Table 2.

Novel EOC risk regions (P < 1.0 × 10−5) with allele-specific effects on lncRNA gene expression

LocusIndependent regions (length, kB)Overlap lncRNAa (ovarian-active?)Top SNPMAFR2OR (95% CI)PSNP hits/eQTL SNPslncRNA eQTL targets (distance, kB)
11p15.5chr11:2116492-2190591 (74)IGF2-AS (Y)rs3741205 (A>C)0.280.990.93 (0.91–0.94)3.94E−064/2FAM99A (429)
AC132217.4 (N)
11p13chr11:36325764-36396678 (71)RP11-514F3.4 (N)rs10501153 (C>T)0.340.820.92 (0.90–0.93)3.76E−0712/8RP11-219O3.2 (50)
16q21chr16:58944508-59028237 (84)RP11-410D17.2 (Y)rs6499994 (A>G)0.090.710.91 (0.89–0.93)8.57E−0828/4CTB-134F13.1 (-791)
RP11-430C1.1 (+861)
16q22.1chr16:67625872-68029739 (404)RP11-167P11.2 (Y)rs12325430 (T>C)0.440.750.92 (0.90–0.93)2.91E−072/2RP11-167P11.2 (0)
CTC-479C5.10 (Y)
CTC-479C5.17 (N)
AC009095.4 (Y)
chr16:67950613-68429047 (478)RP11-96D1.5 (Y)chr16:68187782 (CT>C)0.400.730.92 (0.90–0.93)2.10E−0711/1RP11-167P11.2 (177)
RP11-96D1.9 (N)
RP11-96D1.6 (Y)
RP11-96D1.7 (Y)
RP11-96D1.10 (Y)
RP11-96D1.11 (Y)
RP11-96D1.3 (Y)
RP11-67A1.2 (Y)
CTC-479C5.6 (N)
CTC-479C5.17 (Y)
19q13.12-13chr19:38201712-38474127 (272)CTD-2554C21.3 (N)chr19:38451511 (TA>T)0.140.811.12 (1.09–1.15)5.74E−069/7AC012309.5 (459)
CTD-2554C21.2 (Y)
CTD-2528L19.6 (N)
CTC-244M17.1 (N)
AC016582.2 (N)
  • Abbreviation: R2 = Imputation quality r2.

  • alncRNAs in bold contain SNP hits within their coordinates and non-bolded lncRNAs are in LD with SNP hits.