Table 1.

SNPs associated with epithelial ovarian cancer risk are enriched in lncRNA genes

Tumor Histology	Whole Genome (WG) (15,159,372 SNPs)		13,442 lncRNA Genes (1,757,495 SNPs)				5,287 Ovarian-Active lncRNA Genes (457,227 SNPs)
	SNPs p<10−5	Independent Regionsb	SNPs p<10−5	P-valuea	Independent Regionsb	P-valuec	SNPs p<10−5	P-valued	Independent Regionsb	P-valuee
All Invasive	5294	130	1464	0.047	72	0.0005	873	0.009	46	0.043
Serous	5922	147	1572	0.044	81	0.009	960	0.002	51	0.16
High Grade	5367	178	1467	0.045	89	0.002	899	0.004	50	0.25
Low Grade	1916	1104	219	0.48	385	0.64	50	0.70	169	0.15

^aProportion of risk SNPs within lncRNA genes compared to whole genome distrbution. Empirical p-values based on 10,000 permutations of lncRNA genes across the whole genome.

^bSNPs with r²>0.2 and within a 250kb distance were grouped into independent regions.

^cProportion of regions overlapping lncRNA genes compared to 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 to 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 to all lncRNAs. Empirical p-values based on 10,000 permutations of independent regions that overlapped lncRNAs.