Expression quantitative trait locus (eQTL) analyses were performed for all genes in the 1 MB region spanning the associated SNPs using probe-level gene expression data for breast epithelium samples taken from normal tissue adjacent to the tumor of 135 breast cancer patients of European ancestry from the METABRIC study (21 (
link)). These were assayed using the Illumina
HT12 platform. We also analyzed eQTL data of 387 breast tumors from the Cancer Genome Atlas (TCGA) (303 ER-positive, 81 ER-negative, three unknown) assayed using the Agilent G4502A-07-3 array (35 (
link)). Germline SNP genotypes were available for normal and tumor samples from the Affymetrix
SNP 6.0 platform imputed into 1000 Genomes Project data (March 2012) for the three SNPs of interest: rs2059614 at 11q24.2, and rs148760487 and rs114860916 at 2q24.2 (see Results section). Association between genotype and expression was tested by linear regression with false discovery rate control.
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