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 histology	SNPs P < 10⁻⁵	Independent regions^a	SNPs P < 10⁻⁵	P^b	Independent regions^a	P^c	SNPs P < 10⁻⁵	P^d	Independent regions^a	P^e
All invasive	5,294	130	1,464	0.047	72	0.0005	873	0.009	46	0.043
Serous	5,922	147	1,572	0.044	81	0.009	960	0.002	51	0.16
High grade	5,367	178	1,467	0.045	89	0.002	899	0.004	50	0.25
Low grade	1,916	1,104	219	0.48	385	0.64	50	0.70	169	0.15

↵^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.