eQTL analysis of the remaining 26 loci (69 protein-coding genes) identified 22 SNP-gene combinations that were nominally significant ( t -test P < 0.05) in all, ER+ or ER− breast cancers (Supplementary Data 6 ), nine of which remained significant after taking account of multiple testing (FDR adjusted t -test P < 0.1,Table 3 ).
In addition, there was a highly significant association between levels of expression of CDCA7 and DSS (trend test P = 1.22 × 10 −8 ), which maps just 7 kb from the reported 2q31.1 risk SNP (rs1550623), but while there was a robust eQTL association between rs1550623 and CDCA7 in all cancers (trend tests: nominal P = 0.007, FDR adjusted P = 0.09) there was no association in ER+ cancers alone (both P > 0.1).