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["Supplementary Table 7. Segmental Duplications and Repeat Elements"]
["Gene","Type","CN State","CNV Size (Kb)","ID #a","Exons, Intronsb","Segmental Duplications","Repeat Elements (most)*","CGIc","with enhancers","with active TSS","methylC-seqd ovary vs testes","RNA-Seqe fetal vs adult ovary","H3K27Ac","TFM totalf","chromHMMg Ovary"]
["AHRR","Loss",1,8.766,"D16, D21","intron 4","none ","LINEs, SINEs","none","none","none","similar","slight difference in 5'","yes ",5,"weak"]
["AHRR","Loss",1,14.484,"D12","exon 5","none ","LINEs, SINEs","none ",1,"none ","mC+ ov (enh)","slight difference in 5'","yes ",8,"weak"]
["AHRR","Loss",1,19.77,"D17","exons 5-6 ","none ","LINEs, SINEs","1 (intron 5)",1,"none ","mC+ in ov (enh and CGI)","slight difference in 5'","yes ",15,"weak "]
["ANOS1","Gain",2,7,"D40","intron 2","none ","SINEs, LINEs, LTRs","none","none","none","similar ","different","yes (1)",1,"none"]
["ANOS1","Loss",1,"entire gene","D3","entire gene ","none "]
["AR","Gain",2,8.381,"D31","intron 1 ","none ","LINEs, SINEs, LTRs, DTs","none ","none ","none","similar","different ","none ","none","none"]
["AR","Loss",1,190.517,"D3","exons 2-8 (intron 1)","none ","LINEs, SINEs, LTRs, DTs","none","multiple ","none","similar","similar ","yes ","multiple","weak, strong, WRP"]
["ARX","Gain",4,23,"D44","entire gene ","none ","SR/MS, LCRs, SINE, LINE","7 (each exon, upstream 5')","none ","7 (transcription in all CGIs)","mC++ ov","similar ","none",12,"RP, WRP"]
["ATRX","Gain",2,2.206,"D37","intron 23 ","none ","LINEs, SINEs, DTs","none ","none ","none ","similar ","different ","none ","none ","WRP"]
["ATRX","Gain",3,5.187,"D30","intron 23 ","none ","LINEs, SINEs, DTs","none ","none ","none ","similar","different ","none ","none ","none "]
["ATRX","Gain",2,"entire gene","D10 ","entire gene ","none "]
["AXIN1","Loss",1,2.087,"D51","intron 4","none ","SINE, LINE, DT","none ",1,"none ","mC+ testes (enh)","different ","yes ",1,"strong, weak"]
["AXIN1","Loss",1,12.735,"D42","exons 4-5","none ","SINEs, DTs","1 (orphan exon 5)",1,"none ","mC+ testis (enhancer)","similar ","yes ",4,"strong, weak "]
["AXIN1","Loss",1,6.579,"D34, D44, D52","exon 5","none ","SINEs, LTRs","1 (orphan exon 5)",1,"none","mC+ in testis @ enhancer region (LIMC4 LINE)","similar","yes ",3,"strong"]
["BBS9","Gain",3,30,"D21","exon 1  (RP9)","none ","SINEs, LINEs","1 (5')",2,1,"similar ","similar ","yes (2; 5' both genes)",8,"weak"]
["BNC2","Loss",1,3.702,"D12, D15","intron 1","none ","LINEs, SINE, DT","none","none ","none","similar","RS+ adult","none","none ","weak"]
["BNC2","Gain",4,1.93,"D36","intron 1","none ","SINE, DT","none",1,"none","similar","RS++ adult","none",1,"weak"]
["BNC2","Loss",1,2.069,"D52","intron 2","none ","SINE","none","none","none","similar","different ","none","none ","weak"]
["CAMK1D","Loss",1,6,"D20","intron 1","none ","SINEs, DTs, LINEs","none ","none ","none ","similar ","RS+ adult","yes (1)",3,"none "]
["CHD7","Gain",4,2,"D9","intron 1","none ","SINE","none ","none ","none ","similar ","different ","none ",2,"none"]
["CHD7","Loss",1,11.4,"D1","exons 35-38","none ","SINEs, LINEs","none ","none ","none ","similar ","different ","yes (1)","none ","weak "]
["CNTNAP3","Gain",3,95.708,"D15","exons 1-2","yes (entire) ","LINES, SINEs, LTRs, DTs",1,"none ","none","mC+ ov","none (both)","yes (tall peaks on 5')","none ","none "]
["CNTNAP3","Gain",3,374.048,"D14","exons 19-24","yes (entire) ","LINES, SINEs, LTRs, DTs",1,"none","none","different ","different ","yes (two thin peaks on distal 3')","multiple","none"]
["CNTNAP3","Gain",3,"entire gene","D18","entire gene ","yes (entire) ",{"$nulls":6},"yes (two thin peaks on distal 3')","multiple"]
["CREBBP","Loss",1,5,"D4","intron 2","none ","LINE, SINE","none","none ","none ","similar ","different ","yes (2)",3,"none "]
["CTNNA3","Gain",4,6.612,"D37","intron 5","none ","SINEs","none ",2,"2 (flanking)","mC+ testis (aTSS)","RS+ adult","none ","multiple","weak"]
["CTNNA3","Gain",3,15.582,"D21","intron 7","none ","DTs, SINEs, LINEs","none ","none ","none ","similar ","RS++ adult","none ","none ","none "]
["CTNNA3","Gain",4,14.283,"D14","intron 7","none ","DTs, SINEs, LINEs","none ",2,"2 (flanking)","similar ","different ","none ","multiple"]
["CTNNA3","Loss",1,22.158,"D46","intron 9","none ","DTs, SINEs, LINEs","none ","none ","none ","similar ","different ","none ",2,"none "]
["CTNNA3","Loss",1,92.181,"D43","exon 10 near 5'","none ","DTs, SINEs, LINEs","none ",2,"1 (next to enhancer)","mC+ testis (aTSS/enh, enh)","different ","none ","multiple ","heterochromatin (LIPA13)"]
