Table 3.

Nine CHi-C putative target genes that were statistically significant eQTLs (FDR adjusted P < 0.1)

Cytoband	SNP	Proxy	Gene		All cancers		ER+ cancers		ER− cancers
			Nearest	CHi-C target	P	P adj	P	P adj	P	P adj
2q31.1	rs1550623		CDCA7	CDCA7	0.007	0.087	0.511	0.666	0.330	0.892
11q13.1	rs3903072		SNX32	CTSW	0.006	0.087	0.064	0.326	0.001	0.101
11q13.1	rs3903072		SNX32	SNX32	0.007	0.087	0.032	0.268	0.036	0.506
14q13.3	rs2236007	rs1018464	PAX9	PAX9	0.003	0.066	0.054	0.317	0.248	0.854
14q24.1	rs2588809		RAD51B	ZFP36L1	0.079	0.380	0.004	0.091	0.256	0.854
17q22	rs6504950	rs9902718	STXBP4	COX11	0.002	0.059	0.001	0.032	0.403	0.892
19p13.11	rs8170	rs34084277	BABAM1, ANKLE1*	MRPL34	0.001	0.059	0.011	0.173	0.131	0.829
19p13.11	rs4808801		ELL *	LRRC25	0.009	0.092	0.004	0.091	0.768	0.954
19p13.11	rs4808801		ELL *	SSBP4	0.002	0.059	0.0002	0.016	0.475	0.892

^*In an analysis that included all genes that are nearest genes, regardless of whether they were also a CHi-C target gene, rs4808801 was also associated with expression of ELL (FDR adjusted P = 0.05 for all cancers and P = 0.04 for ER+ cancers) and rs8170 was also associated with expression of ANKLE1 (FDR corrected P = 0.05 for all cancers)

PP-value (1df t-test) per allele association with gene expression, adjusted for methylation and copy number, P_adj P value further adjusted for multiple testing