774783 chr12 51815903 51815903 TCGA-HC-7738 BND 23 36 PATJ TMDD1 chr1 63819123 63819123 chr1 64492396 64492396 TCGA-HC-7738 DUP 43 25 ROR1 CACHD1 chr1 65334728 65334728 chr1 66022388 66022388 TCGA-HC-7738 DUP 32 26 DNAJC6 PDE4B chr1 69928151 69928151 chr1 71492884 71492884 TCGA-HC-7738 DUP 1 28 LRRC7 NEGR1 chr1 70771444 70771444 chr1 70983436 70983436 TCGA-HC-7738 DUP 29 20 LINC01788 PTGER3 chr1 73041656 73041656 chr1 101819756 101819756 TCGA-HC-7738 DEL 1 6 * OLFM3 chr1 78950884 78950884 chr1 79187999 79187999 TCGA-HC-7738 DUP 20 49 ADGRL4 * chr1 84072137 84072137 chr1 86803697 86803697 TCGA-HC-7738 DUP 2 44 * * chr1 99206381 99206381 chr1 101058247 101058247 TCGA-HC-7738 DUP 20 10 AL445433.2 AC093157.1 chr20 10517724 10517724 chr20 10944744 10944744 TCGA-HC-7738 DUP 5 42 SLX4IP AL050403.2 chr20 17304084 17304084 chr20 17622107 17622107 TCGA-HC-7738 DUP 18 10 PCSK2 RRBP1 chr20 33509097 33509097 chr20 33868937 33868937 TCGA-HC-7738 DUP 31 41 CBFA2T2 * chr20 37436210 37436210 chr20 37450690 37450690 TCGA-HC-7738 DUP 24 3 * * chr20 48449799 48449799 chrX 152912007 152912007 TCGA-HC-7738 BND 50 22 * * chr20 49180690 49180690 chr20 51291821 51291821 TCGA-HC-7738 DUP 45 7 STAU1 * chr20 54029929 54029929 chr20 54041604 54041604 TCGA-HC-7738 DEL 21 29 BCAS1 BCAS1 chr20 57512707 57512707 chr20 57778451 57778451 TCGA-HC-7738 DUP 29 12 CTCFL * chr20 926032 926032 chr20 1207329 1207329 TCGA-HC-7738 DUP 48 12 * C20orf202 chr21 31032242 31032242 chr21 31035527 31035527 TCGA-HC-7738 DEL 37 18 * * chr21 36023302 36023302 chr21 36390339 36390339 TCGA-HC-7738 DUP 49 20 * CHAF1B chr21 38053463 38053463 chr21 38332989 38332989 TCGA-HC-7738 DUP 5 4 KCNJ6 LINC01423 chr21 38452398 38452398 chr21 41461982 41461982 TCGA-HC-7738 DEL 17 34 ERG * chr21 38499977 38499977 chr21 41500795 41500795 TCGA-HC-7738 DEL 15 44 ERG TMPRSS2 chr21 41502943 41502949 chr8 127907340 127907346 TCGA-HC-7738 BND 38 37 TMPRSS2 PVT1 chr22 35615610 35615610 chr22 38350567 38350567 TCGA-HC-7738 DUP 27 20 MB TPTEP2 chr22 37910736 37910736 chr22 39031132 39031132 TCGA-HC-7738 DUP 16 9 MICALL1 APOBEC3D chr22 49786598 49786598 chr22 50382223 50382223 TCGA-HC-7738 DUP 33 27 BRD1 PPP6R2 chr22 49898371 49898371 chr22 49997546 49997546 TCGA-HC-7738 DUP 11 13 * IL17REL chr2 103361884 103361885 chr22 47379219 47379219 TCGA-HC-7738 BND 38 8 * * chr2 103540088 103540088 chr2 106001061 106001061 TCGA-HC-7738 DUP 31 28 * * chr2 115284956 115284956 chr2 116510754 116510754 TCGA-HC-7738 DUP 29 5 DPP10 * chr2 116390355 116390355 chr2 118789014 118789014 TCGA-HC-7738 INS 26 10 * LINC01956 chr2 118155007 118155007 chr2 118469323 118469323 TCGA-HC-7738 DUP 44 4 THORLNC * chr2 118582690 118582690 chr2 118946181 118946181 TCGA-HC-7738 DEL 49 1 * MARCO chr2 122799023 122799023 chr2 125805939 125805939 TCGA-HC-7738 INS 45 47 * * chr2 123968494 123968494 chr2 123973312 123973312 TCGA-HC-7738 DEL 19 25 * * chr2 125294435 125294435 chr2 133904918 133904918 TCGA-HC-7738 DEL 8 8 * * chr2 125309429 125309429 chr2 133900135 133900135 TCGA-HC-7738 INS 40 14 * * chr2 129703324 129703324 chr2 130124272 130124272 TCGA-HC-7738 DUP 1 2 * POTEF chr2 149062419 149062419 chr2 149625496 149625496 TCGA-HC-7738 DUP 28 38 LYPD6B MMADHC-DT chr2 153197862 153197862 chr2 153200678 153200678 TCGA-HC-7738 DEL 45 1 AC011901.1 AC011901.1 chr2 154243733 154243733 chr2 154243924 154243924 TCGA-HC-7738 DEL 17 35 GALNT13 GALNT13 chr2 157578379 157578379 chr2 158026789 158026789 TCGA-HC-7738 DUP 28 35 ACVR1C UPP2 chr2 185659383 185659383 chr2 185908010 185908027 TCGA-HC-7738 INV 44 43 * * chr2 185908010 185908027 chr2 185980854 185980854 TCGA-HC-7738 INV 39 25 * * chr2 186911272 186911272 chr2 187586698 187586698 TCGA-HC-7738 INV 49 7 * * chr2 186963302 186963302 chr2 187584567 187584567 TCGA-HC-7738 DUP 38 25 * * chr2 19243322 19243322 chr2 20840826 20840826 TCGA-HC-7738 DUP 11 26 LINC01376 * chr2 193823145 193823145 chr2 193835137 193835137 TCGA-HC-7738 DEL 13 18 * * chr2 204302166 204302166 chr2 206840654 206840654 TCGA-HC-7738 DUP 5 48 * * chr2 205211083 205211083 chr2 205428179 205428179 TCGA-HC-7738 DUP 44 18 PARD3B PARD3B chr2 207337 207337 chr9 28189199 28189199 TCGA-HC-7738 BND 33 18 * LINGO2 chr2 208085644 208085644 chr2 208292883 208292883 TCGA-HC-7738 DUP 20 38 * PIKFYVE chr2 208643141 208643141 chr2 208643712 208643712 TCGA-HC-7738 DEL 31 13 PTH2R PTH2R chr2 209784501 209784501 chr2 211572348 211572348 TCGA-HC-7738 DUP 9 9 UNC80 ERBB4 chr2 210882848 210882848 chr2 211161796 211161796 TCGA-HC-7738 DUP 29 43 * * chr2 212331168 212331168 chr2 214474323 214474323 TCGA-HC-7738 DUP 27 20 ERBB4 AC068051.1 chr2 216170547 216170547 chr2 219273939 219273939 TCGA-HC-7738 DUP 30 38 XRCC5 TUBA4A chr2 217178924 217178924 chr2 218817825 218817825 TCGA-HC-7738 DUP 12 38 * AC009974.1 chr2 217466902 217466902 chr2 219367155 219367155 TCGA-HC-7738 DUP 4 28 DIRC3 * chr2 218980788 218980788 chr2 219320973 219320973 TCGA-HC-7738 DUP 16 39 LINC00608 * chr2 222949786 222949786 chr2 222988259 222988259 TCGA-HC-7738 DEL 33 23 * * chr2 229003619 229003619 chr2 229150922 229150922 TCGA-HC-7738 DUP 38 37 PID1 PID1 chr2 233520049 233520049 chr2 234150787 234150787 TCGA-HC-7738 DUP 20 24 USP40 * chr2 238060943 238060943 chr12 119964156 119964156 TCGA-HC-7738 BND 17 10 UBE2F-SCLY * chr2 238414110 238414110 chr12 119825124 119825124 TCGA-HC-7738 BND 15 19 * CIT chr2 27058458 27058458 chr2 29383929 29383929 TCGA-HC-7738 DUP 47 15 AGBL5 ALK chr2 27250999 27250999 chr2 27314206 27314206 TCGA-HC-7738 DEL 5 35 * MPV17 chr2 38723010 38723010 chr2 39048872 39048872 TCGA-HC-7738 DUP 6 15 GALM SOS1 chr2 49245774 49245774 chr2 50641753 50641753 TCGA-HC-7738 DUP 22 14 AC009975.1 NRXN1 chr2 53207068 53207068 chr2 53635468 53635468 TCGA-HC-7738 DUP 9 16 * ASB3 chr2 537122 537122 chr2 815286 815286 TCGA-HC-7738 DUP 9 30 * LINC01115 chr2 54180924 54180924 chr2 54553790 54553790 TCGA-HC-7738 DUP 42 12 ACYP2 SPTBN1 chr2 56665044 56665044 chr2 57155893 57155893 TCGA-HC-7738 DUP 42 28 * * chr2 58486277 58486277 chr2 60332615 60332615 TCGA-HC-7738 DUP 12 50 LINC01122 * chr2 60578606 60578606 chr2 61330494 61330494 TCGA-HC-7738 DUP 27 37 * USP34 chr2 71411076 71411076 chr2 71714951 71714951 TCGA-HC-7738 DUP 13 50 ZNF638 * chr2 71554311 71554311 chr2 73597877 73597877 TCGA-HC-7738 DUP 34 17 DYSF ALMS1 chr2 99235165 99235165 chr2 99853667 99853667 TCGA-HC-7738 DUP 12 13 AC079447.1 AFF3 chr3 101605610 101605610 chr3 101862642 101862642 TCGA-HC-7738 DUP 24 22 * * chr3 103792356 103792356 chr3 103803730 103803730 TCGA-HC-7738 INV 25 15 * * chr3 105643119 105643119 chr3 105989796 105989796 TCGA-HC-7738 DUP 49 5 * * chr3 122712772 122712772 chr3 124853349 124853349 TCGA-HC-7738 DUP 27 29 PARP14 ITGB5 chr3 125040960 125040960 chr3 127037878 127037878 TCGA-HC-7738 DUP 5 44 HEG1 * chr3 127295087 127295087 chr3 129781634 129781634 TCGA-HC-7738 DUP 1 18 * TMCC1 chr3 13216355 13216355 chr3 16204383 16204383 TCGA-HC-7738 DUP 13 42 IQSEC1 GALNT15 chr3 132200259 132200259 chr3 133262907 133262907 TCGA-HC-7738 DUP 32 27 CPNE4 TMEM108 chr3 132323325 132323325 chr7 13903128 13903128 TCGA-HC-7738 BND 34 46 ACP3 ETV1 chr3 136649815 136649815 chr3 139559837 139559837 TCGA-HC-7738 DUP 2 11 STAG1 AC046134.2 chr3 13763870 13763870 chr3 15169640 15169640 TCGA-HC-7738 DEL 22 25 * COL6A4P1 chr3 139093350 139093350 chr3 139419394 139419394 TCGA-HC-7738 DUP 10 3 MRPS22 AC046134.2 chr3 141988178 141988178 chr3 161116829 161116829 TCGA-HC-7738 DEL 30 10 TFDP2 NMD3 chr3 145468857 145468857 chr3 146216075 146216075 TCGA-HC-7738 DUP 27 43 * PLSCR4 chr3 146919655 146919655 chr3 167437545 167437545 TCGA-HC-7738 DEL 27 32 AC092957.1 * chr3 148180588 148180588 chr3 148183099 148183099 TCGA-HC-7738 DEL 25 43 AC025566.1 AC025566.1 chr3 150123256 150123256 chr3 179168324 179168324 TCGA-HC-7738 DUP 3 50 AC117386.2 PIK3CA chr3 154769863 154769863 chr3 157012777 157012777 TCGA-HC-7738 DUP 50 13 * LEKR1 chr3 155589712 155589712 chr3 156145771 156145771 TCGA-HC-7738 DUP 31 40 PLCH1 KCNAB1 chr3 159861940 159861940 chr3 181447988 181447988 TCGA-HC-7738 DUP 26 43 IQCJ-SCHIP1 SOX2-OT chr3 16282504 16282504 chr3 16463177 16463177 TCGA-HC-7738 DUP 30 19 OXNAD1 RFTN1 chr3 164076591 164076591 chr3 164436678 164436678 TCGA-HC-7738 DUP 29 25 * * chr3 168917324 168917324 chr3 169145291 169145291 TCGA-HC-7738 DUP 46 30 LINC02082 MECOM chr3 170095068 170095068 chr3 170536120 170536120 TCGA-HC-7738 DUP 42 3 PHC3 AC026316.4 chr3 178588177 178588177 chr3 178817453 178817453 TCGA-HC-7738 DUP 19 10 KCNMB2 KCNMB2 chr3 179746308 179746308 chr3 183982205 183982205 TCGA-HC-7738 DUP 19 1 USP13 ABCC5 chr3 193157238 193157238 chr3 193168094 193168094 TCGA-HC-7738 DEL 35 31 VEZF1P1 AC092966.1 chr3 25354036 25354036 chr3 25783326 25783326 TCGA-HC-7738 DUP 47 27 RARB NGLY1 chr3 28316192 28316192 chr3 28623081 28623081 TCGA-HC-7738 DUP 3 50 CMC1 AC098650.1 chr3 30018073 30018073 chr3 30024466 30024466 TCGA-HC-7738 DEL 34 49 * * chr3 32298018 32298018 chr3 32501737 32501737 TCGA-HC-7738 DUP 20 33 CMTM8 CMTM6 chr3 33607280 33607280 chr3 35813584 35813584 TCGA-HC-7738 DUP 28 21 CLASP2 * chr3 40163073 40163073 chr3 41376324 41376324 TCGA-HC-7738 DUP 1 22 MYRIP ULK4 chr3 40227707 40227707 chr3 40511920 40511920 TCGA-HC-7738 DUP 12 18 MYRIP ZNF620 chr3 40367379 40367379 chr3 88599190 88599190 TCGA-HC-7738 INV 19 45 ENTPD3-AS1 * chr3 60861784 60861784 chr3 61456329 61456329 TCGA-HC-7738 DUP 4 18 FHIT * chr3 63559086 63559086 chr3 64737038 64737038 TCGA-HC-7738 DUP 2 32 SYNPR ADAMTS9-AS2 chr3 70390990 70390990 chr3 73226490 73226490 TCGA-HC-7738 DUP 29 28 SAMMSON * chr3 71462154 71462154 chr3 71917993 71917993 TCGA-HC-7738 DUP 32 11 FOXP1 * chr3 72732089 72732089 chr3 73169586 73169586 TCGA-HC-7738 DUP 25 45 * * chr3 74888010 74888010 chr3 76082164 76082164 TCGA-HC-7738 DUP 9 42 * ROBO2 chr3 81469803 81469803 chr3 81470023 81470023 TCGA-HC-7738 DEL 9 39 * * chr3 83430270 83430270 chr3 83430963 83430963 TCGA-HC-7738 DEL 20 2 * * chr3 85575016 85575016 chr3 85651934 85651934 TCGA-HC-7738 DEL 41 14 CADM2 CADM2 chr4 102797218 102797218 chr4 103229326 103229326 TCGA-HC-7738 DUP 30 34 UBE2D3 * chr4 10390320 10390320 chr4 10402579 10402579 TCGA-HC-7738 DEL 49 38 * * chr4 104068767 104068767 chr4 104088958 104088958 TCGA-HC-7738 DEL 37 27 * * chr4 107050580 107050580 chr4 108708036 108708036 TCGA-HC-7738 DUP 50 25 DKK2 * chr4 109695835 109695835 chr4 111207046 111207046 TCGA-HC-7738 INV 11 29 CASP6 * chr4 119325895 119325895 chr4 123219142 123219142 TCGA-HC-7738 DUP 11 48 * SPATA5 chr4 119382320 119382320 chr4 119753497 119753497 TCGA-HC-7738 DUP 42 23 * * chr4 132891561 132891561 chr4 157511082 157511082 TCGA-HC-7738 DEL 1 28 AC115622.1 * chr4 137701714 137701714 chr4 139308796 139308796 TCGA-HC-7738 DUP 4 42 AC131956.2 NAA15 chr4 137883238 137883238 chr4 140298223 140298223 TCGA-HC-7738 DUP 21 8 * SCOC chr4 13951645 13951645 chr4 14105686 14105686 TCGA-HC-7738 DUP 25 20 LINC01182 * chr4 142257569 142257569 chr4 145090228 145090228 TCGA-HC-7738 DUP 23 19 INPP4B AC098588.2 chr4 142827182 142827182 chr4 146524552 146524552 TCGA-HC-7738 DUP 37 32 INPP4B * chr4 148424344 148424344 chr4 154905385 154905385 TCGA-HC-7738 INV 15 35 NR3C2 * chr4 150080506 150080506 chr4 152673800 152673800 TCGA-HC-7738 DUP 20 30 DCLK2 TMEM154 chr4 150513597 150513597 chr4 156616607 156616607 TCGA-HC-7738 INV 39 25 LRBA * chr4 150629986 150629986 chr4 151205073 151205073 TCGA-HC-7738 DUP 33 26 LRBA SH3D19 chr4 162771183 162771185 chr12 85051338 85051340 TCGA-HC-7738 BND 24 16 * LRRIQ1 chr4 162771664 162771666 chr12 87200988 87200990 TCGA-HC-7738 BND 13 2 * * chr4 162775302 162775302 chr11 96520072 96520072 TCGA-HC-7738 BND 48 47 * * chr4 165165123 165165123 chr4 165409416 165409416 TCGA-HC-7738 DUP 33 13 TMEM192 CPE chr4 171045670 171045670 chr4 171687863 171687863 TCGA-HC-7738 DUP 23 46 LINC02431 * chr4 17488402 17488402 chr4 18873908 18873908 TCGA-HC-7738 DUP 12 12 QDPR * chr4 178810160 178810160 chr4 179870915 179870915 TCGA-HC-7738 DUP 49 36 * * chr4 180535636 180535636 chr4 183343968 183343968 TCGA-HC-7738 DUP 30 13 * * chr4 181206081 181206081 chr4 181326139 181326139 TCGA-HC-7738 DUP 7 43 * * chr4 18311512 18311512 chr4 18451631 18451631 TCGA-HC-7738 DUP 1 11 * * chr4 186493316 186493316 chr4 186721874 186721874 TCGA-HC-7738 DUP 43 33 F11-AS1 FAT1 chr4 189771278 189771278 chr4 189924791 189924791 TCGA-HC-7738 DUP 28 50 * FRG1-DT chr4 21589482 21589482 chr4 23965695 23965695 TCGA-HC-7738 DUP 24 30 KCNIP4 * chr4 21885737 21885737 chr4 23556125 23556125 TCGA-HC-7738 DUP 29 39 KCNIP4 * chr4 30065439 30065439 chr4 34103612 34103612 TCGA-HC-7738 DEL 43 7 * * chr4 31017567 31017567 chr4 35101025 35101025 TCGA-HC-7738 INS 28 5 PCDH7 * chr4 31634139 31634139 chr4 31642917 31642917 TCGA-HC-7738 DEL 49 10 * * chr4 31874279 31874279 chr4 35480869 35480869 TCGA-HC-7738 DEL 34 43 * * chr4 32153054 32153054 chr4 34500275 34500275 TCGA-HC-7738 DEL 37 14 LINC02506 * chr4 32188856 32188856 chr4 34188753 34188753 TCGA-HC-7738 INS 15 35 * LINC02484 chr4 32631067 32631067 chr4 32778890 32778890 TCGA-HC-7738 DUP 8 42 * * chr4 33665227 33665227 chr4 34796690 34796690 TCGA-HC-7738 DUP 21 14 * * chr4 35030323 35030323 chr4 35982081 35982081 TCGA-HC-7738 DUP 42 15 * ARAP2 chr4 3575153 3575153 chr4 3590568 3590568 TCGA-HC-7738 DEL 50 45 * LINC00955 chr4 42555622 42555622 chr4 47769772 47769772 TCGA-HC-7738 INS 18 23 ATP8A1 CORIN chr4 43529921 43529921 chr4 43530069 43530069 TCGA-HC-7738 DEL 21 26 * * chr4 46333321 46333322 chr11 55104286 55104287 TCGA-HC-7738 BND 20 42 GABRA2 * chr4 47769772 47769772 chr10 89131869 89131869 TCGA-HC-7738 BND 22 47 CORIN * chr4 48175191 48175191 chr4 48541521 48541521 TCGA-HC-7738 DUP 18 46 TEC FRYL chr4 52684666 52684666 chr4 52826851 52826851 TCGA-HC-7738 DUP 39 42 AC104066.3 * chr4 52713920 52713920 chr4 112790978 112790978 TCGA-HC-7738 INS 38 17 DANCR * chr4 53830433 53830433 chr4 56950924 56950924 TCGA-HC-7738 INV 35 32 AC058822.1 REST chr4 60347639 60347639 chr4 60349208 60349208 TCGA-HC-7738 DEL 1 29 * * chr4 61585277 61585277 chr4 63007967 63007967 TCGA-HC-7738 DUP 45 9 ADGRL3 * chr4 64042056 64042056 chr4 64217958 64217958 TCGA-HC-7738 DUP 50 21 * * chr4 69257718 69257718 chr4 69366718 69366718 TCGA-HC-7738 DEL 35 32 * * chr4 7088618 7088618 chr4 7414084 7414084 TCGA-HC-7738 DUP 31 24 * SORCS2 chr4 72693181 72693181 chr4 76665366 76665366 TCGA-HC-7738 DUP 37 36 * SHROOM3 chr4 73313362 73313362 chr4 75157789 75157789 TCGA-HC-7738 DUP 26 30 AC053527.2 * chr4 73742076 73742076 chr4 75696069 75696069 TCGA-HC-7738 DUP 27 4 CXCL8 G3BP2 chr4 76185333 76185333 chr4 76560791 76560791 TCGA-HC-7738 DUP 47 10 SCARB2 SHROOM3 chr4 7820937 7820937 chr4 10190762 10190762 TCGA-HC-7738 DUP 38 2 AFAP1 * chr4 78500843 78500843 chr4 81010439 81010439 TCGA-HC-7738 DUP 17 45 FRAS1 * chr4 7947963 7947963 chr16 22008108 22008108 TCGA-HC-7738 BND 39 17 * MOSMO chr4 85390036 85390036 chr4 85604923 85604923 TCGA-HC-7738 DUP 44 45 * ARHGAP24 chr4 91593854 91593854 chr4 91831731 91831731 TCGA-HC-7738 DUP 41 4 CCSER1 * chr4 9571934 9571934 chr4 11974951 