We assessed 15 previously reported breast cancer risk loci for the regulatory potential in gene expression of breast cancer cells (Table S4, related to Figure 2). