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Table 1 Genes significant in meta-analysis and identified in CNV-based association tests

From: Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism

Gene Name CNV Type Group 1 Group 2
CNVR(hg19) TagSNP P value Cases # Control # CNV QC Pass/Fail CNVR(hg19) TagSNP P value Cases # Control # CNV QC Pass/Fail
BBS5, KLHL41 Deletion chr2:170354790–170368798 rs3769772 1.86E-11 30 11 PASS chr2:170343083–170840224 rs2592804 0.217885025 1 0 FAIL
CDK19 Deletion chr6:110972494–111696091 rs12198236 0.01327263 3 0 FAIL chr6:111061814–111381468 rs9374202 0.010264833 3 0 PASS
SYNE1 Deletion chr6:152938025–152969462 rs6940651 0.237247353 1 0 FAIL chr6:152511420–152516441 rs7772542 2.04E-09 13 0 FAIL
TARPa Deletion chr7:38357194–38364605 rs11765884 3.74E-05 18 13 PASS chr7:38341226–38341925 rs2736973 2.56E-07 29 26 PASS
TONSL-AS1, TONSLa Deletion chr8:144992103–146235564 rs11136344 0.027970085 7 7 PASS chr8:145660543–145666578 rs2306384 5.04E-05 12 6 PASS
UPF2a Deletion chr10:12028228–12076043 rs7899260 0.00313275 4 0 PASS chr10:12062959–12075960 rs7072007 8.15E-06 9 1 PASS
TET1 Deletion chr10:70342775–70775081 rs7071780 0.05619918 2 0 FAIL chr10:70410630–70432644 rs10762236 9.01E-11 15 0 PASS
MICU1 Deletion chr10:74250792–74534174 rs7912170 0.237133237 1 0 FAIL chr10:74304790–74433626 rs7909573 4.56E-08 11 0 PASS
ADK Deletion chr10:76092179–76099557 rs10824151 5.31E-06 14 5 FAIL chr10:76372037–77001459 rs4746209 0.047420164 2 0 FAIL
NUCB2a Deletion chr11:17300844–17320797 rs12419530 4.08E-05 7 0 PASS chr11:17332461–17339127 rs10466382 0.034028702 3 1 PASS
LARP4 Deletion chr12:49846626–51537196 rs10876136 0.237133237 1 0 FAIL chr12:50768339–50807570 rs7296212 2.21E-05 7 0 PASS
AQR Deletion chr15:34261920–35227613 rs16954263 0.237133237 1 0 FAIL chr15:35233730–35252767 rs4513050 2.33E-09 17 3 FAIL
PIGL Deletion chr17:15043999–16221319 rs7210224 0.237133237 1 0 FAIL chr17:16196056–16207526 rs11868284 2.21E-05 7 0 PASS
PAFAH1B1 Deletion chr17:1811983–2578648 rs9674799 0.056145117 2 0 FAIL chr17:2534710–2561169 rs11078288 0.000478637 5 0 PASS
SLC19A1 Deletion chr21:46298869–47863025 rs2330183 0.138704428 2 1 FAIL chr21:46945024–46953292 rs4819128 9.13E-06 10 2 PASS
FOLH1B Duplication chr11:89123768–89405190 rs7929532 0.237133237 1 0 FAIL chr11:89374850–89405190 rs7112871 3.71E-35 54 2 FAIL
  1. aGenes/loci passed CNV QC in both groups