11974951 TCGA-HC-7738 DUP 16 3 * * chr4 96606124 96606124 chr4 97043959 97043959 TCGA-HC-7738 DUP 23 40 LINC02267 * chr4 97736505 97736505 chr4 99292273 99292273 TCGA-HC-7738 DUP 5 4 STPG2 AP002026.1 chr5 100236303 100236303 chr5 104251560 104251560 TCGA-HC-7738 INS 3 50 * * chr5 100329727 100329727 chr5 106329318 106329318 TCGA-HC-7738 INS 7 25 * * chr5 100522130 100522130 chr5 102698725 102698725 TCGA-HC-7738 DEL 16 47 AC021086.1 * chr5 100873028 100873028 chr5 103347995 103347995 TCGA-HC-7738 DEL 37 16 ST8SIA4 * chr5 100904923 100904923 chr5 107427817 107427817 TCGA-HC-7738 INS 10 35 * EFNA5 chr5 100970416 100970416 chr5 121988340 121988340 TCGA-HC-7738 DEL 14 16 * SRFBP1 chr5 103320968 103320968 chr5 103639056 103639056 TCGA-HC-7738 DUP 22 32 * * chr5 103331797 103331797 chr5 107442812 107442812 TCGA-HC-7738 DEL 12 25 * EFNA5 chr5 106231315 106231315 chr5 107035641 107035641 TCGA-HC-7738 INS 7 35 * * chr5 107254473 107254473 chr5 109307451 109307451 TCGA-HC-7738 DEL 23 15 * AC008467.1 chr5 117132749 117132749 chr5 117141450 117141450 TCGA-HC-7738 DEL 38 7 * * chr5 119175201 119175201 chr5 120931350 120931350 TCGA-HC-7738 DUP 19 44 DMXL1 * chr5 127764273 127764273 chr5 128188112 128188112 TCGA-HC-7738 DUP 1 3 CCDC192 SLC12A2 chr5 12809729 12809729 chr5 12822431 12822431 TCGA-HC-7738 DEL 33 33 * * chr5 141138299 141138299 chr5 141149038 141149038 TCGA-HC-7738 DUP 37 20 AC244517.2 AC244517.2 chr5 143163125 143163125 chr5 143350072 143350072 TCGA-HC-7738 DUP 40 18 ARHGAP26 NR3C1 chr5 145588377 145588377 chr5 147658812 147658812 TCGA-HC-7738 DUP 19 29 PRELID2 JAKMIP2 chr5 159894376 159894376 chr5 161426630 161426630 TCGA-HC-7738 DUP 23 23 ADRA1B GABRB2 chr5 166006906 166006906 chr5 166210349 166210349 TCGA-HC-7738 DEL 15 28 * * chr5 174401280 174401280 chr5 174756776 174756776 TCGA-HC-7738 DUP 38 21 LINC01411 AC113346.2 chr5 176061788 176061788 chr5 178763599 178763599 TCGA-HC-7738 DUP 34 41 FAM153B * chr5 1770678 1770678 chr5 2088142 2088142 TCGA-HC-7738 DUP 7 27 * * chr5 25314239 25314239 chr5 25314988 25314988 TCGA-HC-7738 DEL 42 27 LINC02211 LINC02211 chr5 26076938 26076938 chr5 26349410 26349410 TCGA-HC-7738 DUP 11 9 * * chr5 274047 274047 chr5 488716 488716 TCGA-HC-7738 DUP 16 11 PDCD6 SLC9A3 chr5 2772617 2772617 chr5 3838780 3838780 TCGA-HC-7738 DUP 6 13 * * chr5 50274511 50274511 chr5 100199312 100199312 TCGA-HC-7738 INS 48 20 * * chr5 51035510 51035510 chr5 101815949 101815949 TCGA-HC-7738 DEL 8 20 * * chr5 51312093 51312093 chr5 104586272 104586272 TCGA-HC-7738 DEL 27 33 * AC099520.1 chr5 52993207 52993207 chr5 56072670 56072670 TCGA-HC-7738 DUP 25 18 ITGA2 AC008892.1 chr5 54905385 54905385 chr5 56914645 56914645 TCGA-HC-7738 DUP 24 11 * SETD9 chr5 55397013 55397013 chr5 55822084 55822084 TCGA-HC-7738 DUP 49 7 MTREX * chr5 58027195 58027195 chr5 58037951 58037951 TCGA-HC-7738 DEL 29 33 * * chr5 58928594 58928594 chr5 58992807 58992807 TCGA-HC-7738 DUP 23 7 * PDE4D chr5 62917614 62917614 chr5 63155444 63155444 TCGA-HC-7738 DUP 4 5 * * chr5 66637889 66637889 chr5 82588052 82588052 TCGA-HC-7738 INV 31 45 MAST4 AC026782.2 chr5 89525268 89525268 chr5 91232039 91232039 TCGA-HC-7738 DUP 30 4 * LUCAT1 chr5 95062050 95062050 chr5 96466399 96466399 TCGA-HC-7738 DUP 5 16 MCTP1 AC104123.1 chr5 96916273 96916273 chr5 97304545 97304545 TCGA-HC-7738 INS 12 45 ERAP2 LIX1-AS1 chr5 97664590 97664590 chr5 98748467 98748467 TCGA-HC-7738 INS 8 42 LINC01340 * chr5 98920561 98920561 chr5 101720909 101720909 TCGA-HC-7738 INS 21 47 CHD1 * chr6 100001125 100001125 chr6 100242452 100242452 TCGA-HC-7738 DUP 32 46 MCHR2-AS1 * chr6 100561979 100561979 chr6 102987615 102987615 TCGA-HC-7738 DUP 29 18 ASCC3 * chr6 100677355 100677355 chr6 102220909 102220909 TCGA-HC-7738 DUP 17 50 ASCC3 * chr6 101682387 101682387 chr6 102483233 102483233 TCGA-HC-7738 INV 10 10 GRIK2 * chr6 102366476 102366476 chr6 102757465 102757465 TCGA-HC-7738 DUP 39 46 * * chr6 103827515 103827515 chr6 104513095 104513095 TCGA-HC-7738 DUP 14 14 * * chr6 104427110 104427110 chr6 105726522 105726522 TCGA-HC-7738 DUP 21 38 * AL591518.1 chr6 104455220 104455220 chr6 106091633 106091633 TCGA-HC-7738 DUP 29 39 * ATG5 chr6 104484855 104484855 chr6 104858260 104858260 TCGA-HC-7738 DUP 44 14 * HACE1 chr6 104795923 104795923 chr6 104827370 104827370 TCGA-HC-7738 DEL 4 25 HACE1 HACE1 chr6 126221004 126221004 chr6 126473148 126473148 TCGA-HC-7738 DUP 44 49 * * chr6 141660912 141660912 chr6 141672167 141672167 TCGA-HC-7738 DUP 24 15 * * chr6 141692412 141692412 chr6 143532276 143532276 TCGA-HC-7738 DUP 47 16 * * chr6 147045652 147045652 chr6 147329640 147329640 TCGA-HC-7738 DUP 5 26 STXBP5-AS1 STXBP5 chr6 151172674 151172674 chr6 151562245 151562245 TCGA-HC-7738 DUP 34 47 AL138733.1 CCDC170 chr6 152737564 152737564 chr6 153288037 153288037 TCGA-HC-7738 DUP 15 50 * AL590867.1 chr6 155468527 155468527 chr6 155769250 155769250 TCGA-HC-7738 DUP 43 29 * * chr6 16695891 16695891 chr6 18959193 18959193 TCGA-HC-7738 DUP 37 49 ATXN1 * chr6 24733908 24733908 chr6 26270179 26270179 TCGA-HC-7738 DUP 28 42 * H3C8 chr6 32482938 32482982 chr6 32570692 32570692 TCGA-HC-7738 DEL 26 8 * * chr6 32524905 32524905 chr6 32585162 32585162 TCGA-HC-7738 DEL 10 29 HLA-DRB5 HLA-DRB1 chr6 34828304 34828304 chr6 35123780 35123780 TCGA-HC-7738 DUP 33 36 UHRF1BP1 TCP11 chr6 41308484 41308484 chr6 42177528 42177528 TCGA-HC-7738 DUP 45 50 AL672212.1 GUCA1A chr6 42527477 42527477 chr6 42528965 42528965 TCGA-HC-7738 DEL 3 23 * * chr6 44079551 44079551 chr6 44279791 44279791 TCGA-HC-7738 DUP 18 17 * TMEM151B chr6 49566284 49566284 chr6 51268035 51268035 TCGA-HC-7738 DUP 11 27 CYP2AC1P * chr6 50632786 50632786 chr6 51833915 51833915 TCGA-HC-7738 DUP 44 18 AL135908.1 PKHD1 chr6 55332739 55332739 chr6 58175605 58175605 TCGA-HC-7738 DUP 50 21 GFRAL AL445250.1 chr6 64000209 64000209 chr6 64198091 64198091 TCGA-HC-7738 DUP 42 20 EYS EYS chr6 65542991 65542991 chr6 122872306 122872306 TCGA-HC-7738 DEL 11 15 EYS * chr6 70016655 70016655 chr6 72106400 72106400 TCGA-HC-7738 DUP 31 10 COL19A1 RIMS1 chr6 76850364 76850364 chr6 78456417 78456417 TCGA-HC-7738 DUP 47 18 * * chr6 77679657 77679657 chr6 77886513 77886513 TCGA-HC-7738 DUP 10 2 MEI4 MEI4 chr6 78810510 78810510 chr6 78823335 78823335 TCGA-HC-7738 DEL 6 22 AL450327.1 * chr6 83587904 83587904 chr6 83866001 83866001 TCGA-HC-7738 DUP 12 35 SNAP91 CYB5R4 chr6 89655440 89655440 chr6 90173536 90173536 TCGA-HC-7738 DUP 15 1 MDN1 BACH2 chr6 93854588 93854588 chr6 95512634 95512634 TCGA-HC-7738 DUP 39 8 * * chr7 102512768 102512788 chr7 102611451 102611451 TCGA-HC-7738 DEL 18 39 RASA4B RASA4 chr7 109160387 109160387 chr7 109422291 109422291 TCGA-HC-7738 DUP 20 10 * * chr7 112271606 112271606 chr7 113409729 113409729 TCGA-HC-7738 DUP 17 16 ZNF277 * chr7 114923100 114923100 chr7 115155696 115155696 TCGA-HC-7738 DUP 32 15 MDFIC LINC01392 chr7 115908014 115908014 chr7 115918449 115918449 TCGA-HC-7738 DEL 8 26 * * chr7 134100165 134100165 chr7 134113576 134113576 TCGA-HC-7738 DEL 35 3 * * chr7 14005738 14005738 chr7 14126202 14126202 TCGA-HC-7738 DUP 45 44 * * chr7 144074950 144074950 chr7 146095285 146095285 TCGA-HC-7738 DUP 39 9 OR2A25 * chr7 1594756 1594756 chr20 60315064 60315064 TCGA-HC-7738 BND 28 46 * MIR646HG chr7 16373756 16373756 chr7 17910308 17910308 TCGA-HC-7738 DUP 8 40 CRPPA SNX13 chr7 16518693 16518693 chr7 16825202 16825202 TCGA-HC-7738 DUP 23 21 SOSTDC1 AGR2 chr7 16826974 16826974 chr7 17065200 17065200 TCGA-HC-7738 DUP 46 5 AGR2 AHR chr7 25258697 25258697 chr7 29891638 29891638 TCGA-HC-7738 DUP 22 12 * WIPF3 chr7 30879938 30879938 chr7 31069770 31069770 TCGA-HC-7738 DUP 31 50 MINDY4 ADCYAP1R1 chr7 33055935 33055935 chr7 33355662 33355662 TCGA-HC-7738 DUP 33 30 NT5C3A BBS9 chr7 37933055 37933055 chr8 105888051 105888051 TCGA-HC-7738 BND 19 23 EPDR1 ZFPM2-AS1 chr7 51411228 51411228 chr7 52105176 52105176 TCGA-HC-7738 DUP 1 20 * * chr7 55242979 55242979 chr7 56888842 56888842 TCGA-HC-7738 DUP 45 30 ELDR * chr7 757039 757039 chr7 1542874 1542874 TCGA-HC-7738 DUP 4 11 DNAAF5 MAFK chr7 79607847 79607847 chr7 81745056 81745056 TCGA-HC-7738 DUP 22 4 * HGF chr7 81052291 81052291 chr7 83797753 83797753 TCGA-HC-7738 DUP 40 41 * * chr7 81135079 81135079 chr7 82867215 82867215 TCGA-HC-7738 DUP 2 28 * PCLO chr7 93333826 93333826 chr7 94826692 94826692 TCGA-HC-7738 DUP 26 1 VPS50 * chr7 94359574 94359574 chr7 94664835 94664835 TCGA-HC-7738 DUP 29 25 AC002074.1 PEG10 chr7 94660422 94660422 chr7 94660821 94660821 TCGA-HC-7738 INV 28 24 PEG10 PEG10 chr7 96407526 96407526 chr7 97312544 97312544 TCGA-HC-7738 DUP 39 40 * * chr7 97704540 97704540 chr7 99538059 99538059 TCGA-HC-7738 DUP 8 25 * * chr7 97861403 97861403 chr7 98193440 98193440 TCGA-HC-7738 DUP 1 46 ASNS LMTK2 chr8 101375991 101375991 chr8 101540196 101540196 TCGA-HC-7738 DUP 18 11 * GRHL2 chr8 109411279 109411279 chr8 111778281 111778281 TCGA-HC-7738 DUP 19 5 PKHD1L1 * chr8 110485519 110485519 chr8 110485728 110485728 TCGA-HC-7738 INV 27 25 * * chr8 113435819 113435819 chr8 113562411 113562411 TCGA-HC-7738 DUP 12 37 CSMD3 * chr8 114567869 114567869 chr8 114678084 114678084 TCGA-HC-7738 DUP 49 3 * * chr8 121686303 121686303 chr8 121834676 121834676 TCGA-HC-7738 DUP 4 3 HAS2-AS1 HAS2-AS1 chr8 127555181 127555181 chr8 127555309 127555309 TCGA-HC-7738 INV 22 11 * * chr8 127907398 127907398 chr21 41510953 41510953 TCGA-HC-7738 BND 48 6 PVT1 TMPRSS2 chr8 128371664 128371664 chr8 128371858 128371858 TCGA-HC-7738 INV 12 29 * * chr8 128533202 128533202 chr8 128822224 128822224 TCGA-HC-7738 DUP 47 28 LINC00824 CCDC26 chr8 134351468 134351468 chr8 134869023 134869023 TCGA-HC-7738 DUP 11 37 * AC103764.1 chr8 135015805 135015805 chr8 135015903 135015903 TCGA-HC-7738 INV 36 1 * * chr8 136025201 136025201 chr8 136176472 136176472 TCGA-HC-7738 DUP 47 27 LINC02055 LINC02055 chr8 136680838 136680838 chr8 139206809 139206809 TCGA-HC-7738 DUP 28 23 LINC02055 * chr8 140181940 140181940 chr8 141473191 141473191 TCGA-HC-7738 DUP 11 39 TRAPPC9 MROH5 chr8 141550952 141550952 chr8 141773011 141773011 TCGA-HC-7738 DUP 4 46 * * chr8 16404330 16404330 chr8 16418059 16418059 TCGA-HC-7738 DEL 18 8 MSR1 MSR1 chr8 24892925 24892925 chr8 63542384 63542384 TCGA-HC-7738 INV 1 32 AC120193.1 * chr8 32822159 32822159 chr8 32833918 32833918 TCGA-HC-7738 DEL 32 5 * * chr8 38195132 38195132 chr8 40305304 40305304 TCGA-HC-7738 DUP 20 34 BAG4 SIRLNT chr8 38847509 38847509 chr8 39240182 39240182 TCGA-HC-7738 DUP 30 4 TACC1 ADAM32 chr8 41957061 41957061 chr8 42242935 42242935 TCGA-HC-7738 DUP 34 48 KAT6A AC083973.1 chr8 47801074 47801074 chr15 41709819 41709819 TCGA-HC-7738 BND 41 31 PRKDC MGA chr8 51645486 51645486 chr8 52910486 52910486 TCGA-HC-7738 DUP 42 19 PXDNL * chr8 56858161 56858161 chr8 59362126 59362126 TCGA-HC-7738 DUP 49 13 * * chr8 72144603 72144603 chr8 72458189 72458189 TCGA-HC-7738 DUP 35 46 * * chr8 73567667 73567667 chr8 75545651 75545651 TCGA-HC-7738 DUP 4 47 STAU2 HNF4G chr8 7497260 7497260 chr8 7508877 7508877 TCGA-HC-7738 DEL 48 30 DEFB107B DEFB107B chr8 8387024 8387024 chr8 8647521 8647521 TCGA-HC-7738 DUP 11 1 PRAG1 * chr8 86532028 86532028 chr8 86914336 86914336 TCGA-HC-7738 DUP 7 36 CPNE3 CNBD1 chr8 88048230 88048230 chr8 90279147 90279147 TCGA-HC-7738 DUP 18 7 MMP16 LINC00534 chr8 9164159 9164159 chr8 12136942 12136942 TCGA-HC-7738 INV 1 13 AC022784.1 FAM66D chr8 94499499 94499499 chr8 94873840 94873840 TCGA-HC-7738 DUP 46 14 VIRMA INTS8 chr8 95523756 95523756 chr8 99471573 99471573 TCGA-HC-7738 DUP 40 9 C8orf37-AS1 VPS13B chr8 97072092 97072092 chr8 97315468 97315468 TCGA-HC-7738 DUP 38 29 CPQ * chr8 98225071 98225071 chr8 101492591 101492591 TCGA-HC-7738 DUP 19 10 NIPAL2 GRHL2 chr9 101196062 101196062 chr9 101472165 101472165 TCGA-HC-7738 DUP 31 8 PLPPR1 TMEM246-AS1 chr9 10314942 10314942 chr9 11218984 11218984 TCGA-HC-7738 DUP 48 24 PTPRD * chr9 104287105 104287105 chr9 104289723 104289723 TCGA-HC-7738 DEL 7 41 * * chr9 114621588 114621588 chr17 72128024 72128024 TCGA-HC-7738 BND 3 35 TMEM268 SOX9-AS1 chr9 117581831 117581831 chr17 70316252 70316252 TCGA-HC-7738 BND 44 14 * AC011990.1 chr9 120527170 120527170 chr9 123666534 123666534 TCGA-HC-7738 DUP 19 9 CDK5RAP2 DENND1A chr9 123115518 123115518 chr9 123773326 123773326 TCGA-HC-7738 DUP 46 19 MIR600HG DENND1A chr9 131721801 131721801 chr9 132176019 132176019 TCGA-HC-7738 DUP 27 43 RAPGEF1 NTNG2 chr9 14443458 14443458 chr9 15927454 15927454 TCGA-HC-7738 DUP 20 20 * CCDC171 chr9 19617275 19617275 chr9 20845435 20845435 TCGA-HC-7738 DUP 7 26 SLC24A2 FOCAD chr9 26833866 26833866 chr9 29432824 29432824 TCGA-HC-7738 DUP 15 26 * * chr9 27168716 27168716 chr9 27483638 27483638 TCGA-HC-7738 DUP 31 42 TEK MOB3B chr9 3547838 3547838 chr9 6802259 6802259 TCGA-HC-7738 DUP 28 16 RFX3-AS1 KDM4C chr9 36160207 36160207 chr9 36490052 36490052 TCGA-HC-7738 DUP 31 40 GLIPR2 * chr9 5406647 5406647 chr9 5652195 5652195 TCGA-HC-7738 DUP 36 32 PLGRKT RIC1 chr9 62799867 62799867 chr9 63818712 63818712 TCGA-HC-7738 INV 21 44 * DUX4L50 chr9 72751755 72751755 chr9 74312780 74312780 TCGA-HC-7738 DUP 44 26 TMC1 * chr9 8582133 8582133 chr9 9744762 9744762 TCGA-HC-7738 DUP 26 5 PTPRD PTPRD chr9 9311761 9311761 chr9 9536191 9536191 TCGA-HC-7738 DEL 49 7 PTPRD PTPRD chr9 9450558 9450558 chr9 9473539 9473539 TCGA-HC-7738 DEL 2 25 PTPRD PTPRD chr9 9904780 9904780 chr9 10028224 10028224 TCGA-HC-7738 DUP 48 33 PTPRD PTPRD chrX 101453805 101453805 chrX 101720276 101720276 TCGA-HC-7738 DUP 25 17 ARMCX4 * chrX 132115881 132115881 chrX 134892721 134892721 TCGA-HC-7738 DUP 21 6 FRMD7 MOSPD1 chrX 139912821 139912821 chrX 140101403 140101403 TCGA-HC-7738 DUP 19 23 ATP11C * chrX 145519986 145519986 chrX 146494733 146494733 TCGA-HC-7738 DUP 28 45 * * chrX 150912047 150912047 chrX 151138577 151138577 TCGA-HC-7738 DUP 14 23 * * chrX 155560529 155560529 chrX 155573838 155573838 TCGA-HC-7738 DEL 50 8 TMLHE-AS1 TMLHE-AS1 chrX 38876902 38876902 chrX 39165943 39165943 TCGA-HC-7738 DUP 45 4 * * chrX 43224133 43224133 chrX 43297285 43297285 TCGA-HC-7738 DUP 21 32 PINCR AL023574.1 chrX 5134527 5134527 chrX 6934187 6934187 TCGA-HC-7738 DUP 5 8 * * chrX 56634528 56634528 chrX 56646673 56646673 TCGA-HC-7738 DEL 35 6 * * chrX 62769078 62769078 chrX 62780648 62780648 TCGA-HC-7738 DEL 9 17 * * chrX 66586115 66586115 chrX 67818988 67818988 TCGA-HC-7738 INV 16 11 * * chrX 66831477 66831477 chrX 67083401 67083401 TCGA-HC-7738 DUP 20 25 * * chrX 66894400 66894400 chrX 67147429 67147429 TCGA-HC-7738 DUP 38 36 * * chrX 67818486 67818486 chrX 67942926 67942926 TCGA-HC-7738 INV 35 39 * * chrX 75721757 75721757 chrX 75832250 75832250 TCGA-HC-7738 DUP 11 33 * * chrX 83409629 83409629 chrX 83486128 83486128 TCGA-HC-7738 DUP 25 13 * * chrX 89267128 89267128 chrX 99014171 99014171 TCGA-HC-7738 INV 21 32 * * chrX 95064940 95064940 chrX 95970540 95970540 TCGA-HC-7738 DUP 33 29 * * chrX 9807978 9807978 chrX 10572472 10572472 TCGA-HC-7738 DUP 35 1 SHROOM2 MID1 chr10 18402938 18402938 chr10 34816349 34816349 TCGA-TP-A8TV DEL 43 6 CACNB2 PARD3 chr11 117760287 117760287 chr11 117763392 117763392 TCGA-TP-A8TV DEL 38 14 DSCAML1 DSCAML1 chr12 14785999 14785999 chr12 14786243 14786243 TCGA-TP-A8TV DEL 26 8 WBP11 WBP11 chr12 65511125 65511125 chr12 78563895 78563895 TCGA-TP-A8TV INS 32 38 AC025419.1 * chr13 31627433 31627433 chr13 31635652 31635652 TCGA-TP-A8TV DEL 46 16 * * chr13 40801974 40801974 chr13 40802796 40802796 TCGA-TP-A8TV DEL 45 13 SLC25A15 SLC25A15 chr18 77373395 77373395 chr18 77373596 77373596 TCGA-TP-A8TV DEL 1 47 * * chr18 77602746 77602746 chr18 77607277 77607277 TCGA-TP-A8TV DEL 11 49 * * chr1 163440116 163440116 chr1 165734492 165734492 TCGA-TP-A8TV INS 27 25 * TMCO1 chr20 22247966 22247966 chr20 22248300 22248300 TCGA-TP-A8TV DEL 7 5 * * chr22 20657087 20657087 chr22 20657821 20657821 TCGA-TP-A8TV DEL 47 28 SMPD4P1 SMPD4P1 chr22 20658716 20658716 chr22 20662123 20662123 TCGA-TP-A8TV DEL 12 19 * * chr2 102934676 102934676 chr2 102934936 102934936 TCGA-TP-A8TV DEL 13 11 TMEM182 TMEM182 chr2 8390544 8390544 chr3 23094486 23094486 TCGA-TP-A8TV BND 31 19 * * chr3 144750157 144750157 chr3 144750311 144750311 TCGA-TP-A8TV DEL 26 13 * * chr3 158416854 158416854 chr3 158416954 158416954 TCGA-TP-A8TV DEL 11 45 RSRC1 RSRC1 chr3 167077143 167077143 chr3 167077455 167077455 TCGA-TP-A8TV DEL 49 41 * * chr4 12900405 12900405 chr4 12900946 12900946 TCGA-TP-A8TV DEL 11 39 * * chr4 33183148 33183148 chr4 33184093 33184093 TCGA-TP-A8TV DEL 42 43 * * chr4 66836938 66836938 chr4 66839749 66839749 TCGA-TP-A8TV DEL 4 46 * * chr5 122142609 122142609 chr5 122144448 122144448 TCGA-TP-A8TV DEL 16 8 ZNF474 ZNF474 chr5 99974846 99974846 chr5 99975313 99975313 TCGA-TP-A8TV DEL 45 5 * * chr6 40738728 40738728 chr6 40739547 40739547 TCGA-TP-A8TV DEL 31 36 * * chr8 16892902 16892902 chr8 16893788 16893788 TCGA-TP-A8TV DEL 38 13 AC011586.2 AC011586.2 chr8 97083096 97083096 chr8 97083662 97083662 TCGA-TP-A8TV DEL 21 29 CPQ CPQ chr9 136533072 136533072 chr9 136533344 136533344 TCGA-TP-A8TV DEL 25 2 NOTCH1 NOTCH1 chrX 9003752 9003752 chrX 9003906 9003906 TCGA-TP-A8TV DEL 41 27 * * chr10 123584931 123584931 chr10 123795554 123795554 TCGA-EJ-7789 INS 36 23 * CPXM2 chr10 23104185 23104185 chr10 25944128 25944128 TCGA-EJ-7789 INS 16 3 MSRB2 MYO3A chr10 52374955 52374955 chr10 52558416 52558416 TCGA-EJ-7789 INS 6 48 * LNCAROD chr10 67855286 67855286 chr10 68929119 68929119 TCGA-EJ-7789 INS 9 39 * DDX50 chr11 105194599 105194599 chr20 58264329 58264329 TCGA-EJ-7789 BND 42 8 CARD18 PPP4R1L chr11 105201450 105201450 chr11 105592305 105592305 TCGA-EJ-7789 INS 5 50 CARD18 * chr11 124644217 124644217 chr11 127317949 127317949 TCGA-EJ-7789 INS 3 11 SIAE LINC02712 chr11 45135084 45135084 chrX 87283213 87283213 TCGA-EJ-7789 BND 2 4 PRDM11 * chr11 67172134 67172134 chr11 73146203 73146203 TCGA-EJ-7789 INS 2 11 KDM2A * chr11 81009670 81009670 chr11 81248918 81248918 TCGA-EJ-7789 INS 30 27 * * chr11 90948700 90948700 chr11 91123368 91123368 TCGA-EJ-7789 INS 11 16 * * chr12 26686863 26686863 chr12 27041558 27041558 TCGA-EJ-7789 INS 12 24 ITPR2 MED21 chr12 38386961 38386965 chr6 4408064 4408068 TCGA-EJ-7789 BND 38 46 * AL162718.1 chr12 45341303 45341305 chr8 39868221 39868223 TCGA-EJ-7789 BND 11 23 ANO6 AP005902.1 chr12 54879242 54879242 chr12 58583813 58583813 TCGA-EJ-7789 INS 13 3 * AC020637.1 chr12 66861792 66861792 chr12 70437236 70437236 TCGA-EJ-7789 INS 12 14 GRIP1 * chr12 67194347 67194347 chr12 67207206 67207206 TCGA-EJ-7789 INV 50 31 * * chr12 67194789 67194789 chr12 67205614 67205614 TCGA-EJ-7789 INS 19 36 * * chr12 67198476 67198476 chr12 67207171 67207171 TCGA-EJ-7789 DEL 35 46 * * chr12 67198815 67198815 chr12 67207636 67207636 TCGA-EJ-7789 INV 4 44 * * chr12 78768892 78768892 chr12 83344330 83344330 TCGA-EJ-7789 INS 9 25 * * chr12 90610675 90610675 chr12 91054777 91054777 TCGA-EJ-7789 INS 23 1 * KERA chr13 23647181 23647181 chr13 27481832 27481832 TCGA-EJ-7789 INS 37 49 TNFRSF19 * chr13 75187158 75187158 chr13 75402098 75402098 TCGA-EJ-7789 INS 42 43 * TBC1D4 chr14 24185716 24185716 chr14 24847615 24847615 TCGA-EJ-7789 INS 16 33 IPO4 STXBP6 chr14 30656874 30656874 chr14 34049415 34049415 TCGA-EJ-7789 INS 9 50 SCFD1 EGLN3 chr14 40580417 40580417 chr14 40775736 40775736 TCGA-EJ-7789 INS 30 9 * * chr14 89772630 89772630 chr14 95199711 95199711 TCGA-EJ-7789 INS 14 10 AL137230.2 CLMN chr15 58890500 58890500 chrX 1646950 1646950 TCGA-EJ-7789 BND 37 46 RNF111 * chr15 72697786 72697786 chr15 76901580 76901580 TCGA-EJ-7789 INS 47 7 BBS4 SCAPER chr15 90644077 90644077 chr15 90960767 90960767 TCGA-EJ-7789 INS 34 50 CRTC3 RCCD1 chr15 92281630 92281630 chr15 92630385 92630385 TCGA-EJ-7789 INS 24 26 AC116903.2 FAM174B chr15 96242690 96242690 chr15 96257830 96257830 TCGA-EJ-7789 DEL 14 22 AC012409.2 AC012409.2 chr16 13537335 13537335 chr16 14339768 14339768 TCGA-EJ-7789 INS 16 6 U91319.1 * chr16 1811291 1811291 chr16 4044570 4044570 TCGA-EJ-7789 INS 35 49 HAGH ADCY9 chr16 24736113 24736113 chr1 121743486 121743486 TCGA-EJ-7789 BND 20 5 TNRC6A * chr16 3926072 3926072 chr16 4035149 4035149 TCGA-EJ-7789 INS 35 39 * ADCY9 chr16 3938334 3938334 chr16 3952988 3952988 TCGA-EJ-7789 DEL 32 32 LINC02861 * chr16 3946080 3946080 chr16 4227842 4227842 TCGA-EJ-7789 DEL 35 30 LINC02861 SRL chr16 4041134 4041134 chr16 4228943 4228943 TCGA-EJ-7789 INS 23 5 ADCY9 SRL chr16 4056712 4056712 chr16 4242781 4242781 TCGA-EJ-7789 INS 13 35 ADCY9 SRL chr16 4057678 4057678 chr16 4206834 4206834 TCGA-EJ-7789 DEL 17 15 ADCY9 SRL chr16 4204945 4204945 chr16 31030044 31030044 TCGA-EJ-7789 DEL 20 7 SRL * chr16 70215857 70215857 chr16 71013590 71013590 TCGA-EJ-7789 INS 31 30 * HYDIN chr16 80624954 80624954 chr16 82687879 82687879 TCGA-EJ-7789 DEL 18 46 CDYL2 CDH13 chr16 83660307 83660307 chr16 83933128 83933128 TCGA-EJ-7789 DEL 9 1 CDH13 * chr17 1706445 1706445 chr17 2048749 2048749 TCGA-EJ-7789 INS 18 26 TLCD2 * chr17 22347947 22347947 chr17 27690833 27690833 TCGA-EJ-7789 INS 50 2 * * chr17 27165750 27165750 chr17 27165814 27165814 TCGA-EJ-7789 DEL 48 43 AC129926.2 AC129926.2 chr17 38716546 38716548 chr17 39244399 39244399 TCGA-EJ-7789 INS 26 22 MLLT6 AC015910.1 chr17 51536499 51536499 chr17 53291650 53291650 TCGA-EJ-7789 INS 12 46 * AC034268.2 chr17 52814688 52814688 chr17 54310122 54310122 TCGA-EJ-7789 INS 4 46 * * chr18 2534827 2534827 chr18 3541485 3541485 TCGA-EJ-7789 INS 45 13 * DLGAP1 chr18 30282699 30282699 chr18 34251558 34251558 TCGA-EJ-7789 INS 1 39 * * chr18 43144254 43144254 chr18 47923551 47923551 TCGA-EJ-7789 INS 49 45 * SMAD2 chr19 19235843 19235843 chr19 21750164 21750164 TCGA-EJ-7789 INS 31 20 NCAN ZNF100 chr19 39201293 39201293 chr19 42753958 42753961 TCGA-EJ-7789 INS 46 18 NCCRP1 PSG8 chr19 4419081 4419081 chr19 7246980 7246980 TCGA-EJ-7789 INS 43 32 CHAF1A INSR chr19 56817995 56817995 chr19 57603400 57603400 TCGA-EJ-7789 INS 50 27 ZIM2 ZNF530 chr1 147319027 147319027 chr6 620576 620576 TCGA-EJ-7789 BND 6 30 LINC00624 EXOC2 chr1 153207827 153207827 chr1 155245514 155245514 TCGA-EJ-7789 INS 8 39 * GBA chr1 154251093 154251093 chr1 155533384 155533384 TCGA-EJ-7789 INS 30 1 UBAP2L ASH1L chr1 179374859 179374859 chr1 180512632 180512632 TCGA-EJ-7789 INS 39 49 AXDND1 * chr1 207456267 207456267 chr1 207983928 207983929 TCGA-EJ-7789 INS 32 13 CR2 * chr1 23565538 23565538 chr1 26438392 26438392 TCGA-EJ-7789 INS 4 10 * DHDDS chr1 82303895 82303895 chr1 82851728 82851728 TCGA-EJ-7789 INS 41 38 AL157944.1 * chr1 8715028 8715028 chr1 10610255 10610255 TCGA-EJ-7789 INS 35 29 RERE PEX14 chr1 95317157 95317157 chr1 99193316 99193316 TCGA-EJ-7789 INS 7 40 LINC01760 AL445433.2 chr20 20649460 20649460 chr20 24224738 24224738 TCGA-EJ-7789 INS 36 1 RALGAPA2 * chr20 40499923 40499923 chr20 41757484 41757484 TCGA-EJ-7789 INS 48 13 * * chr20 58265951 58265951 chr11 105194823 105194823 TCGA-EJ-7789 BND 34 45 PPP4R1L CARD18 chr21 23782042 23782044 chr21 24209683 24209683 TCGA-EJ-7789 INS 38 49 * * chr21 31522812 31522812 chr21 34703859 34703859 TCGA-EJ-7789 INS 7 44 TIAM1 CLIC6 chr21 35730491 35730491 chr21 38347604 38347604 TCGA-EJ-7789 INS 32 38 RUNX1 * chr22 24395114 24395114 chr22 25086924 25086924 TCGA-EJ-7789 INS 21 12 SPECC1L KIAA1671 chr22 38337358 38337358 chr22 38648106 38648106 TCGA-EJ-7789 INS 9 37 TPTEP2 FAM227A chr2 104276776 104276776 chr2 105636921 105636921 TCGA-EJ-7789 INS 23 6 * * chr2 11006358 11006358 chr2 13556301 13556301 TCGA-EJ-7789 INS 20 37 * AC073062.1 chr2 140250990 140250990 chr2 140458573 140458573 TCGA-EJ-7789 INS 24 2 LRP1B LRP1B chr2 149860438 149860438 chr2 153652633 153652633 TCGA-EJ-7789 INS 26 21 LINC01931 * chr2 151016609 151016609 chr2 152920585 152920585 TCGA-EJ-7789 INS 1 40 AC023469.1 * chr2 174825100 174825100 chr2 175307714 175307714 TCGA-EJ-7789 INS 50 24 CHN1 AC093459.1 chr2 180511954 180511954 chr2 184169749 184169749 TCGA-EJ-7789 INS 12 27 * * chr2 203167643 203167643 chr2 205255591 205255591 TCGA-EJ-7789 INS 23 3 NBEAL1 PARD3B chr2 234251463 234251463 chr2 237223029 237223029 TCGA-EJ-7789 INS 22 14 * * chr2 25032885 25032885 chr2 29824752 29824752 TCGA-EJ-7789 INS 26 47 DNAJC27-AS1 ALK chr3 100842723 100842723 chr3 101225759 101225759 TCGA-EJ-7789 INS 23 19 ABI3BP IMPG2 chr3 143544711 143544711 chr3 143796141 143796141 TCGA-EJ-7789 INS 23 50 SLC9A9 SLC9A9 chr3 159983914 159983914 chr3 174665399 174665399 TCGA-EJ-7789 DEL 27 10 IL12A-AS1 NAALADL2 chr3 164922138 164922138 chr3 165152790 165152790 TCGA-EJ-7789 INS 33 32 * LINC02023 chr3 169675009 169675009 chr3 173672780 173672780 TCGA-EJ-7789 INS 8 18 * NLGN1 chr3 171804678 171804678 chr3 172790695 172790695 TCGA-EJ-7789 INS 38 14 PLD1 ECT2 chr3 193040228 193040228 chr3 196971456 196971456 TCGA-EJ-7789 INS 16 6 * * chr3 44378404 44378404 chr3 44879845 44879845 TCGA-EJ-7789 INS 3 18 TCAIM TGM4 chr3 4912264 4912264 chr3 5613202 5613202 TCGA-EJ-7789 INS 12 21 BHLHE40-AS1 * chr3 6597735 6597735 chr3 9384892 9384892 TCGA-EJ-7789 INS 47 25 AC069277.1 THUMPD3 chr3 83347907 83347907 chr3 86395584 86395584 TCGA-EJ-7789 INS 47 5 * * chr4 126181545 126181545 chr4 126403768 126403768 TCGA-EJ-7789 INS 38 16 * * chr4 132332401 132332401 chr4 132448908 132448908 TCGA-EJ-7789 INS 37 39 * * chr4 15343450 15343450 chr4 21102886 21102886 TCGA-EJ-7789 INS 23 45 C1QTNF7-AS1 KCNIP4 chr4 180483882 180483884 chr4 180588346 180588346 TCGA-EJ-7789 INS 39 16 * * chr4 18205579 18205579 chr4 18759833 18759833 TCGA-EJ-7789 INS 47 3 * * chr4 183159451 183159451 chr4 183828955 183828955 TCGA-EJ-7789 INS 30 25 WWC2 STOX2 chr4 20321063 20321063 chr4 22757596 22757596 TCGA-EJ-7789 INS 10 40 SLIT2 GBA3 chr4 21863784 21863784 chr4 22485474 22485474 TCGA-EJ-7789 INS 34 48 KCNIP4 ADGRA3 chr4 22197729 22197729 chr4 25859201 25859201 TCGA-EJ-7789 INS 3 36 AC096719.1 SEL1L3 chr4 59669423 59669423 chr4 64308076 64308076 TCGA-EJ-7789 INS 22 50 * TECRL chr4 71775977 71775977 chr4 168837823 168837823 TCGA-EJ-7789 DEL 19 39 GC PALLD chr4 77134055 77134055 chr4 83200931 83200931 TCGA-EJ-7789 INS 25 22 * * chr4 79435810 79435810 chr4 83206578 83206578 TCGA-EJ-7789 INS 46 24 * * chr4 80621266 80621266 chr4 80929610 80929610 TCGA-EJ-7789 INS 22 42 CFAP299 CFAP299 chr4 97845430 97845430 chr4 101117025 101117025 TCGA-EJ-7789 INS 21 3 STPG2 PPP3CA chr5 133830224 133830224 chr5 138294241 138294241 TCGA-EJ-7789 INS 44 7 * CDC25C chr5 163578047 163578047 chr5 164694264 164694264 TCGA-EJ-7789 INS 4 24 * AC109466.1 chr5 164552355 164552355 chr5 164747712 164747712 TCGA-EJ-7789 INS 14 46 AC109466.1 AC109466.1 chr5 21655103 21655103 chr7 68841774 68841774 TCGA-EJ-7789 BND 17 23 AC091946.1 * chr5 30010402 30010402 chr5 30282566 30282566 TCGA-EJ-7789 INS 5 42 * * chr5 51791357 51791357 chr5 51951413 51951413 TCGA-EJ-7789 INS 24 43 * * chr6 114702157 114702157 chr6 114952573 114952573 TCGA-EJ-7789 INS 39 19 * * chr6 124685461 124685461 chr6 128189893 128189893 TCGA-EJ-7789 INS 11 50 NKAIN2 PTPRK chr6 127380548 127380548 chr6 132317060 132317060 TCGA-EJ-7789 INS 11 1 * MOXD1 chr6 130444872 130444872 chr6 131023819 131023819 TCGA-EJ-7789 INS 14 48 * EPB41L2 chr6 153370622 153370622 chr6 156253986 156253986 TCGA-EJ-7789 INS 50 50 * * chr6 19844603 19844603 chr6 22436465 22436465 TCGA-EJ-7789 INS 35 7 * * chr6 21377077 21377083 chr6 24803667 24803667 TCGA-EJ-7789 INS 36 7 * AL512428.1 chr6 30312943 30312943 chr6 32927324 32927324 TCGA-EJ-7789 INS 46 11 HCG17 * chr6 38035630 38035630 chr6 41982757 41982757 TCGA-EJ-7789 INS 2 12 ZFAND3 CCND3 chr6 4408064 4408068 chr12 38386961 38386965 TCGA-EJ-7789 BND 16 13 AL162718.1 * chr6 65807682 65807682 chr16 71155327 71155327 TCGA-EJ-7789 BND 38 47 * HYDIN chr6 89529615 89529615 chr6 89906744 89906744 TCGA-EJ-7789 INS 24 6 ANKRD6 GJA10 chr6 92474047 92474047 chr6 92474512 92474512 TCGA-EJ-7789 DEL 7 20 * * chr7 145832880 145832880 chr7 146208702 146208702 TCGA-EJ-7789 INS 2 35 * CNTNAP2 chr7 157138292 157138292 chr7 157701574 157701574 TCGA-EJ-7789 INS 49 29 UBE3C PTPRN2 chr7 97801646 97801646 chr7 100768267 100768267 TCGA-EJ-7789 INS 4 37 * ZAN chr8 122722015 122722020 chr8 125603508 125603508 TCGA-EJ-7789 INS 17 49 * * chr8 17175101 17175101 chr8 17973649 17973655 TCGA-EJ-7789 INS 50 35 ZDHHC2 PCM1 chr8 39868221 39868223 chr12 45341303 45341305 TCGA-EJ-7789 BND 6 50 AP005902.1 ANO6 chr8 78610582 78610582 chr8 78975546 78975546 TCGA-EJ-7789 INS 28 45 * * chr8 84525085 84525085 chr8 84802195 84802195 TCGA-EJ-7789 INS 10 19 RALYL RALYL chr9 102364306 102364306 chr9 102853821 102853821 TCGA-EJ-7789 INS 39 22 * * chr9 115902651 115902651 chr9 116318770 116318770 TCGA-EJ-7789 INS 35 17 LINC00474 PAPPA chr9 76840255 76840255 chr9 82329679 82329679 TCGA-EJ-7789 INS 35 40 PRUNE2 AL162726.3 chr9 80966424 80966424 chr9 84136031 84136031 TCGA-EJ-7789 INS 47 35 * * chr9 85652369 85652369 chr9 89616185 89616185 TCGA-EJ-7789 INS 46 6 AGTPBP1 * chr9 86409038 86409038 chr9 90764010 90764010 TCGA-EJ-7789 INS 4 24 * * chr9 91871724 91871724 chr9 96425157 96425157 TCGA-EJ-7789 INS 30 49 ROR2 * chrX 124857453 124857453 chrX 126655695 126655695 TCGA-EJ-7789 INS 28 1 TENM1 * chrX 136566377 136566377 chrX 139215447 139215447 TCGA-EJ-7789 INS 21 38 * FGF13 chrX 152242031 152242031 chr18 15095249 15095249 TCGA-EJ-7789 BND 27 1 GABRA3 AP005242.1 chrX 43501843 43501843 chrX 44251525 44251525 TCGA-EJ-7789 INS 40 13 * EFHC2 chrX 86693417 86693417 chrX 90528221 90528221 TCGA-EJ-7789 INS 41 39 DACH2 * chrX 87486989 87486989 chr11 45135282 45135282 TCGA-EJ-7789 BND 47 5 * PRDM11 chr10 115537713 115537713 chr8 47284415 47284415 TCGA-ZG-A9L0 BND 41 12 ATRNL1 SPIDR chr10 36718860 36718860 chr6 158044400 158044400 TCGA-ZG-A9L0 BND 19 12 * SYNJ2 chr10 72357191 72357191 chr10 72357400 72357400 TCGA-ZG-A9L0 INS 35 32 * * chr10 98603450 98603450 chr3 102120425 102120425 TCGA-ZG-A9L0 BND 1 18 HPSE2 ZPLD1 chr11 31841876 31841880 chr11 31848240 31848240 TCGA-ZG-A9L0 DEL 41 50 PAUPAR PAUPAR chr11 31841876 31841880 chr11 31848038 31848038 TCGA-ZG-A9L0 INS 3 36 PAUPAR PAUPAR chr11 37189635 37189635 chr11 37196338 37196338 TCGA-ZG-A9L0 DEL 15 46 * * chr11 37415408 37415408 chr11 38974179 38974179 TCGA-ZG-A9L0 DEL 48 48 * * chr11 40953080 40953080 chr11 40956951 40956951 TCGA-ZG-A9L0 DEL 18 24 LRRC4C LRRC4C chr11 61670910 61670911 chr12 97697386 97697387 TCGA-ZG-A9L0 BND 24 14 * * chr11 61860842 61860842 chr12 109157594 109157594 TCGA-ZG-A9L0 BND 11 10 FADS2 ACACB chr11 61886561 61886561 chr11 70285645 70285645 TCGA-ZG-A9L0 INS 8 50 FADS3 PPFIA1 chr11 68358656 68358657 chr17 17717680 17717681 TCGA-ZG-A9L0 BND 27 6 LRP5 RAI1 chr11 69086073 69086074 chr12 107940665 107940666 TCGA-ZG-A9L0 BND 10 14 TPCN2 * chr11 70230965 70230972 chr12 102412175 102412182 TCGA-ZG-A9L0 BND 14 6 * IGF1 chr11 70893033 70893033 chr11 70895430 70895430 TCGA-ZG-A9L0 DEL 46 25 SHANK2 SHANK2 chr11 77219758 77219758 chr18 35128794 35128794 TCGA-ZG-A9L0 BND 2 45 GDPD4 MAPRE2 chr11 91366477 91366477 chr11 91367351 91367351 TCGA-ZG-A9L0 DEL 5 46 * * chr12 101457409 101457409 chr11 68507578 68507578 TCGA-ZG-A9L0 BND 4 38 * PPP6R3 chr12 102412175 102412182 chr11 70230965 70230972 TCGA-ZG-A9L0 BND 19 29 IGF1 * chr12 108531472 108531472 chr11 70403924 70403924 TCGA-ZG-A9L0 BND 40 29 SART3 CTTN chr12 7233161 7233161 chr12 31218518 31218518 TCGA-ZG-A9L0 DEL 2 41 * * chr12 8064565 8064565 chr12 8909903 8909903 TCGA-ZG-A9L0 INS 12 3 C3AR1 AC006581.2 chr12 84077567 84077567 chr3 75660784 75660784 TCGA-ZG-A9L0 BND 10 44 * RPL23AP49 chr12 9109034 9109034 chr2 21296188 21296188 TCGA-ZG-A9L0 BND 1 46 A2M AC018742.1 chr12 97618066 97618066 chr11 69525458 69525458 TCGA-ZG-A9L0 BND 10 16 * * chr12 97690946 97690946 chr17 18292515 18292515 TCGA-ZG-A9L0 BND 47 7 * TOP3A chr12 97701460 97701460 chr11 70245325 70245325 TCGA-ZG-A9L0 BND 39 41 * * chr13 37288503 37288503 chr13 39468025 39468025 TCGA-ZG-A9L0 INS 39 14 * LHFPL6 chr13 37996156 37996156 chr13 39483232 39483232 TCGA-ZG-A9L0 DEL 2 42 HSPD1P9 LHFPL6 chr13 38562932 38562932 chr13 39488803 39488803 TCGA-ZG-A9L0 DEL 12 48 * LHFPL6 chr13 38590585 38590585 chr13 87612109 87612109 TCGA-ZG-A9L0 INS 21 47 * MIR4500HG chr13 55190560 55190560 chr13 57291876 57291876 TCGA-ZG-A9L0 DEL 34 20 * * chr13 55775922 55775922 chr13 80589198 80589198 TCGA-ZG-A9L0 INS 38 38 * * chr13 57257816 57257816 chr13 81114455 81114455 TCGA-ZG-A9L0 DEL 29 38 * * chr13 57879168 57879168 chr13 57974152 57974152 TCGA-ZG-A9L0 DEL 6 44 * * chr13 68154557 68154557 chr13 68167243 68167243 TCGA-ZG-A9L0 DEL 4 49 * * chr13 77313490 77313490 chr13 77409904 77409904 TCGA-ZG-A9L0 DEL 38 39 MYCBP2 * chr13 86788459 86788459 chr13 91474104 91474104 TCGA-ZG-A9L0 DEL 9 17 * GPC5 chr13 88284435 88284435 chr13 89440133 89440133 TCGA-ZG-A9L0 DEL 26 23 * * chr14 28009747 28009747 chr14 28009909 28009909 TCGA-ZG-A9L0 DEL 29 7 * * chr14 81296947 81296947 chr14 82203074 82203074 TCGA-ZG-A9L0 DEL 46 39 STON2 * chr14 82237435 82237435 chr14 82298043 82298043 TCGA-ZG-A9L0 DEL 17 37 * * chr14 82241198 82241198 chr14 83065379 83065379 TCGA-ZG-A9L0 INS 50 4 * * chr14 82943609 82943609 chr14 82969997 82969997 TCGA-ZG-A9L0 DEL 40 10 * * chr15 45811754 45811754 chr5 31640070 31640070 TCGA-ZG-A9L0 BND 23 38 AC068722.1 PDZD2 chr16 25254895 25254895 chr16 25255027 25255027 TCGA-ZG-A9L0 DEL 31 9 ZKSCAN2 ZKSCAN2 chr17 17208964 17208964 chr11 71544962 71544962 TCGA-ZG-A9L0 BND 19 48 MPRIP * chr17 17757143 17757143 chr11 71385429 71385429 TCGA-ZG-A9L0 BND 7 36 RAI1 ACTE1P chr1 157130664 157130664 chr1 157138475 157138475 TCGA-ZG-A9L0 DEL 24 14 ETV3 ETV3 chr1 165520150 165520150 chr3 102470732 102470732 TCGA-ZG-A9L0 BND 19 2 LRRC52-AS1 ZPLD1 chr1 189848015 189848015 chr1 189861447 189861447 TCGA-ZG-A9L0 DEL 45 38 * * chr1 199285522 199285522 chr1 199287569 199287571 TCGA-ZG-A9L0 DEL 27 21 LINC02789 LINC02789 chr1 236914633 236914633 chr1 236916776 236916776 TCGA-ZG-A9L0 DEL 9 26 * * chr1 240355543 240355543 chr1 241222843 241222843 TCGA-ZG-A9L0 DEL 1 44 FMN2 RGS7 chr1 241204088 241204088 chr1 241316435 241316435 TCGA-ZG-A9L0 INS 8 36 RGS7 RGS7 chr20 49369370 49369370 chrX 86013734 86013734 TCGA-ZG-A9L0 BND 40 9 KCNB1 CHM chr21 38408144 38408144 chr4 189698186 189698186 TCGA-ZG-A9L0 BND 15 43 ERG * chr2 129890563 129890563 chr2 150152761 150152761 TCGA-ZG-A9L0 DEL 17 8 * * chr2 141430195 141430195 chr21 31844524 31844524 TCGA-ZG-A9L0 BND 1 50 LRP1B * chr2 143640000 143640000 chr2 144902693 144902693 TCGA-ZG-A9L0 INS 34 28 ARHGAP15 TEX41 chr2 144318196 144318200 chr2 149496751 149496751 TCGA-ZG-A9L0 INS 41 12 GTDC1 * chr2 145900547 145900547 chr16 62516908 62516908 TCGA-ZG-A9L0 BND 49 45 * * chr2 149508373 149508373 chr2 213950901 213950901 TCGA-ZG-A9L0 INS 32 15 * SPAG16 chr2 155187094 155187094 chr2 187510711 187510711 TCGA-ZG-A9L0 DEL 21 8 * AC007319.1 chr2 20542143 20542143 chr2 24080575 24080575 TCGA-ZG-A9L0 DEL 43 24 * FAM228B chr2 211901098 211901098 chr2 213951447 213951447 TCGA-ZG-A9L0 DEL 41 47 ERBB4 SPAG16 chr2 212577202 212577202 chr2 212578716 212578716 TCGA-ZG-A9L0 DEL 2 17 * * chr2 218223239 218223239 chr2 218224384 218224384 TCGA-ZG-A9L0 DEL 31 31 ARPC2 ARPC2 chr2 23118130 23118131 chr12 8843971 8843972 TCGA-ZG-A9L0 BND 30 1 AC018467.1 A2ML1 chr2 38391085 38391085 chr2 38449204 38449204 TCGA-ZG-A9L0 DEL 38 41 * LINC02613 chr2 39325542 39325542 chr2 39331893 39331893 TCGA-ZG-A9L0 DEL 6 32 MAP4K3 MAP4K3 chr2 40820210 40820210 chr2 40824809 40824812 TCGA-ZG-A9L0 DEL 41 7 * * chr2 81853622 81853622 chr2 81885769 81885769 TCGA-ZG-A9L0 DEL 33 32 * * chr2 82329207 82329207 chr2 87692003 87692003 TCGA-ZG-A9L0 INS 9 21 * AC133644.2 chr3 113103597 113103597 chr3 113103727 113103727 TCGA-ZG-A9L0 DEL 2 50 AC078785.1 AC078785.1 chr3 173998397 173998397 chr3 174017525 174017525 TCGA-ZG-A9L0 DEL 9 32 NLGN1 NLGN1 chr3 67687290 67687291 chr6 138699350 138699351 TCGA-ZG-A9L0 BND 23 48 SUCLG2-AS1 * chr3 93941609 93941609 chr3 94007740 94007740 TCGA-ZG-A9L0 DEL 34 12 PROS1 ARL13B chr3 94929413 94929413 chr3 95235164 95235164 TCGA-ZG-A9L0 DEL 26 5 * * chr3 94966886 94966886 chr5 102834255 102834255 TCGA-ZG-A9L0 BND 16 44 LINC00879 PAM chr3 95217515 95217515 chr3 95303710 95303710 TCGA-ZG-A9L0 DEL 4 38 * * chr4 105435369 105435369 chr8 122358201 122358201 TCGA-ZG-A9L0 BND 5 13 PPA2 * chr4 106943348 106943348 chr4 106946649 106946649 TCGA-ZG-A9L0 DEL 32 42 DKK2 DKK2 chr4 111092519 111092519 chr4 125492668 125492668 TCGA-ZG-A9L0 INS 34 26 * FAT4 chr4 112060212 112060212 chr4 125507450 125507450 TCGA-ZG-A9L0 DEL 32 11 AC004704.1 * chr4 114470887 114470887 chr4 133576438 133576438 TCGA-ZG-A9L0 DEL 25 39 * AC105252.1 chr4 120712384 120712384 chr4 137732904 137732904 TCGA-ZG-A9L0 DEL 9 23 PRDM5 AC131956.2 chr4 123903130 123903130 chr4 129852139 129852139 TCGA-ZG-A9L0 DEL 42 19 LINC01091 LINC02465 chr4 129991151 129991151 chr4 137484079 137484079 TCGA-ZG-A9L0 DEL 49 47 * * chr4 137744639 137744639 chr4 138173329 138173329 TCGA-ZG-A9L0 DEL 17 48 * SLC7A11 chr4 26286305 26286305 chr4 26286473 26286473 TCGA-ZG-A9L0 INS 7 4 RBPJ RBPJ chr4 61403050 61403050 chr4 61425490 61425490 TCGA-ZG-A9L0 DEL 12 34 ADGRL3 ADGRL3 chr4 63313359 63313359 chr4 64268413 64268413 TCGA-ZG-A9L0 DEL 6 41 * * chr4 83900863 83900863 chr12 94599571 94599571 TCGA-ZG-A9L0 BND 30 3 AC079160.1 TMCC3 chr4 91592365 91592365 chr4 91605627 91605627 TCGA-ZG-A9L0 INS 8 1 CCSER1 * chr5 102834255 102834255 chr3 94966886 94966886 TCGA-ZG-A9L0 BND 43 34 PAM LINC00879 chr5 12677981 12677981 chr5 12795045 12795045 TCGA-ZG-A9L0 DEL 9 2 LINC01194 LINC01194 chr5 1950215 1950215 chr5 1957331 1957332 TCGA-ZG-A9L0 DEL 16 13 AC124852.1 AC124852.1 chr5 21645776 21645776 chr5 101451562 101451562 TCGA-ZG-A9L0 DEL 12 40 AC091946.1 * chr5 21837249 21837249 chr5 101542947 101542947 TCGA-ZG-A9L0 INS 4 17 CDH12 * chr5 22825413 22825413 chr5 22825551 22825551 TCGA-ZG-A9L0 DEL 43 16 CDH12 CDH12 chr5 29530093 29530093 chr5 29539962 29539975 TCGA-ZG-A9L0 DEL 11 32 * * chr5 39189798 39189798 chr5 39190451 39190451 TCGA-ZG-A9L0 DEL 14 6 FYB1 FYB1 chr5 89484480 89484480 chr5 165632629 165632629 TCGA-ZG-A9L0 DEL 35 29 * AC008415.1 chr6 158005136 158005136 chr2 43020112 43020112 TCGA-ZG-A9L0 BND 33 29 SYNJ2 * chr6 63861308 63861308 chr6 116460844 116460845 TCGA-ZG-A9L0 DEL 33 30 EYS Z84488.1 chr7 148320039 148320039 chr7 148396006 148396006 TCGA-ZG-A9L0 INS 31 31 CNTNAP2 CNTNAP2 chr7 153963344 153963344 chr7 153964391 153964391 TCGA-ZG-A9L0 INS 48 24 DPP6 DPP6 chr7 79545563 79545563 chr7 79569281 79569281 TCGA-ZG-A9L0 DEL 11 32 NUP35P2 * chr8 10457432 10457432 chr14 106157073 106157073 TCGA-ZG-A9L0 BND 25 40 * * chr8 113784093 113784093 chr8 113784301 113784301 TCGA-ZG-A9L0 DEL 38 24 * * chr8 24938177 24938177 chr16 82860944 82860944 TCGA-ZG-A9L0 BND 1 24 * CDH13 chr8 31480504 31480504 chr8 31480638 31480638 TCGA-ZG-A9L0 DEL 43 6 * * chr8 54397181 54397181 chr8 54397489 54397489 TCGA-ZG-A9L0 DEL 6 17 * * chr8 76365817 76365817 chr8 80963399 80963399 TCGA-ZG-A9L0 DEL 49 8 * * chr8 76539832 76539832 chr8 78483698 78483698 TCGA-ZG-A9L0 DEL 20 7 ZFHX4-AS1 PKIA-AS1 chr8 76711939 76711939 chr8 80942842 80942842 TCGA-ZG-A9L0 INS 10 22 ZFHX4 * chr8 77237211 77237211 chr8 80710669 80710669 TCGA-ZG-A9L0 DEL 44 35 * ZNF704 chr8 78257177 78257177 chr8 81153885 81153885 TCGA-ZG-A9L0 DEL 14 39 * AC079209.1 chr8 78274045 78274045 chr8 79430511 79430511 TCGA-ZG-A9L0 INS 9 24 * * chr8 78496142 78496142 chr8 87392708 87392708 TCGA-ZG-A9L0 DEL 42 14 PKIA-AS1 CNBD1 chr8 79113558 79113558 chr8 80797837 80797837 TCGA-ZG-A9L0 DEL 30 10 * ZNF704 chr8 79241338 79241338 chr8 81260974 81260974 TCGA-ZG-A9L0 DEL 22 11 * * chr8 79271160 79271160 chr8 81204518 81204518 TCGA-ZG-A9L0 INS 35 45 * * chr8 79876167 79876167 chr8 80758269 80758269 TCGA-ZG-A9L0 INS 42 18 * ZNF704 chr8 80596337 80596337 chr8 80943022 80943022 TCGA-ZG-A9L0 DEL 12 50 SLC25A51P3 * chr8 80797091 80797091 chr8 86350608 86350608 TCGA-ZG-A9L0 INS 32 11 ZNF704 WWP1 chr8 81224364 81224364 chr8 86395884 86395884 TCGA-ZG-A9L0 DEL 1 18 * WWP1 chr8 87589065 87589065 chr8 87878897 87878897 TCGA-ZG-A9L0 DEL 33 18 CNBD1 * chr8 98496821 98496821 chr8 98496939 98496939 TCGA-ZG-A9L0 DEL 49 8 STK3 STK3 chr9 30345791 30345791 chr9 30346097 30346097 TCGA-ZG-A9L0 DEL 1 39 * * chr9 9626268 9626268 chr9 9664352 9664352 TCGA-ZG-A9L0 DEL 16 35 PTPRD PTPRD chrX 143450864 143450864 chr2 185386141 185386141 TCGA-ZG-A9L0 BND 45 48 AC239727.1 * chrX 62591915 62591915 chrX 63332695 63332695 TCGA-ZG-A9L0 DEL 23 16 * * chrX 84910795 84910795 chrX 142898071 142898071 TCGA-ZG-A9L0 DEL 45 31 * * chrX 85317596 85317596 chr2 185386971 185386971 TCGA-ZG-A9L0 BND 17 15 POF1B * chrX 85325246 85325246 chrX 142843927 142843927 TCGA-ZG-A9L0 INS 29 21 POF1B * chrX 99267778 99267778 chrX 99268490 99268490 TCGA-ZG-A9L0 DEL 45 41 * * chr10 100517465 100517465 chr10 111799436 111799436 TCGA-EJ-A65M DEL 18 11 SEC31B * chr10 20113472 20113472 chr3 191327153 191327153 TCGA-EJ-A65M BND 3 2 PLXDC2 UTS2B chr10 20200436 20200447 chr3 190997264 190997275 TCGA-EJ-A65M BND 32 12 PLXDC2 * chr10 20280347 20280347 chr10 20649788 20649788 TCGA-EJ-A65M DEL 3 31 PLXDC2 * chr10 21099566 21099577 chr3 164194672 164194683 TCGA-EJ-A65M BND 9 32 NEBL * chr10 21255706 21255706 chr3 190911056 190911056 TCGA-EJ-A65M BND 22 18 * * chr11 101550119 101550119 chr11 101554774 101554774 TCGA-EJ-A65M DEL 3 24 TRPC6 TRPC6 chr11 103331759 103331759 chr11 103338379 103338379 TCGA-EJ-A65M DEL 33 24 DYNC2H1 DYNC2H1 chr11 38281570 38281570 chr11 38292540 38292540 TCGA-EJ-A65M DEL 18 9 * * chr11 38592538 38592542 chr4 182233947 182233951 TCGA-EJ-A65M BND 8 18 * TENM3 chr11 39657071 39657071 chr4 181433988 181433988 TCGA-EJ-A65M BND 30 39 * * chr11 40901005 40901005 chr11 40902282 40902282 TCGA-EJ-A65M DEL 19 33 LRRC4C LRRC4C chr11 45700951 45700951 chr11 49856117 49856117 TCGA-EJ-A65M DEL 13 14 * AP006587.4 chr11 46752181 46752181 chr11 50529268 50529268 TCGA-EJ-A65M DEL 47 30 CKAP5 * chr11 48066933 48066933 chr6 123607119 123607119 TCGA-EJ-A65M BND 18 20 PTPRJ TRDN chr11 48084241 48084241 chr11 48128208 48128208 TCGA-EJ-A65M DEL 2 10 PTPRJ PTPRJ chr11 48313278 48313280 chr6 64663194 64663196 TCGA-EJ-A65M BND 48 42 * EYS chr11 48513342 48513345 chr8 59440633 59440636 TCGA-EJ-A65M BND 15 36 * * chr11 49854567 49854568 chr8 55552685 55552686 TCGA-EJ-A65M BND 49 4 AP006587.4 * chr11 49936285 49936285 chr8 56685509 56685509 TCGA-EJ-A65M BND 28 2 * * chr11 50410440 50410445 chr8 57172455 57172460 TCGA-EJ-A65M BND 46 24 AC024405.1 LINC01606 chr11 55216215 55216216 chr4 189086082 189086083 TCGA-EJ-A65M BND 7 15 * * chr11 55223491 55223491 chr4 178670543 178670543 TCGA-EJ-A65M BND 41 15 * * chr11 90538022 90538022 chr11 90544306 90544306 TCGA-EJ-A65M DEL 50 41 DISC1FP1 DISC1FP1 chr11 99137057 99137057 chr11 100067871 100067871 TCGA-EJ-A65M DEL 18 17 CNTN5 CNTN5 chr11 99824672 99824672 chr11 99880942 99880942 TCGA-EJ-A65M DEL 6 18 CNTN5 CNTN5 chr12 126947275 126947275 chr8 56141576 56141576 TCGA-EJ-A65M BND 32 16 LINC02405 * chr12 128836199 128836199 chr12 129612123 129612123 TCGA-EJ-A65M DEL 5 48 * TMEM132D chr12 129612037 129612037 chr9 28481418 28481418 TCGA-EJ-A65M BND 50 9 TMEM132D LINGO2 chr12 19338497 19338500 chr18 33171103 33171106 TCGA-EJ-A65M BND 34 49 PLEKHA5 CCDC178 chr12 20257265 20257265 chr12 20803176 20803176 TCGA-EJ-A65M DEL 35 36 * * chr12 20264500 20264500 chr18 30215707 30215707 TCGA-EJ-A65M BND 26 18 * * chr12 37504189 37504189 chr12 37529225 37529225 TCGA-EJ-A65M DEL 35 19 * * chr12 37588844 37588844 chr12 37589984 37589984 TCGA-EJ-A65M DEL 38 49 * * chr12 40192980 40192980 chr12 40200892 40200892 TCGA-EJ-A65M DEL 3 31 LINC02471 LRRK2 chr12 71836146 71836146 chr12 80027360 80027360 TCGA-EJ-A65M DEL 35 7 AC089984.2 * chr12 87498020 87498020 chr12 87498199 87498199 TCGA-EJ-A65M DEL 27 29 * * chr13 107168374 107168374 chr13 107168571 107168571 TCGA-EJ-A65M DEL 16 12 FAM155A FAM155A chr13 37027293 37027293 chr13 61766422 61766422 TCGA-EJ-A65M DEL 23 33 SUPT20H * chr13 38961470 38961470 chr13 38962421 38962421 TCGA-EJ-A65M DEL 40 44 * * chr13 61701879 61701879 chr13 62066449 62066449 TCGA-EJ-A65M INS 30 30 * * chr13 61703733 61703733 chr13 62113075 62113075 TCGA-EJ-A65M DEL 38 22 * * chr13 67402474 67402474 chr13 67405176 67405176 TCGA-EJ-A65M DEL 47 17 * * chr13 71945460 71945460 chr13 73705320 73705320 TCGA-EJ-A65M DEL 42 6 * KLF12 chr13 81104720 81104720 chr13 82001313 82001313 TCGA-EJ-A65M DEL 17 8 * * chr13 81985826 81985826 chr7 124492953 124492953 TCGA-EJ-A65M BND 16 32 * * chr13 82371742 82371742 chr13 82372059 82372059 TCGA-EJ-A65M DEL 3 38 * * chr13 82974557 82974557 chr13 84658172 84658172 TCGA-EJ-A65M INS 27 40 * * chr13 83342826 83342826 chr13 85665232 85665232 TCGA-EJ-A65M DEL 28 7 * * chr13 83508419 83508419 chr13 83997944 83997944 TCGA-EJ-A65M INS 19 40 * * chr13 83981246 83981246 chr13 85097051 85097051 TCGA-EJ-A65M INS 46 35 * * chr13 90231966 90231966 chr13 92676247 92676247 TCGA-EJ-A65M DEL 18 1 * GPC5 chr13 90804259 90804261 chr7 124804338 124804340 TCGA-EJ-A65M BND 15 45 * * chr14 37826085 37826085 chr14 37826475 37826475 TCGA-EJ-A65M DEL 4 47 TTC6 TTC6 chr14 42550057 42550074 chr14 42565645 42565645 TCGA-EJ-A65M DEL 2 39 AL442163.1 AL442163.1 chr14 49379222 49379222 chr14 49386628 49386628 TCGA-EJ-A65M DEL 7 45 * * chr14 51118125 51118125 chr4 115018326 115018326 TCGA-EJ-A65M BND 33 39 * NDST4 chr14 52391526 52391526 chr14 52392409 52392409 TCGA-EJ-A65M DEL 35 19 * * chr14 86301458 86301458 chr14 86301611 86301611 TCGA-EJ-A65M DEL 10 45 * * chr15 31818550 31818550 chr15 42329756 42329756 TCGA-EJ-A65M DEL 26 31 OTUD7A GANC chr16 7102682 7102682 chr16 7103341 7103341 TCGA-EJ-A65M DEL 37 34 RBFOX1 RBFOX1 chr17 53089192 53089192 chr17 53715233 53715233 TCGA-EJ-A65M DEL 36 28 * AC034268.2 chr17 53636247 53636249 chr7 10909983 10909985 TCGA-EJ-A65M BND 27 25 AC034268.2 * chr18 29307868 29307868 chr18 33185924 33185924 TCGA-EJ-A65M DEL 25 36 AC074237.1 CCDC178 chr18 29330958 29330958 chr18 29338469 29338469 TCGA-EJ-A65M DEL 30 15 AC074237.1 AC074237.1 chr18 29912453 29912453 chr18 29946407 29946407 TCGA-EJ-A65M DEL 44 29 * * chr18 30196461 30196461 chr18 30333587 30333587 TCGA-EJ-A65M DEL 15 38 * * chr18 33171103 33171106 chr12 19338497 19338500 TCGA-EJ-A65M BND 37 44 CCDC178 PLEKHA5 chr18 33267574 33267574 chr18 33284354 33284354 TCGA-EJ-A65M DEL 19 20 CCDC178 CCDC178 chr18 37056153 37056153 chr18 37058841 37058841 TCGA-EJ-A65M DEL 36 18 KIAA1328 KIAA1328 chr18 37844357 37844357 chr18 41185170 41185170 TCGA-EJ-A65M INS 11 47 * * chr18 41574096 41574096 chr18 43760276 43760276 TCGA-EJ-A65M DEL 40 49 KC6 * chr18 68563640 68563640 chr18 69414937 69414937 TCGA-EJ-A65M INS 1 46 * DOK6 chr18 68882256 68882256 chr5 106494244 106494244 TCGA-EJ-A65M BND 38 2 CCDC102B * chr18 68999237 68999237 chr18 69300803 69300803 TCGA-EJ-A65M DEL 15 24 CCDC102B * chr18 69245477 69245477 chr18 70010912 70010912 TCGA-EJ-A65M INS 3 7 AC090337.2 RTTN chr18 69268195 69268197 chr5 87393204 87393206 TCGA-EJ-A65M BND 1 4 * CCNH chr18 69431034 69431036 chr5 131095088 131095090 TCGA-EJ-A65M BND 7 7 DOK6 * chr18 69767544 69767548 chr5 87871841 87871845 TCGA-EJ-A65M BND 21 7 DOK6 * chr18 70086898 70086898 chr5 88502564 88502564 TCGA-EJ-A65M BND 47 1 RTTN * chr18 70225149 70225149 chr18 70247591 70247591 TCGA-EJ-A65M DEL 11 12 * * chr18 70580089 70580097 chr5 107411887 107411895 TCGA-EJ-A65M BND 41 46 * EFNA5 chr1 104417541 104417541 chr8 12775731 12775731 TCGA-EJ-A65M BND 30 42 * AC123777.1 chr1 105234864 105234864 chr8 25177257 25177257 TCGA-EJ-A65M BND 3 19 * * chr1 105729390 105729394 chr8 24096432 24096436 TCGA-EJ-A65M BND 39 2 * * chr1 106203068 106203068 chr8 8604681 8604681 TCGA-EJ-A65M BND 18 5 * * chr1 107856980 107856980 chr8 23269045 23269045 TCGA-EJ-A65M BND 16 46 VAV3 R3HCC1 chr1 108557255 108557258 chr8 24133555 24133558 TCGA-EJ-A65M BND 43 2 * * chr1 108934426 108934435 chr8 13887949 13887958 TCGA-EJ-A65M BND 40 12 GPSM2 * chr1 147111655 147111655 chr1 155667457 155667457 TCGA-EJ-A65M DEL 4 26 NBPF13P YY1AP1 chr1 147320483 147320483 chr7 54224366 54224366 TCGA-EJ-A65M BND 11 15 LINC00624 * chr1 147640075 147640075 chr1 163194535 163194535 TCGA-EJ-A65M DEL 39 20 ACP6 RGS5 chr1 147817220 147817220 chr1 162730657 162730657 TCGA-EJ-A65M DEL 35 50 * DDR2 chr1 174950338 174950338 chr1 176923326 176923326 TCGA-EJ-A65M DEL 40 8 RABGAP1L ASTN1 chr1 174974285 174974285 chr1 176910112 176910112 TCGA-EJ-A65M INS 22 44 RABGAP1L ASTN1 chr1 178733340 178733340 chr1 194569834 194569834 TCGA-EJ-A65M INS 48 44 RALGPS2 * chr1 192345846 192345846 chr1 196422063 196422063 TCGA-EJ-A65M DEL 39 10 AL390957.1 KCNT2 chr1 193163836 193163837 chr1 240176248 240176248 TCGA-EJ-A65M INS 47 36 CDC73 FMN2 chr1 193316199 193316199 chr1 237611673 237611673 TCGA-EJ-A65M INS 45 28 LINC01031 RYR2 chr1 193407514 193407514 chr1 193408686 193408697 TCGA-EJ-A65M DEL 19 35 * * chr1 193408686 193408697 chr1 194417626 194417626 TCGA-EJ-A65M DEL 15 21 * * chr1 194129000 194129000 chr1 240149091 240149091 TCGA-EJ-A65M INS 31 4 * FMN2 chr1 195517393 195517393 chr1 196374529 196374529 TCGA-EJ-A65M INS 11 50 * KCNT2 chr1 240217298 240217298 chr1 240964299 240964299 TCGA-EJ-A65M DEL 7 28 FMN2 RGS7 chr1 241179270 241179270 chr1 243649389 243649389 TCGA-EJ-A65M DEL 49 46 RGS7 AKT3 chr1 242488005 242488005 chr1 242488766 242488766 TCGA-EJ-A65M DEL 49 33 PLD5 PLD5 chr1 72735925 72735925 chr1 77648586 77648586 TCGA-EJ-A65M INS 48 45 * ZZZ3 chr1 83621680 83621680 chr1 83621772 83621772 TCGA-EJ-A65M DEL 46 15 LINC01725 LINC01725 chr1 95768808 95768808 chr1 95769497 95769497 TCGA-EJ-A65M DEL 28 38 LINC02607 LINC02607 chr20 15900133 15900133 chr20 16224766 16224766 TCGA-EJ-A65M DEL 16 15 MACROD2 PPIAP17 chr20 23950170 23950170 chr20 24008602 24008602 TCGA-EJ-A65M INS 4 25 * * chr22 28669977 28669987 chr4 45972863 45972863 TCGA-EJ-A65M BND 14 16 TTC28 * chr2 114688624 114688624 chr2 115268236 115268236 TCGA-EJ-A65M DEL 36 21 DPP10 DPP10 chr2 116021728 116021728 chr2 116024293 116024293 TCGA-EJ-A65M DEL 47 11 * * chr2 118532772 118532772 chr2 154371758 154371758 TCGA-EJ-A65M INS 40 41 * GALNT13 chr2 118675581 118675581 chr2 118678355 118678355 TCGA-EJ-A65M DEL 4 24 * * chr2 118678786 118678786 chr2 155079039 155079039 TCGA-EJ-A65M DEL 19 6 * * chr2 122560677 122560677 chr2 123104653 123104653 TCGA-EJ-A65M DEL 9 8 * * chr2 122997962 122997962 chr2 123498008 123498008 TCGA-EJ-A65M INS 38 7 * * chr2 123578140 123578140 chr2 212627400 212627400 TCGA-EJ-A65M INS 25 1 * AC093865.1 chr2 133293833 133293833 chr2 137564682 137564682 TCGA-EJ-A65M DEL 14 16 NCKAP5 THSD7B chr2 139451368 139451368 chr2 140693750 140693750 TCGA-EJ-A65M DEL 3 6 * LRP1B chr2 139781457 139781457 chr2 139791168 139791168 TCGA-EJ-A65M DEL 48 6 * * chr2 141687102 141687102 chr2 141708948 141708948 TCGA-EJ-A65M DEL 18 17 LRP1B LRP1B chr2 145516120 145516120 chr2 154038397 154038397 TCGA-EJ-A65M INS 28 41 * GALNT13 chr2 146057114 146057114 chr2 146206711 146206711 TCGA-EJ-A65M DEL 16 45 * * chr2 151215329 151215329 chr2 151223856 151223856 TCGA-EJ-A65M DEL 24 46 * * chr2 153415046 153415046 chr2 153450747 153450747 TCGA-EJ-A65M DEL 48 40 * AC012501.2 chr2 154063442 154063442 chrY 56752210 56752210 TCGA-EJ-A65M BND 44 40 GALNT13 * chr2 165330444 165330444 chr2 228590022 228590022 TCGA-EJ-A65M DEL 30 22 SCN2A LINC01807 chr2 166794942 166794942 chr2 228600827 228600827 TCGA-EJ-A65M DEL 33 44 * LINC01807 chr2 18381735 18381735 chr2 19242161 19242161 TCGA-EJ-A65M DEL 17 2 * LINC01376 chr2 184646534 184646534 chr8 14903487 14903487 TCGA-EJ-A65M BND 35 43 ZNF804A SGCZ chr2 185158779 185158784 chr8 15418534 15418539 TCGA-EJ-A65M BND 11 11 * TUSC3 chr2 185295896 185295896 chr8 15301718 15301718 TCGA-EJ-A65M BND 40 8 * * chr2 20640578 20640578 chr2 23684884 23684884 TCGA-EJ-A65M INS 46 18 HS1BP3 KLHL29 chr2 21678861 21678861 chr2 24305673 24305673 TCGA-EJ-A65M DEL 9 24 AC018742.1 ITSN2 chr2 29889496 29889496 chr2 38394457 38394457 TCGA-EJ-A65M DEL 16 38 ALK * chr2 38960731 38960731 chr2 38961874 38961874 TCGA-EJ-A65M DEL 25 36 ARHGEF33 ARHGEF33 chr2 44078895 44078895 chr2 44079383 44079383 TCGA-EJ-A65M DEL 24 4 * * chr2 51637419 51637419 chr2 76065644 76065644 TCGA-EJ-A65M INS 26 23 AC007402.1 * chr2 51807493 51807493 chr2 52994134 52994134 TCGA-EJ-A65M INS 4 22 AC007402.1 * chr2 52233477 52233477 chr2 145973150 145973150 TCGA-EJ-A65M DEL 28 49 AC007402.1 * chr2 52408424 52408424 chr2 53602408 53602408 TCGA-EJ-A65M INS 43 13 * ASB3 chr2 53063797 53063797 chr2 56920472 56920472 TCGA-EJ-A65M INS 19 24 * * chr2 53564427 53564427 chr2 75874242 75874242 TCGA-EJ-A65M INS 7 42 ASB3 * chr2 53747370 53747370 chr2 56532520 56532520 TCGA-EJ-A65M INS 10 12 ASB3 * chr2 54205737 54205737 chr2 146220486 146220486 TCGA-EJ-A65M INS 40 27 ACYP2 * chr2 56233977 56233977 chr2 146491258 146491258 TCGA-EJ-A65M DEL 46 7 AC007744.1 * chr2 56618045 56618045 chr2 146099913 146099913 TCGA-EJ-A65M INS 11 1 * * chr2 75989083 75989083 chr2 76303376 76303376 TCGA-EJ-A65M INS 25 18 * * chr2 89260356 89260356 chr2 153665331 153665331 TCGA-EJ-A65M DEL 30 44 * * chr3 110236813 110236813 chr3 110237288 110237288 TCGA-EJ-A65M DEL 30 31 * * chr3 17309732 17309732 chr3 17320520 17320520 TCGA-EJ-A65M DEL 44 6 TBC1D5 TBC1D5 chr3 190911056 190911056 chr10 21255706 21255706 TCGA-EJ-A65M BND 5 42 * * chr3 190997264 190997275 chr10 20200436 20200447 TCGA-EJ-A65M BND 35 9 * PLXDC2 chr3 191261521 191261522 chr10 21154647 21154648 TCGA-EJ-A65M BND 33 2 OSTN NEBL chr3 19845009 19845009 chr3 19847525 19847525 TCGA-EJ-A65M DEL 3 1 * * chr3 67714430 67714430 chr3 77459544 77459544 TCGA-EJ-A65M DEL 14 26 SUCLG2-AS1 ROBO2 chr3 77075050 77075050 chr3 79168969 79168969 TCGA-EJ-A65M DEL 49 37 ROBO2 ROBO1 chr3 80074757 80074757 chr3 81776806 81776806 TCGA-EJ-A65M DEL 29 26 * * chr3 81860105 81860105 chr3 83347454 83347454 TCGA-EJ-A65M DEL 8 21 AC129807.1 * chr3 88118695 88118695 chr3 88151273 88151273 TCGA-EJ-A65M DEL 50 16 CGGBP1 CGGBP1 chr3 88509493 88509493 chr3 88649520 88649521 TCGA-EJ-A65M INS 42 41 * * chr3 94345905 94345905 chr3 94348635 94348635 TCGA-EJ-A65M DEL 35 27 * * chr4 111172683 111172683 chr4 115402312 115402312 TCGA-EJ-A65M DEL 43 9 * * chr4 111602376 111602376 chr4 131595185 131595185 TCGA-EJ-A65M DEL 24 46 * * chr4 111715749 111715749 chr4 115400570 115400570 TCGA-EJ-A65M INS 9 10 * * chr4 111952241 111952241 chr4 111953744 111953744 TCGA-EJ-A65M DEL 6 13 AC004704.1 AC004704.1 chr4 114856799 114856799 chr4 114888024 114888024 TCGA-EJ-A65M DEL 26 8 NDST4 NDST4 chr4 117288149 117288149 chr4 164571382 164571382 TCGA-EJ-A65M DEL 28 39 * * chr4 117348938 117348938 chr8 100151383 100151383 TCGA-EJ-A65M BND 40 24 LINC02262 POLR2K chr4 118019454 118019454 chr4 163102519 163102519 TCGA-EJ-A65M INS 25 33 * * chr4 119812746 119812746 chr8 116438131 116438131 TCGA-EJ-A65M BND 2 10 * * chr4 120619922 120619922 chr4 120684796 120684796 TCGA-EJ-A65M DEL 27 25 * * chr4 126154351 126154352 chr5 107909439 107909440 TCGA-EJ-A65M BND 13 29 * FBXL17 chr4 131340775 131340775 chr4 131363519 131363519 TCGA-EJ-A65M DEL 24 30 * * chr4 131637731 131637731 chr4 155514566 155514566 TCGA-EJ-A65M DEL 12 30 * AC107208.1 chr4 132842910 132842910 chr4 135987848 135987848 TCGA-EJ-A65M DEL 1 5 AC115622.1 * chr4 132860847 132860847 chr4 133464552 133464552 TCGA-EJ-A65M INS 26 8 AC115622.1 * chr4 133282636 133282636 chr4 136030504 136030504 TCGA-EJ-A65M INS 21 35 * * chr4 137112478 137112478 chr4 137128823 137128823 TCGA-EJ-A65M DEL 25 33 LINC02511 LINC02511 chr4 157087906 157087907 chr8 113205581 113205582 TCGA-EJ-A65M BND 37 42 GLRB CSMD3 chr4 157101432 157101432 chr4 165633611 165633611 TCGA-EJ-A65M INS 5 19 GLRB * chr4 157412095 157412095 chr4 157447960 157447960 TCGA-EJ-A65M DEL 41 20 * * chr4 157458565 157458565 chr4 157509489 157509489 TCGA-EJ-A65M DEL 33 47 * * chr4 157485673 157485673 chr4 166668404 166668404 TCGA-EJ-A65M DEL 9 40 * * chr4 158017503 158017503 chr8 112508217 112508217 TCGA-EJ-A65M BND 14 40 * CSMD3 chr4 158316832 158316836 chr8 116461577 116461581 TCGA-EJ-A65M BND 7 26 RXFP1 * chr4 159198563 159198566 chr8 117381226 117381229 TCGA-EJ-A65M BND 15 9 RAPGEF2 * chr4 159587920 159587922 chr8 103450694 103450696 TCGA-EJ-A65M BND 18 20 * AC012213.5 chr4 159592205 159592205 chr4 159825214 159825214 TCGA-EJ-A65M INS 36 20 * * chr4 159958641 159958641 chr4 163103864 163103864 TCGA-EJ-A65M DEL 38 3 * * chr4 161939168 161939168 chr4 167162928 167162928 TCGA-EJ-A65M DEL 8 24 FSTL5 SPOCK3 chr4 162687908 162687908 chr4 162716726 162716726 TCGA-EJ-A65M DEL 21 3 * * chr4 163850170 163850173 chr8 103650214 103650217 TCGA-EJ-A65M BND 10 13 MARCHF1 RIMS2 chr4 163861380 163861380 chr4 164301728 164301728 TCGA-EJ-A65M INS 23 15 MARCHF1 MARCHF1 chr4 163971065 163971065 chr4 165635048 165635048 TCGA-EJ-A65M DEL 48 38 MARCHF1 * chr4 164528623 164528623 chr8 104489001 104489001 TCGA-EJ-A65M BND 43 13 * * chr4 166157756 166157759 chr8 111564111 111564114 TCGA-EJ-A65M BND 48 31 * LINC02237 chr4 166538693 166538705 chr8 118667193 118667205 TCGA-EJ-A65M BND 39 33 * SAMD12-AS1 chr4 166657571 166657573 chr8 112861888 112861890 TCGA-EJ-A65M BND 15 1 * CSMD3 chr4 171088765 171088765 chr4 172757889 172757889 TCGA-EJ-A65M DEL 41 43 * GALNTL6 chr4 174670438 174670438 chr4 174677411 174677411 TCGA-EJ-A65M DEL 34 30 GLRA3 GLRA3 chr4 176414391 176414391 chr4 176416188 176416188 TCGA-EJ-A65M DEL 20 39 * * chr4 176736962 176736962 chr4 176737371 176737371 TCGA-EJ-A65M DEL 37 41 VEGFC VEGFC chr4 181089167 181089169 chr11 41428305 41428307 TCGA-EJ-A65M BND 21 5 LINC00290 LRRC4C chr4 181113086 181113086 chr11 39193019 39193019 TCGA-EJ-A65M BND 35 12 LINC00290 * chr4 182221376 182221378 chr11 42048573 42048575 TCGA-EJ-A65M BND 29 7 TENM3 LINC02745 chr4 182233947 182233951 chr11 38592538 38592542 TCGA-EJ-A65M BND 32 28 TENM3 * chr4 188880846 188880846 chr4 189099936 189099936 TCGA-EJ-A65M DEL 42 11 * * chr4 189086082 189086083 chr11 55216215 55216216 TCGA-EJ-A65M BND 3 29 * * chr4 21744381 21744381 chr4 21745530 21745530 TCGA-EJ-A65M DEL 20 16 KCNIP4 KCNIP4 chr4 22363863 22363863 chr4 36592176 36592176 TCGA-EJ-A65M DEL 34 16 ADGRA3 LINC02505 chr4 33102374 33102374 chr4 33404867 33404867 TCGA-EJ-A65M DEL 4 10 * * chr4 55544334 55544334 chr4 57225202 57225202 TCGA-EJ-A65M INS 30 46 CLOCK * chr4 55643011 55643011 chr4 93095293 93095293 TCGA-EJ-A65M INS 6 21 * GRID2 chr4 55795589 55795589 chr4 62342872 62342872 TCGA-EJ-A65M INS 45 12 * * chr4 56056168 56056168 chr4 63470480 63470480 TCGA-EJ-A65M DEL 23 6 CRACD AC093730.1 chr4 56077944 56077945 chr4 58293840 58293840 TCGA-EJ-A65M INS 26 49 CRACD * chr4 56840374 56840374 chr4 61501418 61501418 TCGA-EJ-A65M INS 39 1 * ADGRL3 chr4 56889648 56889648 chr4 64006161 64006161 TCGA-EJ-A65M INS 17 1 * * chr4 57000286 57000286 chr4 67880406 67880406 TCGA-EJ-A65M DEL 33 32 POLR2B UBA6-AS1 chr4 57076870 57076870 chr4 66552286 66552286 TCGA-EJ-A65M DEL 4 14 IGFBP7 * chr4 57087829 57087829 chr4 57267995 57267995 TCGA-EJ-A65M INS 24 49 IGFBP7 * chr4 57830069 57830069 chr4 65697865 65697865 TCGA-EJ-A65M DEL 24 29 * EPHA5-AS1 chr4 58125615 58125615 chr4 93731762 93731762 TCGA-EJ-A65M DEL 45 38 * GRID2 chr4 58151039 58151039 chr4 63646745 63646745 TCGA-EJ-A65M DEL 30 16 * * chr4 58197805 58197805 chr4 62569022 62569022 TCGA-EJ-A65M INS 3 29 * * chr4 58319845 58319845 chr4 59962936 59962936 TCGA-EJ-A65M INS 17 16 * * chr4 58495812 58495812 chr4 63429582 63429582 TCGA-EJ-A65M DEL 2 33 * * chr4 58514076 58514076 chr4 59666768 59666768 TCGA-EJ-A65M INS 21 36 * * chr4 58693267 58693267 chr4 60248765 60248765 TCGA-EJ-A65M DEL 34 17 * * chr4 59989762 59989762 chr4 60213558 60213558 TCGA-EJ-A65M INS 25 15 * * chr4 60066066 60066066 chr4 61624751 61624751 TCGA-EJ-A65M DEL 38 33 * ADGRL3 chr4 60419858 60419858 chr4 65744812 65744812 TCGA-EJ-A65M INS 39 43 * * chr4 60497302 60497302 chr4 62489940 62489940 TCGA-EJ-A65M INS 32 32 * AC074087.1 chr4 61416626 61416626 chr4 65753805 65753805 TCGA-EJ-A65M DEL 14 49 ADGRL3 * chr4 61742247 61742247 chr4 61744462 61744462 TCGA-EJ-A65M DEL 45 2 ADGRL3 ADGRL3 chr4 62227845 62227845 chr4 67797945 67797945 TCGA-EJ-A65M INS 27 30 * UBA6-AS1 chr4 62571770 62571770 chr4 93810129 93810129 TCGA-EJ-A65M INS 27 44 * GRID2 chr4 62709814 62709814 chr4 63746418 63746418 TCGA-EJ-A65M DEL 30 17 * * chr4 63176010 63176010 chr4 91644092 91644092 TCGA-EJ-A65M INS 1 22 * * chr4 63449331 63449331 chr4 93540942 93540942 TCGA-EJ-A65M DEL 17 37 * GRID2 chr4 65250598 65250598 chr4 93488829 93488829 TCGA-EJ-A65M INS 47 39 * GRID2 chr4 66544557 66544557 chr4 92144231 