["CTNNA3","Loss",1,31.747,"D10","intron 12 ","none ","DTs, SINEs, LINEs","none ",2,"none ","mC+ testis (enhancer)","RS++ adult","none ",4,"weak"]
["CTNNA3","Loss",1,7.416,"D27","intron 13","none ","SINEs, SR/MS","none ","none ","none ","similar ","RS++ adult","none ","none ","none "]
["CTNNB1","Gain",3,12.571,"D14","intron 1 ","none ","LINEs, DTs, SINEs","none ","multiple ","multiple","similar","different ","yes ",4,"weak"]
["CTNNB1","Gain",3,19.067,"D18","exons 8-17","none ","LINEs, SINEs, DTs","none ","3 (enh, genic enh)","none ","mC+ testis (Charlie18a DT)","similar","yes ",5,"strong, weak"]
["CTNNB1","Gain",3,10.332,"D16, D17","exons 9-15","none ","LINEs, SINEs, DTs","none","2 (genic)","none","different ","RS++ fetal","yes ","none","strong, weak "]
["CTNNB1","Gain",4,9.628,"D21","exons 9-14","none ","LINEs, SINEs, DTs","none ","2 (genic)","none","similar ","similar ","yes ","none "]
["CXCL12","Gain",4,6.895,"D17","disrupted exon 4 (3')","none ","DTs, LINE, SINE","none ","1  (distal 3')","none","mc+ testis (enh 5' distal)","similar ","yes ",1,"strong, weak "]
["CXCL12","Gain",3,8.082,"D21","exon 4","none ","DTs, LINE, SINE","none ","1  (distal 3')","none","mc+ testis (enh 5' distal)","similar ","yes ",1,"strong, weak "]
["DHRSX","Loss",1,5.369,"D25","intron 1 ","yes ","LINEs, SINEs, DTs","none",1,"none ","mC++ ov","different","yes ",3,"weak"]
["DHRSX","Loss",1,3.006,"D25","intron 1 ","yes ","LINEs, SINEs, DTs","none","none ","none ","similar ","RS+ adult","yes ",2,"none"]
["DHRSX","Loss",1,14.427,"D26","intron 1 ","yes ","LINEs, SINEs, DTs","none ",2,"none ","mC++ ov","different","yes ",8,"weak "]
["DHRSX","Loss",1,1.195,"D32","intron 1 ","yes ","LINEs, SINEs, DTs","none","none ","none ","similar ","RS+ adult","yes ",1,"none"]
["DHRSX","Loss",1,2.047,"D41","intron 1 ","yes ","LINEs, SINEs, DTs","none","none ","none ","similar ","RS+ adult","yes ",2,"none"]
["DHRSX","Loss",1,14.715,"D48","intron 1 ","yes ","LINEs, SINEs, DTs","none ",2,"none ","mC++ ov","different","yes ",8,"weak "]
["DHRSX","Loss",1,1.858,"D51","intron 1 ","yes ","LINEs, SINEs, DTs","none",1,"none ","mC++ ov","different","yes ",3,"weak"]
["DHRSX","Gain",3,9.178,"D36","intron 1 ","yes ","LINEs, SINEs, DTs","none",1,"none ","mC++ ov","different","yes ",4,"weak"]
["DHRSX","Gain",3,16.755,"D45","intron 1 ","yes ","LINEs, SINEs, DTs","none ",2,"none ","mC++ ov","different","yes ",8,"weak "]
["DHRSX","Loss",1,48.838,"D46","exons 2-3","yes ","LINEs, SINEs, DTs","none ",1,"none ","mC+ testis (enhancer)","similar ","yes ","multiple","strong, weak, Zn genes and repeats"]
["DHRSX","Loss",1,1.343,"D26","exon 3","yes ","LINEs, SINEs, DTs","none","none","none","different ","different ","none ","none ","strong, weak"]
["DHRSX","Loss",1,1.831,"D40","intron 3","yes ","LINEs, SINEs, DTs","none ","none","none","similar ","different ","none ",3,"weak"]
["DHRSX","Loss",1,24.485,"D46","intron 3","yes ","LINEs, SINEs, DTs","none ","none ","none ","mC+ ovary (middle)","different ","yes ","multiple","weak"]
["DHRSX","Gain",4,1.118,"D31","intron 3","yes ","LINEs, SINEs, DTs","none ","none","none","similar ","different ","none ",1,"weak"]
["DHRSX","Gain",3,1.174,"D25","intron 3","yes ","LINEs, SINEs, DTs","none ","none ","none","similar ","RS++ adult","none ",2,"weak "]
["DMD","Loss",1,4.061,"D29","intron 1 ","yes ","SINEs, LINEs, LTRs","none","none ","none ","similar","different","none ","none ","none "]
["DMD","Gain",2,3.874,"D36","intron 1 ","yes ","SINEs, LINEs, LTRs","none","none ","none ","similar","different","none ",2,"none "]
["DMD","Gain",2,5.569,"D30","intron 1 ","yes ","SINEs, LINEs, LTRs","none","none ","none ","similar","different","none ","none ","none "]
["DMD","Gain",3,5.571,"D34","intron 1","yes ","SINEs, LINEs, LTRs","none","none ","none ","similar","different","none ","none ","none "]
["DMD","Gain",2,2.449,"D23, D37","intron 2 ","yes ","LINEs, SINEs, DTs","none ","none ","none","similar","RS+ adult","none ","none ","none"]
["DMD","Gain",2,9.609,"D28","intron 2 ","yes ","LINEs, SINEs, DTs","none ","none","none ","mC+ ov (LINE)","different ","yes ","1 (5') ","none"]
["DMD","Gain",2,9.618,"D30","intron 2 ","yes ","LINEs, SINEs, DTs","none ","none","none","mC+ ov ","different","yes (2)","1 (5') ","none"]
["DMD","Loss",1,9.823,"D29","intron 2 ","yes ","LINEs, SINEs, DTs","none","none","none","mC+ ov","different ","yes ","1 (5') ","none"]
["DMD","Loss",0,2.617,"D32","intron 2 ","yes ","LINEs, SINEs, DTs","none","none","none","similar ","different ","none ","none ","none "]
