To further investigate the likely genes underlying the susceptibility variants, we examined associations between the lead SNPs and the RNA expression of neighboring genes in 473 primary breast tumors and 61 normal breast tissue samples in The Cancer Genome Atlas (TCGA) database. We found strong evidence for an association between rs616402 (a surrogate for rs616488; r2 = 0.66) and expression of PEX14 in both tumor (P = 4.7 × 10−12) and normal tissue (P = 0.00018; Supplementary Table 8), between rs3760983 (a surrogate for rs3760982; r2 = 1) and expression of both ZNF404 (P = 1.2 × 10−6 in tumors) and ZNF283 (P = 0.0089) and between rs3903072 and expression of CTSW (P = 4.9 × 10−5). SNP rs3760982 was also found to be associated with the expression of ZNF45 (P = 0.0077), ZNF283 (P = 0.05) and ZNF222 (P = 0.01) in lymphoblastoid cell lines from HapMap samples using the Genevar database35 (Supplementary Table 8c). After adjustment for the SNP in the region most strongly associated with expression, SNP rs616488 and PEX14 (P = 0.0071) as well as rs1217396