92144231 TCGA-EJ-A65M DEL 20 45 * * chr4 67037766 67037766 chr4 67289103 67289103 TCGA-EJ-A65M INS 10 47 * * chr4 89980036 89980036 chr4 173851955 173851955 TCGA-EJ-A65M DEL 46 4 * * chr4 96552048 96552048 chr4 97699719 97699719 TCGA-EJ-A65M INS 26 41 LINC02267 STPG2 chr4 96789890 96789890 chr4 170721470 170721470 TCGA-EJ-A65M DEL 20 7 LINC02267 * chr4 97361326 97361326 chr4 97361595 97361595 TCGA-EJ-A65M DEL 39 31 STPG2 STPG2 chr4 97773480 97773480 chr4 172813399 172813399 TCGA-EJ-A65M INS 38 30 STPG2 GALNTL6 chr4 97951873 97951873 chr4 174124562 174124562 TCGA-EJ-A65M DEL 22 40 STPG2 LINC02268 chr4 99921264 99921264 chr4 99928233 99928233 TCGA-EJ-A65M DEL 16 39 DNAJB14 DNAJB14 chr5 106897029 106897029 chr5 106942007 106942007 TCGA-EJ-A65M DEL 22 38 LINC01950 LINC01950 chr5 107104491 107104491 chr18 69917563 69917563 TCGA-EJ-A65M BND 24 50 * CD226 chr5 107134346 107134346 chr5 130613026 130613026 TCGA-EJ-A65M INS 18 11 * * chr5 107909439 107909440 chr4 126154351 126154352 TCGA-EJ-A65M BND 42 18 FBXL17 * chr5 107911242 107911242 chr5 107913853 107913853 TCGA-EJ-A65M DEL 32 4 FBXL17 FBXL17 chr5 108709981 108709981 chr5 108713697 108713697 TCGA-EJ-A65M DEL 11 29 * * chr5 110477123 110477123 chr5 110477247 110477247 TCGA-EJ-A65M DEL 8 32 TMEM232 TMEM232 chr5 114924093 114924093 chr7 85946608 85946608 TCGA-EJ-A65M BND 39 12 * * chr5 115239654 115239654 chr5 115726471 115726471 TCGA-EJ-A65M DEL 36 38 PGGT1B * chr5 115291676 115291676 chr7 90534517 90534517 TCGA-EJ-A65M BND 19 36 CCDC112 CDK14 chr5 116366353 116366353 chr7 87483026 87483026 TCGA-EJ-A65M BND 28 46 COMMD10 * chr5 117220342 117220345 chr7 89862768 89862771 TCGA-EJ-A65M BND 30 31 * * chr5 117604640 117604640 chr7 88710385 88710385 TCGA-EJ-A65M BND 36 20 * AC002069.2 chr5 117623219 117623224 chr7 86513111 86513116 TCGA-EJ-A65M BND 43 31 * * chr5 12245247 12245247 chr5 13356415 13356415 TCGA-EJ-A65M DEL 33 27 * * chr5 130464841 130464841 chr18 68998517 68998517 TCGA-EJ-A65M BND 7 31 * CCDC102B chr5 131095088 131095090 chr18 69431034 69431036 TCGA-EJ-A65M BND 4 16 * DOK6 chr5 147565014 147565015 chr5 147568021 147568021 TCGA-EJ-A65M DEL 42 21 JAKMIP2-AS1 JAKMIP2-AS1 chr5 156413091 156413091 chr5 157660516 157660516 TCGA-EJ-A65M INS 13 45 SGCD SOX30 chr5 24744243 24744243 chr5 26453932 26453932 TCGA-EJ-A65M INS 30 27 * * chr5 24807971 24807971 chr5 28402243 28402243 TCGA-EJ-A65M DEL 13 8 * * chr5 25612886 25612886 chr5 27017274 27017274 TCGA-EJ-A65M DEL 41 3 * CDH9 chr5 26071881 26071881 chr7 120913695 120913695 TCGA-EJ-A65M BND 27 24 * * chr5 26497806 26497806 chr5 26562395 26562395 TCGA-EJ-A65M DEL 49 17 * * chr5 26793951 26793951 chr5 27548044 27548044 TCGA-EJ-A65M INS 34 14 * * chr5 26845992 26846005 chr7 120172433 120172447 TCGA-EJ-A65M BND 39 35 * AC004946.2 chr5 26998136 26998136 chr7 120841609 120841609 TCGA-EJ-A65M BND 34 33 CDH9 TSPAN12 chr5 27897505 27897505 chr7 120909754 120909754 TCGA-EJ-A65M BND 5 49 * * chr5 46160518 46160518 chr5 46163980 46163980 TCGA-EJ-A65M DEL 36 5 * * chr5 85088121 85088121 chr7 123612185 123612185 TCGA-EJ-A65M BND 50 34 * ASB15 chr5 86561201 86561201 chr5 86659353 86659353 TCGA-EJ-A65M DEL 27 41 * * chr5 86622658 86622658 chr5 89022254 89022254 TCGA-EJ-A65M INS 28 32 * MEF2C-AS1 chr5 86723957 86723957 chr5 108218388 108218388 TCGA-EJ-A65M DEL 11 7 * FBXL17 chr5 87393204 87393206 chr18 69268195 69268197 TCGA-EJ-A65M BND 37 46 CCNH * chr5 87473579 87473579 chr5 131161356 131161356 TCGA-EJ-A65M INS 22 30 AC018754.1 HINT1 chr5 87532916 87532923 chr18 70033339 70033346 TCGA-EJ-A65M BND 47 30 * RTTN chr5 87536284 87536284 chr5 131379477 131379477 TCGA-EJ-A65M INS 13 26 * CDC42SE2 chr5 87555005 87555010 chr18 69754659 69754664 TCGA-EJ-A65M BND 47 4 * DOK6 chr5 87871841 87871845 chr18 69767544 69767548 TCGA-EJ-A65M BND 41 15 * DOK6 chr5 87909893 87909893 chr5 131080155 131080155 TCGA-EJ-A65M INS 9 7 * * chr5 88424558 88424558 chr5 88786976 88786976 TCGA-EJ-A65M DEL 38 31 TMEM161B-AS1 MEF2C chr5 88702574 88702574 chr5 131321068 131321068 TCGA-EJ-A65M DEL 3 50 MEF2C-AS2 CDC42SE2 chr5 97775615 97775615 chr5 97785631 97785631 TCGA-EJ-A65M DEL 9 20 * * chr6 114183088 114183088 chr10 99734273 99734273 TCGA-EJ-A65M BND 43 36 HDAC2-AS2 CUTC chr6 121901805 121901805 chr6 123589470 123589470 TCGA-EJ-A65M DEL 45 35 * TRDN chr6 123592847 123592848 chr8 57475667 57475668 TCGA-EJ-A65M BND 5 40 TRDN * chr6 123607119 123607119 chr11 48066933 48066933 TCGA-EJ-A65M BND 23 44 TRDN PTPRJ chr6 123968789 123968790 chr8 58399339 58399340 TCGA-EJ-A65M BND 21 15 NKAIN2 * chr6 123969317 123969320 chr8 55172622 55172625 TCGA-EJ-A65M BND 40 35 NKAIN2 XKR4 chr6 153451993 153451993 chr6 153452801 153452801 TCGA-EJ-A65M DEL 30 41 * * chr6 159414771 159414771 chr6 159417019 159417019 TCGA-EJ-A65M DEL 34 45 * * chr6 165251256 165251256 chr6 165635634 165635634 TCGA-EJ-A65M DEL 46 28 * PDE10A chr6 4339553 4339553 chr6 31060564 31060564 TCGA-EJ-A65M DEL 27 45 AL162718.1 * chr6 48869603 48869603 chr6 48870100 48870100 TCGA-EJ-A65M DEL 28 20 * * chr6 58358044 58358044 chr6 58359899 58359899 TCGA-EJ-A65M DEL 37 42 AL445250.1 AL445250.1 chr6 61506930 61506930 chr6 61509609 61509609 TCGA-EJ-A65M DEL 25 24 * * chr6 62649755 62649755 chr8 60122942 60122942 TCGA-EJ-A65M BND 3 14 * * chr6 63558320 63558320 chr8 56579349 56579349 TCGA-EJ-A65M BND 45 25 PTP4A1 * chr6 64105605 64105608 chr8 118479694 118479697 TCGA-EJ-A65M BND 21 42 EYS SAMD12 chr6 64519861 64519861 chr6 64756338 64756338 TCGA-EJ-A65M DEL 37 38 EYS EYS chr6 64608221 64608221 chr8 118070996 118070996 TCGA-EJ-A65M BND 1 36 EYS EXT1 chr6 64710938 64710939 chr8 118131201 118131202 TCGA-EJ-A65M BND 25 14 EYS * chr6 65197196 65197196 chr8 59903087 59903087 TCGA-EJ-A65M BND 8 2 EYS * chr6 65939306 65939306 chr6 123555532 123555532 TCGA-EJ-A65M DEL 8 42 * TRDN chr6 77922097 77922097 chr6 77922236 77922236 TCGA-EJ-A65M DEL 25 21 MEI4 MEI4 chr6 83284959 83284959 chr6 84905365 84905365 TCGA-EJ-A65M DEL 4 35 ME1 * chr6 95603163 95603163 chr6 95615050 95615050 TCGA-EJ-A65M DEL 21 47 MANEA * chr7 10294400 10294400 chr7 10772075 10772075 TCGA-EJ-A65M DEL 33 42 * MGC4859 chr7 10317403 10317403 chr7 18351444 18351444 TCGA-EJ-A65M INS 41 15 * HDAC9 chr7 120172433 120172447 chr5 26845992 26846005 TCGA-EJ-A65M BND 40 3 AC004946.2 * chr7 120841609 120841609 chr5 26998136 26998136 TCGA-EJ-A65M BND 36 21 TSPAN12 CDH9 chr7 123771117 123771117 chr7 124901877 124901877 TCGA-EJ-A65M INS 18 28 * POT1 chr7 124196472 124196472 chr7 125172250 125172250 TCGA-EJ-A65M DEL 27 10 AC006148.1 POT1-AS1 chr7 124352863 124352863 chr7 124794863 124794863 TCGA-EJ-A65M INS 40 19 AC006148.1 * chr7 125237877 125237879 chr7 125802016 125802016 TCGA-EJ-A65M DEL 27 6 AC019155.2 * chr7 17939238 17939238 chr7 18014660 18014660 TCGA-EJ-A65M DEL 34 6 SNX13 * chr7 18499356 18499356 chr7 18554913 18554913 TCGA-EJ-A65M DEL 48 27 HDAC9 HDAC9 chr7 18709124 18709124 chr7 20115540 20115540 TCGA-EJ-A65M INS 17 41 HDAC9 AC005062.1 chr7 33228317 33228320 chrX 109048472 109048475 TCGA-EJ-A65M BND 28 1 BBS9 * chr7 33271369 33271371 chrX 147020352 147020354 TCGA-EJ-A65M BND 41 45 BBS9 * chr7 33616245 33616245 chr7 33618407 33618407 TCGA-EJ-A65M DEL 20 1 * * chr7 33679107 33679107 chr7 33808630 33808630 TCGA-EJ-A65M DEL 34 45 * * chr7 33682554 33682562 chrX 147861032 147861040 TCGA-EJ-A65M BND 12 35 * * chr7 33810587 33810588 chrX 145741668 145741669 TCGA-EJ-A65M BND 15 49 * * chr7 34667760 34667760 chrX 110271410 110271410 TCGA-EJ-A65M BND 20 15 NPSR1 AMMECR1 chr7 43401513 43401513 chr7 43409491 43409491 TCGA-EJ-A65M DEL 32 42 HECW1 HECW1 chr7 49284378 49284381 chr1 147170151 147170154 TCGA-EJ-A65M BND 11 15 * PRKAB2 chr7 55895424 55895424 chr1 197673000 197673000 TCGA-EJ-A65M BND 36 41 ZNF713 DENND1B chr7 62356394 62356394 chr8 64083062 64083062 TCGA-EJ-A65M BND 18 13 * LINC01414 chr7 79590514 79590514 chr7 79617629 79617629 TCGA-EJ-A65M DEL 18 27 * * chr7 84221515 84221515 chr7 84223869 84223869 TCGA-EJ-A65M DEL 43 28 SEMA3A SEMA3A chr7 86487160 86487160 chr7 88498177 88498177 TCGA-EJ-A65M DEL 40 47 * * chr7 86513111 86513116 chr5 117623219 117623224 TCGA-EJ-A65M BND 20 10 * * chr7 87440557 87440557 chr7 89430436 89430436 TCGA-EJ-A65M DEL 37 21 ABCB4 * chr7 87645850 87645850 chr5 117255364 117255364 TCGA-EJ-A65M BND 29 30 ABCB1 * chr7 87648761 87648761 chr7 88477185 88477185 TCGA-EJ-A65M INS 11 40 ABCB1 * chr7 88130849 88130849 chr7 88425228 88425228 TCGA-EJ-A65M DEL 4 47 ADAM22 * chr7 88202110 88202110 chr7 89306088 89306088 TCGA-EJ-A65M INS 13 18 ADAM22 ZNF804B chr7 89276365 89276371 chr5 116686736 116686742 TCGA-EJ-A65M BND 6 21 ZNF804B * chr7 89862768 89862771 chr5 117220342 117220345 TCGA-EJ-A65M BND 24 48 * * chr7 90483780 90483781 chr5 117716170 117716171 TCGA-EJ-A65M BND 44 43 CLDN12 * chr8 100147838 100147847 chr4 159840697 159840706 TCGA-EJ-A65M BND 28 40 * * chr8 100574587 100574587 chr4 181386261 181386261 TCGA-EJ-A65M BND 32 36 SNX31 * chr8 100787252 100787252 chr4 161236694 161236694 TCGA-EJ-A65M BND 2 13 * * chr8 102426319 102426321 chr4 119831837 119831839 TCGA-EJ-A65M BND 41 43 * * chr8 102450075 102450075 chr4 164525669 164525669 TCGA-EJ-A65M BND 16 48 * * chr8 102453674 102453674 chr4 117355984 117355984 TCGA-EJ-A65M BND 50 1 * LINC02262 chr8 103829536 103829536 chr8 113215307 113215307 TCGA-EJ-A65M DEL 27 12 RIMS2 CSMD3 chr8 103831629 103831629 chr8 111559122 111559122 TCGA-EJ-A65M INS 28 28 RIMS2 LINC02237 chr8 104493114 104493114 chr4 164312343 164312343 TCGA-EJ-A65M BND 26 9 LRP12 MARCHF1 chr8 105776213 105776213 chr8 112814253 112814253 TCGA-EJ-A65M INS 41 20 ZFPM2 CSMD3 chr8 105806508 105806508 chr4 163260126 163260126 TCGA-EJ-A65M BND 38 16 ZFPM2-AS1 * chr8 111256807 111256807 chr8 112307209 112307209 TCGA-EJ-A65M INS 43 35 * CSMD3 chr8 111463209 111463209 chr8 118667246 118667246 TCGA-EJ-A65M DEL 4 32 LINC02237 SAMD12-AS1 chr8 113046745 113046745 chr4 121440665 121440665 TCGA-EJ-A65M BND 46 49 CSMD3 * chr8 113205581 113205582 chr4 157087906 157087907 TCGA-EJ-A65M BND 12 7 CSMD3 GLRB chr8 113258198 113258198 chr8 113275460 113275460 TCGA-EJ-A65M DEL 14 27 CSMD3 CSMD3 chr8 116461577 116461581 chr4 158316832 158316836 TCGA-EJ-A65M BND 33 44 * RXFP1 chr8 117381226 117381229 chr4 159198563 159198566 TCGA-EJ-A65M BND 47 20 * RAPGEF2 chr8 118019996 118020001 chr4 166511212 166511217 TCGA-EJ-A65M BND 44 15 EXT1 AC097487.1 chr8 118131201 118131202 chr6 64710938 64710939 TCGA-EJ-A65M BND 40 17 * EYS chr8 118360938 118360938 chr11 45729706 45729706 TCGA-EJ-A65M BND 21 36 SAMD12 AC044839.1 chr8 118476105 118476105 chr6 64114062 64114062 TCGA-EJ-A65M BND 30 20 SAMD12 EYS chr8 118667193 118667205 chr4 166538693 166538705 TCGA-EJ-A65M BND 29 41 SAMD12-AS1 * chr8 119437648 119437651 chr4 121450912 121450915 TCGA-EJ-A65M BND 25 20 AC021733.2 TUBB4BP5 chr8 119455847 119455847 chr4 159997774 159997774 TCGA-EJ-A65M BND 45 32 AC021733.2 * chr8 127013475 127013475 chr8 127166117 127166117 TCGA-EJ-A65M INS 26 3 PCAT1 PCAT1 chr8 12775676 12775676 chr1 105760635 105760635 TCGA-EJ-A65M BND 24 28 AC123777.1 * chr8 129378961 129378961 chr1 194653778 194653778 TCGA-EJ-A65M BND 35 16 CCDC26 * chr8 132604064 132604064 chr8 132604357 132604357 TCGA-EJ-A65M DEL 46 39 LRRC6 LRRC6 chr8 13352338 13352338 chr1 108972045 108972045 TCGA-EJ-A65M BND 20 10 DLC1 WDR47 chr8 137488476 137488476 chr8 137494483 137494483 TCGA-EJ-A65M DEL 35 19 * * chr8 14115794 14115795 chr1 104471277 104471278 TCGA-EJ-A65M BND 44 19 SGCZ * chr8 14504529 14504529 chr2 184649709 184649709 TCGA-EJ-A65M BND 41 11 SGCZ ZNF804A chr8 14863091 14863091 chr8 16115714 16115714 TCGA-EJ-A65M INS 5 44 SGCZ MSR1 chr8 15301718 15301718 chr2 185295896 185295896 TCGA-EJ-A65M BND 18 48 * * chr8 15418534 15418539 chr2 185158779 185158784 TCGA-EJ-A65M BND 23 34 TUSC3 * chr8 24096432 24096436 chr1 105729390 105729394 TCGA-EJ-A65M BND 6 11 * * chr8 24133555 24133558 chr1 108557255 108557258 TCGA-EJ-A65M BND 8 16 * * chr8 25177257 25177257 chr1 105234864 105234864 TCGA-EJ-A65M BND 9 39 * * chr8 3014387 3014387 chr8 3744327 3744327 TCGA-EJ-A65M DEL 7 22 CSMD1 CSMD1 chr8 4220217 4220219 chr8 4232738 4232738 TCGA-EJ-A65M DEL 39 3 CSMD1 CSMD1 chr8 51265202 51265202 chr8 51851867 51851867 TCGA-EJ-A65M INS 21 5 AC012413.1 PCMTD1 chr8 52338962 52338962 chr8 56826912 56826912 TCGA-EJ-A65M DEL 33 22 ST18 * chr8 55002943 55002943 chr8 56642615 56642615 TCGA-EJ-A65M INS 28 22 * AC009597.1 chr8 55056109 55056109 chr8 63002402 63002402 TCGA-EJ-A65M INS 48 18 * * chr8 55144057 55144057 chr8 55982183 55982183 TCGA-EJ-A65M DEL 34 38 XKR4 LYN chr8 55172622 55172625 chr6 123969317 123969320 TCGA-EJ-A65M BND 16 22 XKR4 NKAIN2 chr8 55552685 55552686 chr11 49854567 49854568 TCGA-EJ-A65M BND 28 10 * AP006587.4 chr8 55570319 55570319 chr8 55924903 55924903 TCGA-EJ-A65M INS 39 4 * LYN chr8 55792825 55792828 chr6 62652774 62652777 TCGA-EJ-A65M BND 9 36 TGS1 * chr8 55811774 55811774 chr8 57343622 57343622 TCGA-EJ-A65M INS 48 6 TGS1 AC068075.1 chr8 55916920 55916920 chr8 56082227 56082227 TCGA-EJ-A65M INS 47 40 LYN * chr8 56522754 56522754 chr11 49936798 49936798 TCGA-EJ-A65M BND 4 23 AC012349.1 * chr8 56960438 56960445 chr11 47674602 47674609 TCGA-EJ-A65M BND 25 5 BPNT2 AGBL2 chr8 57475667 57475668 chr6 123592847 123592848 TCGA-EJ-A65M BND 28 21 * TRDN chr8 57652291 57652291 chr8 59391840 59391840 TCGA-EJ-A65M INS 41 10 AC104051.1 * chr8 58399339 58399340 chr6 123968789 123968790 TCGA-EJ-A65M BND 39 9 * NKAIN2 chr8 59999031 59999031 chr11 50467547 50467547 TCGA-EJ-A65M BND 48 48 * * chr8 60006106 60006106 chr8 118573264 118573264 TCGA-EJ-A65M INS 21 37 * SAMD12 chr8 60117396 60117396 chr8 63012526 63012526 TCGA-EJ-A65M DEL 49 40 * AC120042.1 chr8 63497424 63497424 chr8 63522928 63522928 TCGA-EJ-A65M DEL 19 46 * * chr8 64077304 64077304 chr8 78924593 78924593 TCGA-EJ-A65M DEL 44 33 LINC01414 AC083837.1 chr8 77572288 77572288 chr19 28876784 28876784 TCGA-EJ-A65M BND 1 36 * AC007795.1 chr9 19258557 19258557 chr9 19274137 19274137 TCGA-EJ-A65M DEL 32 31 DENND4C DENND4C chr9 19675849 19675849 chr9 20003088 20003088 TCGA-EJ-A65M DEL 27 44 SLC24A2 * chr9 72797251 72797251 chr9 72801342 72801342 TCGA-EJ-A65M DEL 3 36 TMC1 TMC1 chr9 9014395 9014395 chr9 9014784 9014784 TCGA-EJ-A65M DEL 24 8 PTPRD PTPRD chrX 108692544 108692544 chrX 110273603 110273603 TCGA-EJ-A65M DEL 18 28 COL4A5 AMMECR1 chrX 109048472 109048475 chr7 33228317 33228320 TCGA-EJ-A65M BND 30 11 * BBS9 chrX 110271410 110271410 chr7 34667760 34667760 TCGA-EJ-A65M BND 29 37 AMMECR1 NPSR1 chrX 110486023 110486023 chr7 34703580 34703580 TCGA-EJ-A65M BND 44 10 * NPSR1 chrX 145588073 145588073 chr7 33824730 33824730 TCGA-EJ-A65M BND 12 11 * * chrX 147020352 147020354 chr7 33271369 33271371 TCGA-EJ-A65M BND 30 30 * BBS9 chrX 147861032 147861040 chr7 33682554 33682562 TCGA-EJ-A65M BND 40 31 * * chrX 32167520 32167520 chrX 33767801 33767801 TCGA-EJ-A65M INS 45 6 DMD AL591501.1 chrX 7109454 7109454 chrX 7110099 7110099 TCGA-EJ-A65M DEL 33 21 PUDP PUDP chrX 97113866 97113866 chrX 99404580 99404580 TCGA-EJ-A65M DEL 34 42 DIAPH2 * chr10 81379540 81379540 chr10 108789932 108789932 