Table 1.

SNPs associated with EOC risk are enriched in lncRNA genes

Whole genome (15,159,372 SNPs)13,442 lncRNA genes (1,757,495 SNPs)5,287 ovarian-active lncRNA genes (457,227 SNPs)
Tumor histologySNPs P < 10−5Independent regionsaSNPs P < 10−5PbIndependent regionsaPcSNPs P < 10−5PdIndependent regionsaPe
All invasive5,2941301,4640.047720.00058730.009460.043
Serous5,9221471,5720.044810.0099600.002510.16
 High grade5,3671781,4670.045890.0028990.004500.25
 Low grade1,9161,1042190.483850.64500.701690.15
  • aSNPs with r2 > 0.2 and within a 250-kb distance were grouped into independent regions.

  • bProportion of risk SNPs within lncRNA genes compared with whole-genome distribution. Empirical P values based on 10,000 permutations of lncRNA genes across the whole genome.

  • cProportion of regions overlapping lncRNA genes compared with whole-genome distribution. Empirical P values based on 10,000 permutations of independent regions across the whole genome.

  • dProportion of risk SNPs in ovarian-active lncRNA genes compared with all lncRNAs. Empirical P values based on 10,000 permutations of active/inactive classification of lncRNAs.

  • eProportion of regions overlapping ovarian-active lncRNA genes compared with all lncRNAs. Empirical P values based on 10,000 permutations of independent regions that overlapped lncRNAs.