["DMD","Loss",0,4.432,"D38","intron 2 ","yes ","LINEs, SINEs, DTs","none","none","none","similar ","different ","none ","none ","none "]
["DMD","Gain",2,1.623,"D31","intron 7","yes ","LINEs, SINEs, LTRs","none","none","none ","different ","different ","none ","none ","WRP"]
["DMD","Loss",0,1.085,"D40","intron 7","yes ","LINEs, SINEs, LTRs","none","none","none ","different ","different ","none ","none ","none"]
["DMD","Loss",1,1.111,"D29","intron 7","yes ","LINEs, SINEs, LTRs","none","none","none ","different ","different ","none ","none ","none"]
["DMD","Loss",1,1.88,"D52","intron 7","yes ","LINEs, SINEs, LTRs","none","none","none ","different ","different ","none ","none ","none"]
["DMD","Loss",1,3.564,"D52","exons 8-9","yes ","SR/MS","none","none","none ","different ","different ","none ","none ","none"]
["DMD","Loss",1,3.633,"D29","exons 8-9","yes ","SR/MS ","none","none","none ","different ","different ","none ","none ","none"]
["DMD","Loss",1,2.014,"D52","intron 9 ","yes ","LINEs, SINEs, LTRs","none","none ","none ","mC+ ov","different ","none ","none ","none"]
["DMD","Loss",1,7.032,"D29","intron 9 ","yes ","LINEs, SINEs, LTRs","none ","none ","none ","mC+ ov (middle)","different ","none ","none ","none "]
["DMD","Loss",0,5.091,"D48","intron 9 ","yes ","LINEs, SINEs, LTRs","none ","none ","none ","mC+ ov (middle)","different ","none ","none ","none "]
["DMD","Loss",0,5.099,"D42","intron 9 ","yes ","LINEs, SINEs, LTRs","none ","none ","none ","mC+ ov (middle)","different ","none ","none ","none "]
["DMD","Loss",0,6.299,"D48, D52","intron 17","yes ","LINEs, SINEs, LTRs","none ","none ",1,"mC+ @ aTSS testis","RS++ adult @aTSS; RS++ fetal at distal side","none ",3,"WRP"]
["DMD","Loss",0,1.686,"D40","exon 18","yes ","LINEs, SINEs, LTRs","none ","none ","none ","similar ","different ","none ","none ","WRP"]
["DMD","Loss",0,3.89,"D41","exons 40-41","yes ","LINE, DT, SR/MS","none","none ","none ","similar ","similar ","none ","none ","none "]
["DMD","Loss",0,5.741,"D41","exon 48","yes ","SINE, LINE, LTR","none ",2,"none","mC+ testis (tnxn site)","similar ","none ","1 (intron 48)","WRP"]
["DMD","Gain",2,17.369,"D30","intron 44","yes ","SINEs, LINEs, DTs","none","1 (5' shorter transcript)","none ","similar ","different ","none ",1,"none"]
["DMD","Gain",4,3.509,"D29","intron 44","yes ","SINEs, LINEs, DTs","none","none","none","similar ","RS+ adult","none ","none ","none "]
["DMD","Gain",4,3.728,"D34","intron 44","yes ","SINEs, LINEs, DTs","none","none","none","similar ","RS+ adult","none ","none ","none "]
["DMD","Gain",4,3.731,"D44","intron 44","yes ","SINEs, LINEs, DTs","none","none","none","similar ","RS+ adult","none ","none ","none "]
["DMD","Loss",0,5.023,"D23","exon 48","yes ","SINE, LINE, LTR","none",2,"none","similar ","similar ","none ","1 (intron 48)","WRP, weak"]
["DMD","Loss",0,5.159,"D50","exon 48","yes ","SINE, LINE, LTR","none",2,"none","similar ","similar ","none ","1 (intron 48)","WRP, weak"]
["DMD","Loss",0,2.816,"D42, D52","intron 55","yes ","LINEs, SINEs, DTs","none","none ","none ","similar","RS+ adult","none ","1 (5') ","WRP"]
["DMD","Loss",0,9.647,"D48","intron 55","yes ","LINEs, SINEs, DTs","none","none ","none ","similar ","different ","none ",2,"WRP"]
["DMD","Loss",1,1.303,"D52","intron 55","yes ","LINEs, SINEs, DTs","none","none ","none ","similar ","different ","none ","none ","WRP"]
["DMD","Loss",1,9.846,"D44","intron 55","yes ","LINEs, SINEs, DTs","none ","none","none ","similar","different ","none ",2,"WRP (2)"]
["DMD","Loss",0,2.172,"D48","intron 59","yes ","DTs, LINEs, SINEs","none ","none ","none ","similar","different ","none ",1,"none "]
["DMD","Loss",0,1.177,"D20","intron 59 ","yes ","DTs, LINEs, SINEs","none ","none ","none ","similar","different ","none ","1 (5') ","none "]
["DMD","Gain","4, 2",1.395,"D34, D42, D44, D52","intron 59","yes ","DTs, LINEs, SINEs","none ","none","none ","similar","none (both)","none ","none ","none "]
["DMD","Loss",1,1.519,"D52","intron 60 ","yes ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","none ","none ","none "]
["DMD","Loss",1,3.142,"D29","intron 60 ","yes ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","none ","none ","none "]
["DMD","Loss",1,4.72,"D51","intron 60 ","yes ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","none ","none ","none "]
["DMD","Loss",1,5.495,"D44","intron 60 ","yes ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","none ","none ","none "]