TCGA-M7-A722 DEL 38 15 * LINC02661 chr11 123855575 123855575 chr11 123863818 123863818 TCGA-M7-A722 DEL 13 10 * OR6M3P chr12 22376684 22376684 chr12 22942154 22942154 TCGA-M7-A722 DEL 6 32 ST8SIA1 AC084816.1 chr13 31493007 31493007 chr13 102090504 102090504 TCGA-M7-A722 DEL 19 31 * FGF14 chr13 36675233 36675233 chr13 86137782 86137782 TCGA-M7-A722 DEL 49 41 SERTM1 AL354994.1 chr1 100750867 100750867 chr1 100772445 100772445 TCGA-M7-A722 DEL 23 12 * * chr1 158467254 158467254 chr1 181354851 181354851 TCGA-M7-A722 INS 49 31 OR10K1 CACNA1E chr1 180881280 180881280 chr1 180887149 180887149 TCGA-M7-A722 DEL 9 29 XPR1 XPR1 chr2 198673501 198673501 chr2 209710619 209710619 TCGA-M7-A722 INS 50 49 AC019330.1 MAP2 chr2 199622626 199622626 chr2 210096498 210096498 TCGA-M7-A722 DEL 22 14 LINC01877 KANSL1L chr4 113215759 113215759 chr4 135258509 135258509 TCGA-M7-A722 DEL 17 41 ANK2 * chr4 27542272 27542272 chr4 27542337 27542337 TCGA-M7-A722 DEL 24 29 * * chr5 103612553 103612553 chr5 103877423 103877423 TCGA-M7-A722 DEL 12 37 * * chr5 23513754 23513754 chr5 23590595 23590595 TCGA-M7-A722 DEL 21 9 PRDM9 * chr5 46382688 46382688 chr5 46388499 46388499 TCGA-M7-A722 DEL 6 25 * * chr5 60376507 60376507 chr5 60377563 60377563 TCGA-M7-A722 DEL 33 28 PDE4D PDE4D chr5 84264086 84264086 chr5 86388145 86388145 TCGA-M7-A722 INS 44 17 EDIL3 * chr5 86392646 86392646 chr5 105324777 105324777 TCGA-M7-A722 INS 42 12 * AC099520.1 chr5 96318870 96318870 chr5 96353292 96353292 TCGA-M7-A722 DEL 18 50 AC104123.1 AC104123.1 chr5 96630006 96630006 chr5 103640579 103640579 TCGA-M7-A722 DEL 6 2 AC104123.1 * chr6 120847926 120847926 chr6 123295308 123295308 TCGA-M7-A722 INS 6 34 * TRDN chr6 54568048 54568048 chr6 54569193 54569193 TCGA-M7-A722 DEL 7 10 * * chr6 62446296 62446296 chr6 65623316 65623316 TCGA-M7-A722 DEL 44 14 * EYS chr6 63953349 63953349 chr6 121867517 121867517 TCGA-M7-A722 DEL 5 6 EYS * chr7 50692045 50692045 chr7 50888852 50888852 TCGA-M7-A722 INS 12 3 GRB10 AC004830.2 chr12 79349856 79349856 chr12 79754688 79754688 TCGA-ZG-A9L6 DEL 29 17 SYT1 AC073569.2 chr12 80610086 80610090 chr7 154012397 154012401 TCGA-ZG-A9L6 BND 15 10 PTPRQ DPP6 chr12 80987196 80987198 chr7 119203063 119203065 TCGA-ZG-A9L6 BND 19 48 ACSS3 * chr12 81267642 81267642 chr12 81397075 81397075 TCGA-ZG-A9L6 DEL 23 43 PPFIA2 PPFIA2 chr12 84654286 84654286 chr7 152392483 152392483 TCGA-ZG-A9L6 BND 33 27 * KMT2C chr12 85283026 85283026 chr12 85322394 85322394 TCGA-ZG-A9L6 DEL 16 44 ALX1 LINC02820 chr12 85411411 85411420 chr7 153581973 153581982 TCGA-ZG-A9L6 BND 45 7 * * chr12 86778437 86778437 chr12 87467208 87467208 TCGA-ZG-A9L6 DEL 45 34 MGAT4C * chr13 107994935 107994935 chr5 98062040 98062040 TCGA-ZG-A9L6 BND 18 9 * * chr13 108004917 108004917 chr5 98223318 98223318 TCGA-ZG-A9L6 BND 49 42 * * chr13 45804460 45804460 chr13 45860728 45860728 TCGA-ZG-A9L6 DEL 2 16 SIAH3 * chr13 45820428 45820428 chr5 98688316 98688316 TCGA-ZG-A9L6 BND 14 19 SIAH3 * chr13 45871330 45871330 chr5 98090987 98090987 TCGA-ZG-A9L6 BND 22 44 * LINC01846 chr13 46302061 46302061 chr5 96928469 96928469 TCGA-ZG-A9L6 BND 49 38 * AC009126.1 chr13 47340670 47340671 chr5 97973601 97973602 TCGA-ZG-A9L6 BND 5 45 * * chr13 47485187 47485187 chr13 106327102 106327102 TCGA-ZG-A9L6 INS 12 42 * * chr13 83711072 83711072 chr13 83723329 83723329 TCGA-ZG-A9L6 DEL 50 29 * * chr15 22204034 22204034 chr15 22213129 22213129 TCGA-ZG-A9L6 DEL 24 42 AC025884.3 * chr15 87784670 87784670 chr15 87795256 87795256 TCGA-ZG-A9L6 DEL 41 1 * * chr17 27211244 27211244 chr3 197596286 197596286 TCGA-ZG-A9L6 BND 29 18 * AC132008.2 chr17 43619056 43619056 chr17 43761708 43761710 TCGA-ZG-A9L6 INS 9 24 * * chr17 43619575 43619575 chr17 43761708 43761710 TCGA-ZG-A9L6 DEL 46 49 * * chr17 59798213 59798213 chr17 59884815 59884815 TCGA-ZG-A9L6 INS 33 48 VMP1 TUBD1 chr1 209338364 209338364 chr1 209340811 209340811 TCGA-ZG-A9L6 DEL 43 10 * * chr1 99334221 99334221 chr1 121742880 121742880 TCGA-ZG-A9L6 INS 39 50 * * chr21 26070283 26070283 chr21 26070380 26070380 TCGA-ZG-A9L6 INS 4 50 APP APP chr2 117672640 117672640 chr2 117684032 117684032 TCGA-ZG-A9L6 DEL 21 28 * * chr2 138344978 138344978 chr2 138357349 138357349 TCGA-ZG-A9L6 DEL 9 21 * * chr2 140719591 140719591 chr2 140731621 140731621 TCGA-ZG-A9L6 DEL 49 47 LRP1B LRP1B chr2 186469085 186469085 chr2 186487407 186487407 TCGA-ZG-A9L6 DEL 31 2 * ZC3H15 chr2 199110166 199110166 chr3 18050983 18050983 TCGA-ZG-A9L6 BND 27 29 * TBC1D5 chr3 17980316 17980316 chr2 180427127 180427127 TCGA-ZG-A9L6 BND 49 23 TBC1D5 * chr3 63336785 63336785 chr3 63342218 63342218 TCGA-ZG-A9L6 DEL 13 41 SYNPR SYNPR chr4 103460819 103460819 chr4 103759035 103759035 TCGA-ZG-A9L6 DEL 9 18 * * chr4 113336414 113336414 chr4 118243931 118243931 TCGA-ZG-A9L6 INS 8 2 ANK2 NDST3 chr4 115061380 115061380 chr4 118255888 118255888 TCGA-ZG-A9L6 DEL 27 29 NDST4 NDST3 chr4 116361643 116361643 chr4 116890696 116890696 TCGA-ZG-A9L6 DEL 44 41 * * chr4 116368764 116368764 chr4 116888833 116888833 TCGA-ZG-A9L6 INS 22 16 * * chr4 121643255 121643255 chr5 160052040 160052040 TCGA-ZG-A9L6 BND 14 7 * TTC1 chr4 122035155 122035155 chr5 162376190 162376190 TCGA-ZG-A9L6 BND 32 2 * * chr4 128954070 128954070 chr4 129526488 129526488 TCGA-ZG-A9L6 DEL 30 32 SCLT1 * chr4 161342543 161342543 chr4 161342657 161342657 TCGA-ZG-A9L6 DEL 49 40 * * chr4 43770830 43770830 chr4 43773018 43773018 TCGA-ZG-A9L6 DEL 36 16 * * chr4 46423330 46423330 chr4 46423506 46423506 TCGA-ZG-A9L6 DEL 9 50 GABRA2 GABRA2 chr4 60266265 60266265 chr4 61123850 61123850 TCGA-ZG-A9L6 DEL 37 11 * * chr4 60705147 60705147 chr5 160189279 160189279 TCGA-ZG-A9L6 BND 44 22 * FABP6 chr4 65351730 65351730 chr4 65352045 65352045 TCGA-ZG-A9L6 DEL 3 34 EPHA5 EPHA5 chr4 90316953 90316953 chr5 160431679 160431679 TCGA-ZG-A9L6 BND 11 3 CCSER1 * chr4 93330521 93330522 chr5 161172024 161172025 TCGA-ZG-A9L6 BND 29 37 GRID2 * chr4 94665349 94665349 chr5 160412580 160412580 TCGA-ZG-A9L6 BND 8 50 PDLIM5 SLU7 chr4 94782201 94782201 chr5 159987714 159987714 TCGA-ZG-A9L6 BND 5 40 BMPR1B * chr4 94956648 94956648 chr5 167849913 167849913 TCGA-ZG-A9L6 BND 30 47 BMPR1B TENM2 chr4 98710904 98710905 chr5 160433850 160433851 TCGA-ZG-A9L6 BND 13 40 * * chr5 101096128 101096128 chr5 101097400 101097400 TCGA-ZG-A9L6 DEL 13 17 * * chr5 107056254 107056254 chr5 107078174 107078174 TCGA-ZG-A9L6 DEL 28 10 * * chr5 159987714 159987714 chr4 94782201 94782201 TCGA-ZG-A9L6 BND 42 14 * BMPR1B chr5 160046270 160046270 chr5 161173571 161173571 TCGA-ZG-A9L6 DEL 1 38 TTC1 * chr5 160137367 160137383 chr4 60286545 60286559 TCGA-ZG-A9L6 BND 9 39 * * chr5 160433850 160433851 chr4 98710904 98710905 TCGA-ZG-A9L6 BND 17 18 * * chr5 161172024 161172025 chr4 93330521 93330522 TCGA-ZG-A9L6 BND 47 24 * GRID2 chr5 162365014 162365016 chr4 93331243 93331245 TCGA-ZG-A9L6 BND 34 40 * GRID2 chr5 162376190 162376190 chr4 122035155 122035155 TCGA-ZG-A9L6 BND 1 10 * * chr5 162400070 162400070 chr5 167359728 167359728 TCGA-ZG-A9L6 DEL 11 37 * TENM2 chr5 167849913 167849913 chr4 94956648 94956648 TCGA-ZG-A9L6 BND 25 33 TENM2 BMPR1B chr5 21208510 21208510 chr5 21248155 21248155 TCGA-ZG-A9L6 DEL 15 24 * * chr5 96956133 96956141 chr13 45804528 45804536 TCGA-ZG-A9L6 BND 19 18 LNPEP SIAH3 chr5 97211801 97211801 chr5 146337770 146337770 TCGA-ZG-A9L6 DEL 49 5 LIX1-AS1 AC091959.1 chr5 97852765 97852765 chr13 46389175 46389175 TCGA-ZG-A9L6 BND 20 37 * RUBCNL chr5 97973601 97973602 chr13 47340670 47340671 TCGA-ZG-A9L6 BND 6 50 * * chr5 98062040 98062040 chr13 107994935 107994935 TCGA-ZG-A9L6 BND 50 32 * * chr5 98136766 98136766 chr12 80147744 80147744 TCGA-ZG-A9L6 BND 38 3 LINC01846 OTOGL chr5 98688316 98688316 chr13 45820428 45820428 TCGA-ZG-A9L6 BND 35 17 * SIAH3 chr5 98693875 98693875 chr13 47399399 47399399 TCGA-ZG-A9L6 BND 21 43 * * chr6 153689028 153689028 chr6 153950467 153950467 TCGA-ZG-A9L6 DEL 1 1 * * chr6 154471351 154471351 chr6 154473661 154473661 TCGA-ZG-A9L6 DEL 40 42 CNKSR3 CNKSR3 chr6 64700935 64700935 chr6 64707095 64707095 TCGA-ZG-A9L6 DEL 18 24 EYS EYS chr6 65141042 65141042 chr6 123601246 123601246 TCGA-ZG-A9L6 DEL 20 28 EYS TRDN chr7 117387464 117387464 chr7 119281927 119281927 TCGA-ZG-A9L6 INS 32 31 ASZ1 * chr7 119203063 119203065 chr12 80987196 80987198 TCGA-ZG-A9L6 BND 33 21 * ACSS3 chr7 119289065 119289065 chr7 153553851 153553851 TCGA-ZG-A9L6 INS 43 48 * * chr7 120136243 120136243 chr7 120163419 120163419 TCGA-ZG-A9L6 DEL 6 46 * * chr7 152392483 152392483 chr12 84654286 84654286 TCGA-ZG-A9L6 BND 8 39 KMT2C * chr7 152672557 152672557 chr7 154153250 154153250 TCGA-ZG-A9L6 INS 25 37 XRCC2 DPP6 chr7 90701503 90701503 chr10 65474233 65474233 TCGA-ZG-A9L6 BND 22 27 CDK14 * chr8 102514217 102514217 chr8 103378652 103378652 TCGA-ZG-A9L6 INS 16 33 * CTHRC1 chr8 51042306 51042306 chr8 51042640 51042640 TCGA-ZG-A9L6 DEL 40 5 * * chr10 87216120 87216120 chr10 88066654 88066654 TCGA-FC-7961 DEL 6 21 AL157893.1 * chr10 9329392 9329392 chr20 8754106 8754132 TCGA-FC-7961 BND 49 50 * PLCB1 chr11 108221290 108221290 chr9 124385800 124385800 TCGA-FC-7961 BND 8 38 NPAT PSMB7 chr11 95383875 95383875 chr11 95428479 95428479 TCGA-FC-7961 DEL 5 29 * * chr11 9670906 9670906 chr11 10049908 10049908 TCGA-FC-7961 DUP 45 13 SWAP70 SBF2 chr11 97626780 97626780 chr11 98109633 98109633 TCGA-FC-7961 INS 11 23 * * chr11 97974977 97974977 chr11 98274414 98274414 TCGA-FC-7961 DEL 38 29 * * chr11 98949286 98949286 chr11 133185504 133185504 TCGA-FC-7961 DEL 47 23 * OPCML chr12 102078340 102078340 chr4 26526906 26526906 TCGA-FC-7961 BND 9 42 NUP37 * chr12 10497903 10497903 chr12 21000684 21000684 TCGA-FC-7961 DEL 35 49 * SLCO1B3-SLCO1B7 chr12 109342807 109342809 chr12 113113705 113113706 TCGA-FC-7961 DEL 38 24 * RASAL1 chr12 113015136 113015156 chr14 60478427 60478440 TCGA-FC-7961 BND 37 8 AC004551.1 C14orf39 chr12 122047221 122047221 chr12 122081922 122081922 TCGA-FC-7961 INV 1 17 BCL7A MLXIP chr12 41776244 41776244 chr12 45838077 45838077 TCGA-FC-7961 INV 50 4 * ARID2 chr12 60963855 60963855 chr12 61363385 61363385 TCGA-FC-7961 DEL 19 20 * * chr12 79546246 79546246 chr12 79761784 79761784 TCGA-FC-7961 DEL 3 15 AC027288.1 AC073569.2 chr13 21542273 21542273 chr16 84990922 84990922 TCGA-FC-7961 BND 21 48 MICU2 ZDHHC7 chr13 22933473 22933473 chr13 24356814 24356814 TCGA-FC-7961 DUP 38 26 * * chr13 28181287 28181287 chr4 115821686 115821686 TCGA-FC-7961 BND 47 40 PAN3 * chr13 48302948 48302948 chr13 48304834 48304834 TCGA-FC-7961 DEL 23 2 RB1 RB1 chr13 71141531 71141531 chr13 73000703 73000703 TCGA-FC-7961 INS 7 25 LINC00348 PIBF1 chr13 88403798 88403798 chr13 90800477 90800477 TCGA-FC-7961 INS 48 32 * * chr13 89128951 89128951 chr13 92388826 92388826 TCGA-FC-7961 DEL 50 13 * GPC5 chr14 105568898 105568911 chr14 105689169 105689169 TCGA-FC-7961 DUP 46 10 * * chr14 105568937 105568981 chr14 105690653 105690653 TCGA-FC-7961 DUP 45 12 * * chr14 105569370 105569370 chr14 105690273 105690273 TCGA-FC-7961 DUP 13 37 * * chr14 105569607 105569622 chr14 105689530 105689530 TCGA-FC-7961 DEL 40 21 * * chr14 105569693 105569693 chr14 105690481 105690481 TCGA-FC-7961 DEL 34 24 * * chr14 37586172 37586172 chr7 13932415 13932415 TCGA-FC-7961 BND 2 50 * ETV1 chr14 45923718 45923718 chr14 45957566 45957566 TCGA-FC-7961 DEL 8 26 * LINC00871 chr14 87205650 87205650 chr14 87953891 87953891 TCGA-FC-7961 DEL 37 23 * GALC chr15 86632809 86632809 chr11 70563473 70563473 TCGA-FC-7961 BND 29 23 AGBL1 SHANK2 chr16 27139616 27139616 chr17 66798960 66798980 TCGA-FC-7961 BND 2 4 * PRKCA chr16 7096559 7096559 chr16 7096888 7096888 TCGA-FC-7961 DEL 13 27 RBFOX1 RBFOX1 chr16 7459306 7459306 chr16 7505111 7505111 TCGA-FC-7961 DEL 23 3 RBFOX1 RBFOX1 chr16 88929330 88929331 chr17 59829641 59829642 TCGA-FC-7961 BND 20 12 CBFA2T3 VMP1 chr17 57123116 57123116 chr17 59211236 59211236 TCGA-FC-7961 DEL 9 5 * AC099850.2 chr18 48002528 48002528 chr18 76728238 76728245 TCGA-FC-7961 INV 11 22 * * chr18 48002582 48002582 chr21 38489896 38489896 TCGA-FC-7961 BND 29 18 * ERG chr19 50013926 50013926 chr8 127733147 127733147 TCGA-FC-7961 BND 19 32 VRK3 CASC11 chr1 102384546 102384546 chr1 209121708 209121708 TCGA-FC-7961 DEL 49 26 AC114485.1 * chr1 104372434 104372434 chr1 191954326 191954326 TCGA-FC-7961 INS 20 22 * LINC02770 chr1 109381222 109381222 chr1 210111434 210111434 TCGA-FC-7961 INS 22 41 SORT1 SYT14 chr1 110302410 110302410 chr1 158185086 158185086 TCGA-FC-7961 DEL 42 22 RBM15-AS1 * chr1 121616337 121616337 chr1 121740911 121740911 TCGA-FC-7961 DEL 50 19 * * chr1 158268019 158268019 chr6 90959790 90959790 TCGA-FC-7961 BND 17 41 HMGN1P5 * chr1 163870273 163870273 chr1 189027771 189027771 TCGA-FC-7961 INS 19 10 * LINC01035 chr1 172092201 172092201 chr1 174383486 174383490 TCGA-FC-7961 DEL 27 13 DNM3 RABGAP1L chr1 174670947 174670947 chr10 89244601 89244601 TCGA-FC-7961 BND 50 17 RABGAP1L LIPA chr1 174690869 174690869 chr10 87741191 87741192 TCGA-FC-7961 BND 50 35 RABGAP1L PAPSS2 chr1 180276728 180276728 chr1 191870009 191870009 TCGA-FC-7961 DEL 41 38 LHX4 AL359081.1 chr1 192587731 192587731 chr1 215118546 215118546 TCGA-FC-7961 DEL 18 34 AL390957.1 KCNK2 chr1 196325510 196325510 chr1 210057137 210057137 TCGA-FC-7961 DEL 48 37 KCNT2 SYT14 chr1 31896162 31896162 chr1 36189260 36189260 TCGA-FC-7961 DEL 10 21 AL136115.2 * chr1 60589534 60589534 chr1 182817079 182817079 TCGA-FC-7961 INS 23 25 LINC01748 NPL chr1 73994578 73994578 chr1 77652795 77652795 TCGA-FC-7961 DEL 43 20 * ZZZ3 chr1 81461933 81461933 chr2 75849313 75849313 TCGA-FC-7961 BND 21 49 ADGRL2 * chr1 8225040 8225040 chr1 69838121 69838121 TCGA-FC-7961 INS 18 12 * LRRC7 chr1 93774172 93774172 chr1 232909583 232909583 TCGA-FC-7961 INS 12 40 BCAR3 * chr1 96144207 96144207 chr1 188971093 188971093 TCGA-FC-7961 INS 46 34 * LINC01035 chr1 97154876 97154877 chr1 97267764 97267764 TCGA-FC-7961 DEL 37 27 DPYD DPYD chr20 13766239 13766239 chr20 14742530 14742530 TCGA-FC-7961 DUP 47 21 ESF1 MACROD2 chr21 10427230 10427230 chr21 31784962 31784962 TCGA-FC-7961 DUP 19 22 BAGE2 * chr21 18476791 18476791 chr21 18501949 18501949 TCGA-FC-7961 DEL 27 12 TMPRSS15 * chr21 22371697 22371698 chr5 161925984 161925985 TCGA-FC-7961 BND 48 14 AP000561.1 LINC01202 chr21 23344557 23344557 chr5 160587895 160587895 TCGA-FC-7961 BND 28 23 * ATP10B chr21 26630672 26630672 chr21 26855584 26855584 TCGA-FC-7961 DEL 31 12 * * chr21 26664740 26664740 chr4 42779314 42779314 TCGA-FC-7961 BND 9 8 * * chr21 38489036 38489036 chr21 41495437 41495437 TCGA-FC-7961 DEL 34 44 ERG TMPRSS2 chr21 38496116 38496116 chr21 41501700 41501700 TCGA-FC-7961 DEL 7 42 ERG TMPRSS2 chr21 38669255 38669255 chr21 41499244 41499250 TCGA-FC-7961 DEL 31 36 * TMPRSS2 chr22 48816921 48816921 chr22 48848469 48848469 TCGA-FC-7961 INV 32 2 TAFA5 TAFA5 chr2 1155108 1155108 chr2 1159363 1159363 TCGA-FC-7961 INV 16 31 SNTG2 SNTG2 chr2 116220737 116220737 chr2 116224786 116224786 TCGA-FC-7961 INV 46 2 * * chr2 122673428 122673428 chr2 122730227 122730227 TCGA-FC-7961 DEL 10 23 * * chr2 124844473 124844475 chrX 28166951 28166953 TCGA-FC-7961 BND 1 10 CNTNAP5 * chr2 126205401 126205401 chr2 