To compare the genetic determinants of gene expression in different subtypes of breast cancer, we performed a cis-eQTL analysis for 48 ER-negative breast cancer samples. Based on the model described above, we identified 380 significant cis-associations (FDR < 0.1), mapping to 380 SNP loci and 179 target genes (Table S3). Notably, only 43 target genes (24.0%) from ER-positive tumors are represented in the significant associations in ER-negative tumors.