["DMD","Gain",4,2.239,"D34","intron 60 ","yes ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","none ","none ","none "]
["DMD","Gain",4,2.371,"D30","intron 60 ","yes ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","none ","none ","none "]
["DMD","Gain",2,6.423,"D31","intron 62","yes ","LINEs, SINEs, DTs","none ","none ","none ","similar ","different ","yes ",4,"WRP"]
["DMD","Loss",0,2.775,"D38","intron 62","yes ","LINEs, SINEs, DTs","none","none","none","similar ","different ","none ","none ","none"]
["DMD","Gain",4,1.973,"D29","intron 74","yes ","SINE","none","none","none","similar ","different ","none ",2,"none"]
["DMD","Gain",4,2.695,"D44","intron 74","yes ","SINE","none ","none ","none ","similar ","different ","none ",4,"weak "]
["DMD","Gain",2,5.031,"D30","exons 75-76","yes ","SINE, LINE, LTR","none ","none ","none ","similar ","similar ","none ","none ","strong, weak"]
["EP300","Gain",4,3.107,"D29, D48","exons 7-8","none ","SINEs","none","none ","none","similar","RS++ fetal (exon 7)","none ","none ","strong "]
["EP300","Loss",1,3.581,"D13","exons 8-10","none ","SINEs","none ","none ","none ","similar ","RS++ fetal","none ","none ","strong "]
["ESR1","Loss",1,28,"D27","intron 7","none ","LINEs, LTRs, SINEs","none ",1,"none ","similar ","different ","none",4,"weak "]
["ESR1","Gain",3,25,"D30","intron 7","none ","LINEs, LTRs, SINEs","none ","none","none ","similar ","different ","none",4,"weak "]
["ESR2","Gain",3,8.583,"D13","exons 7-8","none ","SINEs","none ","none ","none ","similar ","similar ","yes ","2 (exon 8, intron 6)","weak "]
["ESR2","Gain",4,4.786,"D42, D44","exon 9","none ","SINEs, LINEs, DTs","none ","none ","none ","similar ","similar","yes ","1 (intron 9)","weak"]
["ESR2","Loss",1,12.839,"D13","exon 9","none ","SINEs, LINEs, DTs","none ","none ","none ","similar ","similar","yes ","1 (intron 9)","weak"]
["ESR2","Gain",4,10.456,"D34","exon 9","none ","SINEs, LINEs, DTs","none ","none ","none ","similar ","similar","yes ","1 (intron 9)","weak"]
["ESR2","Loss",1,1.469,"D42","intron 9 ","none ","SINEs, LINEs, DTs","none","none","none","similar ","different ","none","none ","none "]
["ESR2","Loss",1,2.983,"D1","intron 12","none ","SINEs, LINEs, DT","none",1,"none","similar ","different","none",1,"weak"]
["ESR2","Loss",1,3.243,"D9","intron 12","none ","SINEs, LINEs, DT","none",1,"none","similar ","different","none",1,"weak"]
["ESR2","Loss",1,3.383,"D10","intron 12","none ","SINEs, LINEs, DT","none",1,"none","similar ","different","none",1,"weak"]
["ESR2","Loss",1,3.607,"D13","intron 12","none ","SINEs, LINEs, DT","none ",1,"none","similar ","different","none",1,"weak"]
["ESR2","Gain",3,1.805,"D15, D16","disrupted exon 13 ","none ","SINEs, LINEs, DT","none","1 (MIR3 SINE)","none ","mC+ in testis (enhancer)","different ","yes ","1 (intron 12)","weak "]
["ESR2","Gain",3,7.276,"D21","exon 13","none ","SINEs, LINEs, DT","none","1 (MIR3 SINE)","none ","mC+ in testis (enhancer)","different ","yes ","2 (introns, 13)","strong, weak "]
["FAM167A-AS1 (C8orf12)","Loss",1,15.888,"D13","intron 1","none ","SINEs, DTs, LINEs","none ","none ","none ","different ","different","none ",2,"WRP"]
["FAM167A-AS1 (C8orf12)","Loss",1,19.164,"D14","intron 1","none ","SINEs, DTs, LINEs","none ","none ","none ","different ","different","none ",2,"WRP"]
["FGD1 (WNK3, PHF8, FAM120C)","Loss",1,507,"D3","exons 13-18","none ","SINEs, LINEs","none ",2,1,"mC++ testis","different ","yes (1)","multiple","strong, weak"]
["FGF7","Loss",1,139,"D51","exons 3-4  (FAM227B)","yes (5')","LINEs, SINEs, LTRs","none",4,1,"different ","different ","none ","multiple","strong, weak, 4 heterochromatin"]
["FGFR2","Gain",4,6,"D38","intron 5","none ","SINEs","none ",1,"none ","different (enh)","different ","yes (2)","none","weak"]
["FGFR2","Loss",1,6,"D4","exons 14-15","none ","LINEs","none ","none ","none ","similar ","different ","yes (1)",2,"weak"]
["FLNA","Gain",3,22.858,"D1","exons 6-48","yes (3')","SINEs, LINEs","2 (exon 29, distal 3')","none ","none ","similar ","similar ","none ","multiple ","none "]
["FLNA","Gain",2,16.012,"D21","disrupted exon 22; exons 22-48","yes (3')","SINEs","2 orphans","none ","none ","similar ","similar ","none ","multiple ","strong, weak"]
["FLNA","Gain",2,10.732,"D9","disrupted exon 48","yes (entire) ","SINEs, LINEs","2 orphans (3' end disrupted; 3' distal)","none ","none ","mC+ ov (distal CGI)","different ","yes ",2,"weak"]
["FLT1","Loss",1,2.417,"D4","exon 24","none ","DTs ","none","none ","none ","similar ","similar ","none ",2,"none "]
["FLT1","Loss",1,11.378,"D4","intron 3","none ","SINEs, LINEs, SR/MS","none ",1,"none ","mC+ ov (enh)","RS++ adult","yes ","multiple","WRP"]