126812027 126812027 TCGA-FC-7961 DEL 33 14 * * chr2 126215613 126215613 chr2 186717804 186717804 TCGA-FC-7961 INS 25 37 * FAM171B chr2 126783576 126783579 chrX 27145726 27145729 TCGA-FC-7961 BND 6 20 * AC112493.1 chr2 128340308 128340308 chr17 66799365 66799383 TCGA-FC-7961 BND 29 17 * PRKCA chr2 13840327 13840327 chr2 46383074 46383075 TCGA-FC-7961 DEL 32 7 LINC00276 EPAS1 chr2 138903934 138903934 chr2 138958355 138958355 TCGA-FC-7961 DEL 21 41 AHCYP4 * chr2 139031308 139031308 chr2 139919406 139919406 TCGA-FC-7961 DEL 29 28 * * chr2 140255043 140255043 chr2 142891948 142891948 TCGA-FC-7961 DEL 32 50 LRP1B KYNU chr2 143159232 143159234 chrX 15075778 15075780 TCGA-FC-7961 BND 39 27 ARHGAP15 * chr2 15307737 15307738 chr2 46477643 46477643 TCGA-FC-7961 DUP 12 5 NBAS AC016912.2 chr2 166132872 166132872 chr4 14112143 14112143 TCGA-FC-7961 BND 35 23 SCN1A LINC01085 chr2 166438157 166438157 chr4 14110786 14110786 TCGA-FC-7961 BND 43 41 SCN7A LINC01085 chr2 166507341 166507341 chr2 166512096 166512096 TCGA-FC-7961 INS 20 33 * * chr2 234868526 234868526 chr21 18683508 18683508 TCGA-FC-7961 BND 22 2 AC010148.1 MIR548XHG chr2 236586097 236586097 chr16 72820554 72820554 TCGA-FC-7961 BND 42 36 * ZFHX3 chr2 238870630 238870630 chr9 89371903 89371904 TCGA-FC-7961 BND 49 27 TWIST2 SEMA4D chr2 241990547 241990562 chr9 134685194 134685194 TCGA-FC-7961 BND 49 45 LINC01237 COL5A1 chr2 38150558 38150558 chr9 134823968 134823968 TCGA-FC-7961 BND 47 2 CYP1B1-AS1 COL5A1 chr2 40999371 40999374 chr2 41348045 41348045 TCGA-FC-7961 INV 14 40 * * chr2 40999371 40999374 chr2 41017911 41017911 TCGA-FC-7961 INV 28 27 * * chr2 41017470 41017470 chr2 42082831 42082831 TCGA-FC-7961 DUP 16 47 * * chr2 41343536 41343536 chr2 42086627 42086627 TCGA-FC-7961 DEL 2 18 * * chr2 50460149 50460149 chr2 50460220 50460220 TCGA-FC-7961 INS 10 27 NRXN1 NRXN1 chr2 75856977 75856995 chr2 128194994 128194994 TCGA-FC-7961 INV 3 28 * UGGT1 chr2 83661016 83661016 chr2 83668274 83668274 TCGA-FC-7961 DEL 35 15 * * chr3 164142651 164142651 chr3 193227752 193227752 TCGA-FC-7961 INS 9 27 * * chr3 169087744 169087744 chr3 169088790 169088790 TCGA-FC-7961 DEL 5 19 MECOM MECOM chr3 16918767 16918767 chr3 18091954 18091954 TCGA-FC-7961 DEL 20 38 PLCL2 TBC1D5 chr3 192102487 192102487 chr3 192127582 192127582 TCGA-FC-7961 DEL 46 38 * * chr3 2735597 2735597 chr3 18061154 18061154 TCGA-FC-7961 INS 15 17 CNTN4 TBC1D5 chr3 4179162 4179162 chr3 5925239 5925239 TCGA-FC-7961 DEL 29 19 SUMF1 * chr3 4758655 4758655 chr3 7232106 7232117 TCGA-FC-7961 DEL 27 1 ITPR1 GRM7 chr3 5655888 5655888 chr3 7320468 7320468 TCGA-FC-7961 INS 39 8 * GRM7 chr3 6874601 6874601 chr3 7232106 7232117 TCGA-FC-7961 INS 30 6 GRM7 GRM7 chr3 80566878 80566878 chr3 80678997 80678997 TCGA-FC-7961 DUP 18 24 * * chr4 115917358 115917358 chr4 116856215 116856215 TCGA-FC-7961 DEL 13 34 * * chr4 115926861 115926861 chr4 117352410 117352410 TCGA-FC-7961 INS 40 11 AC027613.1 LINC02262 chr4 116843918 116843918 chr4 117353056 117353056 TCGA-FC-7961 DEL 39 18 * LINC02262 chr4 12375964 12375964 chr4 12400252 12400252 TCGA-FC-7961 DEL 36 18 * * chr4 12567922 12567922 chr4 14685921 14685921 TCGA-FC-7961 DEL 33 3 * LINC00504 chr4 13285394 13285394 chr2 166570364 166570364 TCGA-FC-7961 BND 11 11 * * chr4 13307570 13307570 chr4 15098828 15098828 TCGA-FC-7961 INS 6 2 * C1QTNF7-AS1 chr4 13684622 13684635 chr2 166508880 166508896 TCGA-FC-7961 BND 31 44 LINC01182 * chr4 14110786 14110786 chr2 166438157 166438157 TCGA-FC-7961 BND 20 50 LINC01085 SCN7A chr4 14112120 14112120 chr4 14858975 14858975 TCGA-FC-7961 DEL 19 20 LINC01085 LINC00504 chr4 16492951 16492951 chr4 16495833 16495833 TCGA-FC-7961 DEL 8 26 AC097515.1 AC097515.1 chr4 42370260 42370261 chr5 99768426 99768427 TCGA-FC-7961 BND 17 29 AC024022.1 * chr4 42633318 42633318 chr21 28240424 28240424 TCGA-FC-7961 BND 48 25 ATP8A1 * chr4 42967007 42967007 chr4 44242333 44242333 TCGA-FC-7961 DEL 32 43 GRXCR1 KCTD8 chr4 43238784 43238787 chr5 153695849 153695851 TCGA-FC-7961 BND 30 21 * GRIA1 chr4 44874311 44874311 chr4 44908469 44908469 TCGA-FC-7961 DEL 34 34 * * chr4 49486965 49486965 chr4 49568688 49568688 TCGA-FC-7961 INV 50 9 AC119751.3 * chr4 6170179 6170179 chr4 6260149 6260149 TCGA-FC-7961 DUP 29 50 C4orf50 * chr5 103243723 103243723 chr13 72872851 72872851 TCGA-FC-7961 BND 35 3 * PIBF1 chr5 104157503 104157503 chr5 104167016 104167016 TCGA-FC-7961 DEL 25 28 * * chr5 111184292 111184292 chr5 111187988 111187988 TCGA-FC-7961 DEL 20 22 * * chr5 122788909 122788909 chr5 122795093 122795093 TCGA-FC-7961 DEL 43 25 SNX2 SNX2 chr5 153077449 153077449 chr21 27782302 27782302 TCGA-FC-7961 BND 22 8 LINC01470 * chr5 153667541 153667542 chr4 42389192 42389193 TCGA-FC-7961 BND 47 38 GRIA1 AC024022.1 chr5 153695849 153695851 chr4 43238784 43238787 TCGA-FC-7961 BND 48 49 GRIA1 * chr5 160563643 160563643 chr21 24154910 24154910 TCGA-FC-7961 BND 50 36 ATP10B * chr5 161925984 161925985 chr21 22371697 22371698 TCGA-FC-7961 BND 19 9 LINC01202 AP000561.1 chr5 17208607 17208611 chr20 8754106 8754132 TCGA-FC-7961 BND 12 38 BASP1 PLCB1 chr5 175924714 175924714 chr5 177956847 177956847 TCGA-FC-7961 DUP 12 40 THOC3 AC106795.3 chr5 99766909 99766909 chr21 26854352 26854352 TCGA-FC-7961 BND 9 47 * * chr6 112640042 112640042 chr17 19504348 19504348 TCGA-FC-7961 BND 22 45 * SLC47A1 chr6 112733037 112733037 chr21 30046697 30046697 TCGA-FC-7961 BND 19 44 * * chr6 118180856 118180856 chr6 118183734 118183734 TCGA-FC-7961 DEL 2 18 SLC35F1 SLC35F1 chr6 143762856 143762856 chr7 150737614 150737615 TCGA-FC-7961 BND 23 21 PHACTR2 GIMAP5 chr6 143765038 143765038 chr6 144423558 144423561 TCGA-FC-7961 DEL 40 25 PHACTR2 UTRN chr6 144424007 144424007 chr20 35872408 35872409 TCGA-FC-7961 BND 46 18 UTRN PHF20 chr6 17920445 17920446 chr12 116820318 116820318 TCGA-FC-7961 BND 14 4 KIF13A RNFT2 chr6 17920918 17920918 chr8 75372066 75372066 TCGA-FC-7961 BND 13 10 KIF13A * chr6 73728816 73728816 chr6 126039537 126039537 TCGA-FC-7961 DEL 25 37 CD109 TRMT11 chr7 155892006 155892006 chr14 89361179 89361179 TCGA-FC-7961 BND 9 25 * FOXN3 chr7 156995904 156995904 chr7 157645663 157645663 TCGA-FC-7961 INS 30 15 MNX1 PTPRN2 chr7 38413460 38413461 chr7 41945384 41945384 TCGA-FC-7961 DEL 2 12 AMPH * chr7 68949225 68949225 chr7 68949361 68949361 TCGA-FC-7961 INS 43 50 * * chr8 11930685 11930685 chr8 12035842 12035842 TCGA-FC-7961 DUP 29 9 OR7E161P AC107918.1 chr8 127299713 127299732 chr8 127742732 127742739 TCGA-FC-7961 DUP 3 27 PCAT1 * chr8 142150658 142150658 chr12 132349911 132349911 TCGA-FC-7961 BND 32 7 * * chr8 16160786 16160786 chr8 16160903 16160903 TCGA-FC-7961 INV 25 21 MSR1 MSR1 chr8 22280762 22280763 chr8 25130329 25130329 TCGA-FC-7961 DEL 41 24 PIWIL2 * chr8 47837658 47837658 chr8 47932598 47932599 TCGA-FC-7961 DEL 24 9 PRKDC PRKDC chr8 49518793 49518793 chr8 50264434 50264434 TCGA-FC-7961 INS 13 31 * SNTG1 chr8 49774837 49774837 chr8 49809500 49809500 TCGA-FC-7961 DEL 4 16 * * chr8 51973305 51973305 chrX 58528034 58528034 TCGA-FC-7961 BND 19 43 AC064807.2 * chr8 581478 581478 chr8 3216323 3216323 TCGA-FC-7961 DUP 14 33 * CSMD1 chr8 74447121 74447121 chr8 79112819 79112819 TCGA-FC-7961 DEL 37 15 GDAP1 * chr9 104416086 104416086 chr9 109313967 109313967 TCGA-FC-7961 DEL 36 36 * EPB41L4B chr9 113797099 113797099 chr15 34816959 34816959 TCGA-FC-7961 BND 22 35 * * chr9 123397937 123397938 chr9 123485527 123485527 TCGA-FC-7961 DEL 36 17 DENND1A DENND1A chr9 29770533 29770533 chr9 29784842 29784842 TCGA-FC-7961 DEL 38 33 * * chr9 29846560 29846560 chr15 20664824 20664824 TCGA-FC-7961 BND 20 16 * NBEAP1 chr9 42564019 42564019 chr9 42566150 42566150 TCGA-FC-7961 INV 15 50 * * chr9 61533258 61533258 chr9 61992107 61992107 TCGA-FC-7961 INV 21 25 * * chr9 61533703 61533705 chr9 61993079 61993079 TCGA-FC-7961 INV 7 49 * * chr9 61534150 61534150 chr9 61992066 61992074 TCGA-FC-7961 INV 3 3 * * chr9 61534198 61534198 chr9 61993197 61993197 TCGA-FC-7961 INV 20 20 * * chrX 107109214 107109225 chrX 107823288 107823288 TCGA-FC-7961 DEL 6 3 RBM41 * chrX 142079604 142079605 chrX 143735773 143735777 TCGA-FC-7961 DUP 3 42 * * chrX 28166951 28166953 chr2 124844473 124844475 TCGA-FC-7961 BND 34 3 * CNTNAP5 chrX 314656 314656 chrX 320691 320691 TCGA-FC-7961 DEL 44 6 GTPBP6 LINC00685 chrX 43525530 43525530 chrX 46859638 46859638 TCGA-FC-7961 DEL 50 13 * RP2 chrX 62493214 62493214 chr8 50270483 50270483 TCGA-FC-7961 BND 46 49 * SNTG1 chrX 66771727 66771728 chrX 66990317 66990318 TCGA-FC-7961 DUP 14 21 * * chrX 66990317 66990318 chrX 67076210 67076210 TCGA-FC-7961 DEL 16 42 * * chrX 84089786 84089786 chrX 94907173 94907193 TCGA-FC-7961 DEL 34 3 RPS6KA6 * chrX 94905973 94905973 chrX 94911072 94911072 TCGA-FC-7961 INS 24 8 * * chrX 94907173 94907193 chrX 94911124 94911124 TCGA-FC-7961 DEL 7 32 * * chr13 39231655 39231655 chr7 39622566 39622566 TCGA-VP-AA1N BND 38 32 LHFPL6 RALA chr14 86136205 86136207 chr4 180708235 180708237 TCGA-VP-AA1N BND 13 16 * * chr15 25921341 25921341 chr15 26114883 26114883 TCGA-VP-AA1N INS 39 19 LINC02346 LINC00929 chr16 16858583 16858583 chr22 34111152 34111152 TCGA-VP-AA1N BND 32 3 * LINC01643 chr16 16899530 16899530 chr1 12309358 12309358 TCGA-VP-AA1N BND 19 5 * VPS13D chr16 69348266 69348266 chr16 69374830 69374830 TCGA-VP-AA1N INS 33 40 AC026464.3 TERF2 chr18 2750255 2750255 chr18 2795801 2795801 TCGA-VP-AA1N DEL 26 31 SMCHD1 SMCHD1 chr18 2789725 2789725 chr18 8336965 8336965 TCGA-VP-AA1N INS 45 25 SMCHD1 PTPRM chr18 8339479 8339479 chr20 39994588 39994588 TCGA-VP-AA1N BND 35 13 PTPRM * chr1 112676228 112676228 chr1 112683454 112683454 TCGA-VP-AA1N DEL 16 5 MOV10 MOV10 chr1 31028808 31028808 chr16 14303329 14303329 TCGA-VP-AA1N BND 30 48 PUM1 MIR193BHG chr1 31030163 31030166 chr22 32532196 32532199 TCGA-VP-AA1N BND 26 23 PUM1 SYN3 chr20 39994468 39994468 chr20 40139727 40139727 TCGA-VP-AA1N DEL 40 49 * * chr20 39994588 39994588 chr18 8339479 8339479 TCGA-VP-AA1N BND 47 21 * PTPRM chr20 40139876 40139876 chr18 2750099 2750099 TCGA-VP-AA1N BND 44 27 * SMCHD1 chr22 32530646 32530646 chr1 113694229 113694229 TCGA-VP-AA1N BND 43 25 SYN3 * chr22 32532196 32532199 chr1 31030163 31030166 TCGA-VP-AA1N BND 25 32 SYN3 PUM1 chr2 241676466 241676466 chr16 13917329 13917329 TCGA-VP-AA1N BND 8 5 DTYMK * chr3 17019189 17019192 chr6 73101596 73101599 TCGA-VP-AA1N BND 47 8 PLCL2 KCNQ5 chr3 170317916 170317916 chr3 170318547 170318548 TCGA-VP-AA1N DEL 41 11 * * chr3 17166638 17166638 chr6 72996911 72996911 TCGA-VP-AA1N BND 17 45 TBC1D5 KCNQ5 chr3 173768026 173768026 chr3 173768769 173768769 TCGA-VP-AA1N DEL 20 39 NLGN1 NLGN1 chr3 97929100 97929102 chr3 99189437 99189437 TCGA-VP-AA1N INS 33 10 CRYBG3 * chr4 139026873 139026873 chr2 75686743 75686743 TCGA-VP-AA1N BND 32 18 NOCT MRPL19 chr4 180706592 180706597 chr14 86142085 86142090 TCGA-VP-AA1N BND 8 12 * * chr4 49121049 49121049 chr22 24515203 24515203 TCGA-VP-AA1N BND 31 36 * UPB1 chr5 60219403 60219403 chr5 60996745 60996745 TCGA-VP-AA1N INS 4 8 PDE4D NDUFAF2 chr5 85182718 85182718 chr5 85184623 85184623 TCGA-VP-AA1N DEL 21 23 * * chr6 73101596 73101599 chr3 17019189 17019192 TCGA-VP-AA1N BND 1 48 KCNQ5 PLCL2 chr9 94603480 94603480 chr5 124023878 124023878 TCGA-VP-AA1N BND 10 6 PCAT7 * chr10 102506924 102506924 chr10 131965403 131965403 TCGA-XK-AAIW DEL 50 11 SUFU * chr10 79965544 79965544 chr10 79967655 79967655 TCGA-XK-AAIW DEL 29 2 SFTPD SFTPD chr11 111551153 111551160 chr5 157734391 157734398 TCGA-XK-AAIW BND 41 23 LAYN THG1L chr11 112719628 112719628 chr11 112719789 112719789 TCGA-XK-AAIW INS 2 7 AP003100.2 AP003100.2 chr11 114402628 114402632 chr17 43544063 43544067 TCGA-XK-AAIW BND 45 36 RBM7 DHX8 chr11 114402995 114402995 chr17 17230265 17230265 TCGA-XK-AAIW BND 4 14 RBM7 FLCN chr11 78483458 78483458 chr11 78483547 78483547 TCGA-XK-AAIW DEL 40 38 NARS2 NARS2 chr14 41751709 41751709 chr14 41752517 41752517 TCGA-XK-AAIW DEL 1 2 LRFN5 LRFN5 chr15 25194707 25194707 chr15 29733013 29733013 TCGA-XK-AAIW DEL 8 1 SNHG14 TJP1 chr15 25337110 25337111 chr5 151656417 151656418 TCGA-XK-AAIW BND 35 6 SNHG14 * chr17 15388088 15388092 chr5 141058952 141058956 TCGA-XK-AAIW BND 9 28 AC005703.3 PCDHB1 chr17 42797844 42797844 chr17 42797991 42797991 TCGA-XK-AAIW DEL 33 50 COA3 COA3 chr17 43544432 43544434 chr8 133240706 133240708 TCGA-XK-AAIW BND 47 47 DHX8 NDRG1 chr17 73328247 73328247 chr1 107443392 107443392 TCGA-XK-AAIW BND 39 41 * NTNG1 chr19 42201928 42201928 chr19 50878182 50878182 TCGA-XK-AAIW DEL 7 1 DEDD2 KLK2 chr19 50871322 50871322 chr19 50881491 50881491 TCGA-XK-AAIW DEL 46 25 KLK2 * chr1 37512997 37512997 chr8 109777204 109777204 TCGA-XK-AAIW BND 39 18 MEAF6 AC023245.2 chr1 8849416 8849416 chr3 48517308 48517308 TCGA-XK-AAIW BND 13 18 * * chr2 113749340 113749340 chr2 149165536 149165536 TCGA-XK-AAIW DEL 19 21 SLC35F5 LYPD6B chr2 11573245 11573245 chr6 3992684 3992684 TCGA-XK-AAIW BND 13 19 GREB1 * chr2 140830020 140830020 chr2 149559501 149559501 TCGA-XK-AAIW DEL 7 48 LRP1B * chr2 149165448 149165448 chr2 149168969 149168969 TCGA-XK-AAIW DEL 2 22 LYPD6B LYPD6B chr2 149168944 149168944 chr2 151892819 151892819 TCGA-XK-AAIW DEL 6 9 LYPD6B CACNB4 chr2 149555900 149555900 chr2 149556024 149556024 TCGA-XK-AAIW INS 9 15 * * chr2 162305485 162305485 chr2 168117241 168117241 TCGA-XK-AAIW DEL 22 35 IFIH1 STK39 chr2 191952597 191952597 chr2 191970294 191970294 TCGA-XK-AAIW DEL 6 23 CAVIN2-AS1 CAVIN2-AS1 chr3 48513843 48513843 chr1 8746101 8746101 TCGA-XK-AAIW BND 3 25 * RERE chr3 70985021 70985021 chr3 71230990 71230990 TCGA-XK-AAIW DEL 48 22 FOXP1 FOXP1 chr3 96058400 96058400 chr3 97765702 97765702 TCGA-XK-AAIW DEL 49 17 * ARL6 chr4 177059364 177059368 chrX 11713825 11713829 TCGA-XK-AAIW BND 24 40 * AC004554.1 chr5 112726218 112726218 chr5 113652134 113652134 TCGA-XK-AAIW DEL 49 20 APC * chr5 124633723 124633723 chr5 125671107 125671107 TCGA-XK-AAIW INS 4 38 * * chr5 126324009 126324009 chr5 154802771 154802771 TCGA-XK-AAIW DEL 50 41 * LARP1 chr5 141058952 141058956 chr17 15388088 15388092 TCGA-XK-AAIW BND 16 9 PCDHB1 AC005703.3 chr5 141134304 141134307 chr8 123751498 123751501 TCGA-XK-AAIW BND 24 26 AC244517.2 * chr5 151656341 151656341 chr15 25319051 25319051 TCGA-XK-AAIW BND 8 22 * SNHG14 chr5 151656417 151656418 chr15 25337110 25337111 TCGA-XK-AAIW BND 9 28 * SNHG14 chr5 154802696 154802696 chr5 154806093 154806093 TCGA-XK-AAIW DEL 5 26 LARP1 LARP1 chr5 92968958 92968958 chr5 121964011 121964011 TCGA-XK-AAIW INS 38 4 * SRFBP1 chr5 97411108 97411108 chr5 99148896 99148896 TCGA-XK-AAIW INS 44 42 LIX1-AS1 * chr5 98129496 98129496 chr5 121964214 121964214 TCGA-XK-AAIW DEL 16 21 LINC01846 SRFBP1 chr5 99131632 99131632 chr5 118818008 118818008 TCGA-XK-AAIW INS 9 12 * * chr7 122063458 122063458 chr15 85739714 85739714 TCGA-XK-AAIW BND 45 20 * AKAP13 chr7 4438875 4438875 chr7 129492791 129492791 TCGA-XK-AAIW INS 43 44 * * chr8 123751498 123751501 chr5 141134304 141134307 TCGA-XK-AAIW BND 38 23 * AC244517.2 chr8 29024859 29024859 chr8 29026501 29026501 TCGA-XK-AAIW DEL 20 16 HMBOX1 HMBOX1 chrX 11713825 11713829 chr4 177059364 177059368 TCGA-XK-AAIW BND 18 15 AC004554.1 *