Breast cancer TCGA RNA-seq data from 177 individuals were evaluated for the relationship between genotypic status at the risk alleles and AI (Table S7, related to Figure 3, Table S4). After removing cases with somatic copy number alterations, our results demonstrated that the 6q25 and 8q24 risk loci are significantly associated with allelic specific expression of ESR1 and MYC, respectively (P = 0.017 for rs2046210/ESR1 and P = 0.035 for rs418269/MYC; Figures 3A, B). As expected, the AI is greatest in individuals heterozygous for the risk variant. No significant association was observed for KLF4, however the power was limited due to fewer informative variants in the transcribed region (Figure 3C).