["FRAS1 ","Loss",1,11.475,"D22, D24, D26, D42","exon 30","none ","LINEs, SINEs, DTs","none","none ","none ","similar","RS+ in fetal (exon 30), RS+ in adult 3' distal","yes ","1 (intron 4)","none "]
["FRG1BP","Gain",3,121.375,"D15","entire gene ","yes ","SINEs, LINEs, LCRs",{"$nulls":3},"mC++ ov (CGI)","similar ","yes ","multiple"]
["FRG1BP","Gain",3,345.158,"D18","entire gene ","yes ","SINEs, LINEs, LCRs",{"$nulls":3},"mC++ ov (CGI)","similar ","yes ","multiple "]
["GATA4","Loss",1,7,"D12","intron 2","none ","SINEs, LTRs, LINEs","none ",5,3,"mC++ ov","different","yes (1)",5,"weak"]
["GFRA1","Gain",3,18.277,"D14","exon 5","none ","SINEs, LINEs, DTs","none ","1 (exon 5)","none ","different ","RS++ adult","yes ","multiple","none "]
["GFRA1","Gain",3,21.989,"D19","exon 5","none ","SINEs, LINEs","none ","1 (exon 5)","none ","different ","RS++ adult","yes ","multiple","none "]
["GNRH1 ","Gain",3,64,"D13","entire gene (DOCK5, KCTD9, CDCA2)","yes (5')","SINEs, LINEs, DTs","other genes","1 (genic)","2 (CDCA2)","mC++ testis","different","yes (4)","multiple ","weak, strong"]
["GRIP1 ","Loss",1,23.926,"D15","intron 1","none ","LINEs, SINEs, DTs","none ","none ","none ","different ","different ","yes ",11,"WRP"]
["GRIP1 ","Gain",4,8.432,"D5","intron 5","none ","SINE, LINE, DT, LCR","none ","none ","none ","similar ","RS+ fetal","none ","none ","none "]
["GRIP1 ","Loss",1,15.333,"D1","exon 14","none ","LINEs, SINEs, DTs","none ","none ","none ","similar ","RS++ adult","yes ",1,"none "]
["HHAT","Loss",1,3,"D31","intron 7","none ","LINEs, LTRs, SINE","none ","none ","none ","similar ","RS+ adult","none","none ","none"]
["HSD17B3","Gain",4,7,"D18","intron 2 ","none ","LTRs, SINEs","none ","none ","none ","similar ","different ","none",2,"none "]
["INSR","Loss",1,13.98,"D24","intron 2 ","yes (5')","SINEs, DTs, LINEs","none ",4,"none ","mC+ testis","RS++ adult","yes ",7,"weak"]
["INSR","Loss",1,29.054,"D14","disrupted exon 22 (with ZNF557)","yes (5')","DTs","1 (distal 3' bw INSR ZNF557)",1,"none ","mC+ testis INSR, none in CGI (both) ","RS++ fetal","yes ",8,"weak (ZNF557 Zn genes repeats, heterochromatin)"]
["KANK1 ","Loss",1,4.123,"D43","intron 5","none ","SINEs, LINEs, SR/MS","none ","none ","none ","similar ","different ","yes ",1,"none "]
["KANK1 ","Gain",3,15.615,"D17","intron 6","none ","SINEs, LINEs","none",3,3,"mC+ testis","different ","yes ",5,"weak"]
["KANK1 ","Gain",3,5.594,"D20","intron 6","none ","SINEs, LINEs","none",1,3,"mC+ testis","different ","yes ",2,"weak"]
["KANK1 ","Gain",4,5.354,"D16","intron 6","none ","SINEs, LINEs","none",1,3,"mC+ testis","different ","yes ",2,"weak"]
["KANK1 ","Gain",3,32.062,"D18","exon 6","none ","SINEs, LINEs","none ",4,"3 intron 6 (1 near exon 6, 2 flank, aTSS)","mC+ testis (aTSS)","similar ","yes ","multiple ","weak "]
["KRAS","Gain",3,4.197,"D2","disrupted exon 4","yes (3')","SINEs, DTs","none","none","none ","similar ","similar ","none ","none ","weak"]
["KRAS","Gain",3,12.167,"D7","disrupted exon 4; exons 4-5","yes (3')","SINEs, DTs","none","none","none ","similar","none (both)","none ","none ","weak"]
["KRAS","Gain",3,8.5,"D6, D19","disrupted exon 5","yes (3')","SINEs, DTs","none","none","none ","similar","none (both)","none ","none ","weak"]
["MOV10L1","Loss",1,6.774,"D13","intron 2 ","none ","SINEs, LINEs, DTs","none ","none ","none ","similar ","RS++ adult","none ","none ","WRP"]
["MOV10L1","Loss",1,4.586,"D14","intron 2 ","none ","SINEs, LINEs, DTs","none ","none ","none ","similar ","RS++ adult","none ","none ","WRP"]
["MOV10L1","Loss",1,9.97,"D33, D35, D37, D46","exons 16-19","none ","SINEs, LINEs, DTs","none ","1 (exon 16, AT-rich)","none ","mC+ in testis at enchancer region, intron 19 (MER33 DT)","RS++ fetal (enh)","none ",5,"none "]
["MTHFR","Loss",1,31,"D15","entire gene  (CLCN6)","none ","SINEs, LINEs, DTs","1 (CLCN6)",9,"7 (5', 3')","mC++ testis","similar","yes (multiple)",9,"strong, weak"]
["NLGN4X","Gain",2,2.038,"D25","intron 2 ","none ","SR/MS, SINE","none ",1,"none ","similar ","different ","none ","none ","heterochromatin, weak"]
["NLGN4X","Gain",2,1.526,"D31","intron 2 ","none ","SR/MS, SINE","none ","none","none ","similar ","different ","none ","none ","none"]
["NLGN4X","Gain, Loss","4, 1",1.53,"D29, D34, D44","intron 2 ","none ","SR/MS, SINE","none ","none","none ","similar ","different ","none ","none ","none"]
["NLGN4X","Loss",0,3.23,"D40","intron 3","none ","LINEs, SINEs, LTRs","none","none ","none ","similar ","different","none ",1,"weak"]
