We performed cis-eQTL analysis between 816,362 SNP loci (22 autosomes and X chromosome) and corresponding mRNA transcripts in ER-positive breast cancer and ER-negative breast cancer respectively. To control for the false predictions, we excluded genes with absent call in over 90% of the samples; and genes of which the probes sets are affected by one or multiple known SNP loci. We also excluded the HLA locus given the high levels of polymorphism in this region. The Benjamini-Hochberg method was used to correct the raw P-values and a significant association was based on a threshold of false discovery rate (FDR) of 0.1.