["NLGN4X","Loss",0,3.109,"D48","intron 3","none ","LINEs, SINEs, LTRs","none","none ","none ","similar ","different","none ",1,"weak"]
["NLGN4X","Loss",1,4.77,"D29","intron 3","none ","LINEs, SINEs, LTRs","none ","none ","none ","similar ","RS++ adult","none ",1,"weak"]
["NLGN4X","Gain ",2,"entire gene","D10","entire gene ","none "]
["NOTCH1","Loss",0,4.371,"D29, D32, D52","intron 2","none ","DT, LINE","1 (orphan)","none ","none ","similar","different ","yes ",5,"weak"]
["NOTCH2","Loss",1,29,"D41","intron 1","yes ","SINEs, DTs, LINEs","none ",6,1,"mC++ testis (aTSS)","different ","yes (multiple)",7,"weak"]
["NOTCH3","Gain",4,2.786,"D16, D17, D18","exon 1","none ","SR/MS, SR",1,"none ","1 (CGI 5' end)","none @ aTSS in both","different in 5', RS+ @3' in adult","yes ",1,"none"]
["NOTCH3","Gain",4,2.495,"D19","exon 1","none ","SR/MS, SR","1 (5')","none ",1,"mC++ ov","RS++ adult","yes ",1,"none"]
["NOTCH3","Gain",3,22.15,"D21","exons 1-20","none ","SINEs, DTs, LTRs",4,1,"2 (5', orphan)","different mC++","similar ","yes ","multiple","weak"]
["NOTCH3","Gain",3,19.822,"D12, D15","exons 2-20","none ","SINEs, DTs, LTRs",3,"1 (orphan CGI, intron 2)","1 (orphan CGI, intron 2, enh)","mC+ in ovary @ aTSS, exons 7-11, 18-20","similar ","yes ","multiple","weak"]
["NOTCH3","Gain",3,27.041,"D6","exons 13-33","none ","SINEs, DTs, LTRs","3 (orphan)","none ","2 (intron 22 and CGI)","mC+ ov (none in aTSS)","similar ","yes ","multiple","strong, weak"]
["NR0B1","Gain",2,4.932,"D30","disrupted exon 1 ; exons 1-2","none ","AT-rich, LINEs",1,1,3,"mC+ ov (CGI)","similar","none ",2,"WRP"]
["NR0B1","Gain",2,5.64,"D28","entire gene ","none ","LINEs, DTs, LCRs","1 (5')",1,3,"mC+ ov","similar ","none ",2,"WRP"]
["NR0B1","Gain ",2,"entire gene","D10","entire gene ","none "]
["NR5A1","Loss",1,18,"D9","exons 1-4 (includes NR6A1)","none ","SINEs, LINEs","1 (orphan)","4 (intra, upstream of 5')",7,"mC+ ovary (CGI)","RS++ adult","yes (2)","multiple ","strong, weak"]
["NR5A2","Loss",1,1.112,"D25","intron 5","none ","SINEs, LCRs","none ","none ","none ","similar","different ","none ","none ","none "]
["NR5A2","Loss",1,4.529,"D25","intron 7","none ","SINEs, AT-rich","none ","none ","none ","similar ","RS+ adult","none ",1,"WRP"]
["NR5A2","Loss",1,2.896,"D28","intron 7","none ","SINEs, AT-rich","none ","none ","none ","similar ","RS+ adult","none ",1,"WRP"]
["OCA2","Gain",4,2.422,"D42","intron 2 ","none ","SINE","none ","none ","none ","similar ","none (both)","none ",3,"none "]
["OCA2","Gain",4,11.157,"D16, D18, D21","intron 19","none ","LTRs, LINEs","none ","none","none","similar","RS++ fetal","none ",2,"none"]
["OCA2","Gain",3,29.279,"D21","intron 23 ","none ","LINEs, SINEs","2 (orphan)","none ","none ","mC+ in ov (2 CGI, 1 het)","different ","none ","multiple","3 heterochromatin"]
["PBX1","Gain",4,7.081,"D38","intron 2 ","none ","SINEs, SR/MS","none ",2,"none ","different (5' enhancer)","different ","yes ",3,"weak "]
["PBX1","Gain",4,1.253,"D34, D42, D44, D52","intron 2 ","none ","SINEs","none","1  (MIR SINE 3')","none","different ","different ","none ","none ","weak"]
["PBX1","Gain",4,1.253,"D48","intron 2 ","none ","SINEs","none","1  (MIR SINE 3')","none","different ","different ","none ","none ","weak"]
["PCDH17","Loss",1,6.653,"D5, D9","intron 3","none ","SRs, LINE, DT","none ","none","none","similar ","different ","none ",1,"WRP"]
["PCSK1","Loss",1,24.849,"D10","exons 1-3","none ","LINEs, SINEs, DTs","1 (5')",5,2,"similar (mC- ov tes)","different ","yes ",6,"RP, WRP"]
["PCSK1","Loss",1,"entire gene","D9","entire gene ","none ",{"$nulls":6},"yes ","multiple "]
["PDGFRA","Gain",3,18.745,"D17","exons 13-23","yes (small)","LINEs, LTRs, SINEs, DTs ","none ","2 (genic, exons 13-17)","none","mC+ @ enhancer exon 14, intron 17 in testis ","different ","yes ",5,"strong, weak"]
["PDGFRA","Gain",3,18.881,"D18, D21","exons 13-23","yes (small)","LINEs, LTRs, SINEs, DTs ","none ","2 (genic, exons 13-17)","none","mC+ @ enhancer exon 14, intron 17 in testis ","different ","yes ",5,"strong, weak"]
["PDGFRA","Gain",3,2.859,"D6","disrupted exon 23 ","yes (small)","LINEs, LTRs, SINEs, DTs ","none ","none ","none ","similar ","similar ","none ","none ","strong "]
["PIP5K1B","Gain",4,1.665,"D15, D18","intron 7","none ","LINEs, SINEs","none ","none","none","similar","none (both)","none ","none ","none"]
["PIP5K1B","Gain",4,3.522,"D27","intron 9","none ","LINEs, SINEs","none ","none","none","similar","different","none ",1,"none"]
["PIP5K1B","Loss",1,4.136,"D46","exon 13","none ","LINEs, SINEs","none ","none","none","similar","different","none ",2,"none"]
["POR","Loss",1,15,"D23","intron 1","yes (3')","SINEs, DTs","1 (5', MIR4651)","2 (5', distal 5')","1 (5')","different (5', distal enh)","different","yes (5)",6,"none"]
["PTCH1","Gain",4,4.356,"D42","exons 1-2","none ","SR/MS, LCRs, SINEs",1,"none",1,"none @ aTSS in both","similar ","yes ","multiple ","none"]
["PTCH1","Gain",3,14.621,"D4","intron 2 ","none ","SINEs, DTs, LINEs","none",5,"none","mC++ ov","similar","yes ","multiple ","weak"]
["PTCH1","Gain",3,16.368,"D7","intron 2 ","none ","SINEs, DTs, LINEs","1 (5' shorter transcripts)",5,"none","mC+ ov (middle), mC- (aTSS)","similar ","yes ","multiple ","weak "]
["PTCH1","Gain",3,3.713,"D12","intron 2 ","none ","LINEs, SINE","none",1,1,"similar","different","yes ",2,"none"]
["PTCH1","Gain",4,4.117,"D21","exons 11-12","none ","SINEs, LINEs, LCRs","none ","none ","none ","similar ","similar ","yes ",1,"strong "]
["PTCH1","Gain",4,4.047,"D21","exons 14-15","none ","LINEs","none ","1 (genic)","none ","similar ","similar ","yes ","none ","strong "]
["PTPN11","Loss",1,16.373,"D24","exon 1 (includes entire RPL6)","yes (3')","SINEs, LINEs","1 (1)","none (1 genic)","yes (yes)","none @ aTSS in both (none @ aTSS)","different ","yes (yes)","1 (3) several upstream","none (strong, weak)"]
["PTPN11","Gain",3,37.014,"D14, D15, D16, D18, D21","exons 11-16","yes (3')","SINEs, LINEs, DTs","none ","none ","none","similar","similar ","none ",2,"strong, weak"]
["RAF1","Loss",1,8.433,"D7","intron 1 ","none ","SINEs, DTs, LINEs, SR/MS","none ","multiple ","none ","similar","different","yes ",5,"weak"]
["RAF1","Gain",4,3.837,"D7","intron 1 ","none ","LINEs, DTs","none ","none ","none ","similar","different","none ","none ","weak "]
["RAF1","Gain",3,13.598,"D18","exons 3-6","none ","SINEs, LINEs","none ","1 (genic)","none ","similar ","similar ","yes ",5,"strong, weak "]
["ROCK2","Loss",1,28.091,"D1","intron 1","none ","LINEs, SINEs, DTs","none ","multiple ",1,"mC+ tes (aTSS)","different","yes ","multiple ","weak "]
["ROCK2","Loss",1,42.161,"D15","exons 31-33 (entire PQLC3)","none ","SINEs, LINEs, SR/MS","none ","2 (PQLC3)","2 (PQLC3)","similar 3' (mC- both PQLC3)","similar","yes ","none ","weak "]
["SHOX","Gain",4,41.547,"D12","exons 4-6","yes (entire) ","SINEs, LTRs, SR/MS","4 (3' end of short long transcripts)","none ","none ","mC++ ov distal 3'), mC++ tes within ","different","yes ","2 (CGIs)","RP, WRP, heterochromatin"]
["SHOX","Loss",1,41.663,"D46","exon 6","yes (entire) ","SINEs, LTRs, SR/MS",{"$nulls":3},"similar ","different ","yes ","2 (CGIs)"]
["SHOX","Gain",3,"entire gene","D10","entire gene ","yes (entire) "]
["SNRPN","Gain",3,14.752,"D21","intron 2","yes (middle) ","LINEs, SINEs, DTs, LTRs","none ","none ","none ","similar","similar","yes (tall wide peaks intron 2)","multiple","WRP"]
["SNRPN","Gain",3,36.457,"D12","exon 3 (introns 2, 3)","yes (middle) ","LINEs, SINEs, DTs, LTRs","1 (orphan)","none ","1 (orphan CGI)","mC++ ov (CGI)","RS++ adult","yes (tall wide peaks intron 2)","multiple","WRP"]
["SOS1","Loss",1,18,"D16","intron 1","none ","SINEs, LINEs, DTs","none",6,"none ","similar ","different ","yes (5)",8,"weak"]
["SOX9","Loss",1,6,"D25, D46, D52","PE","none ","SINEs","none",1,"none","mC++ testis (enh)","RS+ fetal","yes (1)",3,"weak"]
["SOX9","Loss",1,1.6,"D38","PE  (LINC00459)","none ","DT","none ","none ","none ","similar ","RS+ fetal","none",2,"WRP"]
["SRD5A2","Loss",1,6.909,"D30, D39","disrupted exon 6; exons 4-6","none ","DTs, LINEs, LTRs","none ","none","none","similar","different ","none ","none ","none"]
["SRD5A2","Gain",3,265.744,"D47","entire gene ","none ","DTs, LINEs, LTRs",{"$nulls":3},"mC++ ov (CGI)","different ","none ","multiple "]
["SUPT3H","Loss",0,9.773,"D38","intron 2  (RUNX2)","none ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","yes ",1,"weak "]
["SUPT3H","Loss",1,9.989,"D48","intron 2  (RUNX2)","none ","SINEs, LINEs, DTs","none ","none ","none ","similar ","different ","yes ",1,"weak "]
["TGFB1","Gain",4,4.015,"D18, D21","exons 6-7","none ","SINEs, SR/MS, SRs",null,"none","none","mC+ @3' end in ovary","similar","yes ",2,"strong "]
["TP63","Loss",1,4.149,"D16","intron 1 ","none ","LINEs, SINEs, LTRs, DTs (RNA repeat)","none","none ","none","similar","RS+ adult","none ",3,"none (tRNA-lys-AAG)"]
["TP63","Loss",1,11.13,"D22","intron 1 ","none ","LINEs, SINEs, LTRs, DTs (RNA repeat)","none","none ","none","similar","different","none ",2,"none"]
["TP63","Loss",1,3.886,"D42","intron 1 ","none ","LINEs, SINEs, LTRs, DTs (RNA repeat)","none","none ","none","similar","different","none ","none ","none"]
["TP63","Loss",1,11.223,"D45","intron 1 ","none ","LINEs, SINEs, LTRs, DTs (RNA repeat)","none","none ","none","similar","different","none ",2,"none"]
["TP63","Loss",1,8.299,"D38","intron 1 ","none ","LINEs, SINEs, LTRs, DTs (RNA repeat)","none","none","none","similar","RS+ adult","none ",2,"none"]
["TP63","Loss",1,8.299,"D52","intron 1 ","none ","LINEs, SINEs, LTRs, DTs (RNA repeat)","none","none","none","similar","RS+ adult","none ",2,"none"]
["TP63","Gain",4,4.56,"D27, D34, D43, D48","exons 5-7","none ","SINEs, LINEs","none","none","none","similar","different","none ","none ","none"]
["TP63","Gain",3,11.795,"D41","exons 5-7","none ","SINEs, LINEs","none ","none ","none ","similar ","different ","yes ",1,"none "]
["TP63","Gain",4,1.352,"D42","exon 7","none ","SINEs, LINEs","none ","none ","none ","similar","similar","none ","none ","none "]
["TP63","Loss",1,10.208,"D2","exons 8-10","none ","DTs, SINEs","none ","none ","none ","similar","similar","yes ","none ","none "]
["VAMP7","Loss",1,1.493,"D36","intron 6","yes (entire) ","LINEs, SR/MS, DTs, LTRs, SINEs","none","none","none","similar ","different ","none ","none ","weak"]
["VAMP7","Loss",1,94.31,"D46","exons 6-8 (3')","yes (entire) ","LINEs, SR/MS, DTs, LTRs, SINEs","none ","2 (distal 3')","none ","similar ","similar ","none ",2,"3' - strong, weak, Zn genes repeats, heterochromatin"]
["WNT2","Loss",1,6,"D34","intron 3","none ","LINEs, SINEs","none ","none ","none ","similar ","different","none",2,"WRP"]
["WWOX","Loss",1,8.076,"D22","intron 4","none ","SINEs, LINEs, LTRs, DTs","none","none ","none ","mC+ ov","RS++ adult","none ",1,"none "]
["WWOX","Loss",0,8.165,"D29, D38, D39, D41, D43","intron 5","none ","SINEs, LINEs, LTRs, DTs","none","none","none","mC+ in ovary","RS++ adult","none ",1,"none"]
["WWOX","Loss",0,8.836,"D2, D8, D9, D10, D16, D20, D21","intron 5","none ","SINEs, LINEs, LTRs, DTs",null,"none","none","mC+ in ovary","RS++ adult","none ",1,"none"]
["WWOX","Loss",0,4.495,"D12","intron 5","none ","SINEs, LINEs, LTRs, DTs","none ","none ","none ","mC+ ov","different ","none ",1,"none"]
["WWOX","Loss",0,3.748,"D12","intron 5","none ","SINEs, LINEs, LTRs, DTs","none ","none ","none ","mC+ ov","different ","none ","none ","none"]
["WWOX","Loss",0,4.899,"D18","intron 5","none ","SINEs, LINEs, LTRs, DTs","none ","none ","none ","mC+ ov","different ","none ","none ","none"]
["WWOX","Loss",0,7.236,"D26, D32","intron 5","none ","SINEs, LINEs, LTRs, DTs","none ","none","none","mC+ in ovary","RS++ adult","none ",1,"none"]
["WWOX","Loss",1,6.976,"D42","intron 5","none ","SINEs, LINEs, LTRs, DTs","none ","none","none","mC+ in ovary","RS++ adult","none ",1,"none"]
["WWOX","Gain",3,52.788,"D17","intron 5","none ","SINEs, LINEs, LTRs, DTs","none ","2 (orphan)","none ","mC+ ov in 3'","different ","none ","multiple","weak "]
["WWOX","Gain",3,36.886,"D21","intron 5","none ","SINEs, LINEs, LTRs, DTs","none","2 (orphan)","none","similar","different ","none ","multiple","none"]
["WWOX","Gain",3,12.391,"D33","intron 5","none ","SINEs, LINEs, LTRs, DTs","none","none","none ","similar","different ","none ","multiple","none "]
["WWOX","Gain",3,12.128,"D45","intron 5","none ","SINEs, LINEs, LTRs, DTs","none","none","none ","similar","different ","none ",1,"none "]
["WWOX","Loss",1,1.795,"D14","intron 8","none ","SINEs, LINEs, LTRs, DTs","none","none","none ","similar ","RS++ adult","none ",1,"none "]
["WWOX","Gain",3,14.11,"D18","intron 8","none ","SINEs, LINEs, LTRs, DTs","none ","multiple ","2 (orphan)","different ","RS++ adult","none ",2,"weak "]
["WWOX","Gain",4,4.643,"D2","intron 8","none ","SINEs, LINEs, LTRs, DTs","none ",8,"none ","mC+ tes (5 enh)","RS++ adult","none ",2,"weak "]
["WWOX","Loss",1,148.179,"D45","exon 9","none ","SINEs, LINEs, LTRs, DTs","none ","multiple ","2 (3', orphan)","different ","RS++ adult","none ","multiple ","weak "]
["ahighlighted ID# recurrent CNVs in 2 patients "]
["bgene in a parenthesis - another gene included in the CNV"]
["cCGI - CpG island"]
["dmC - methyl-C profile for DNA (CGI methylation) - mC+ (present)"]
["eRNA-seq - RS++ (higher), RS+ (present), RS- (absent) predicted RNA expression "]
["fentry in parenthesis - number or location of peaks"]
["gChromHMM - ChIP Seq data for predicting chromatin states (strong or weak transcription; WRP/RP, weak/repressed polycomb)"]
["*SINE - short interspersed element, LINE - long interspersed element, LTR - long terminal repeat, DT - DNA transposon, SR/MS - satellite repeats/microsatellite "]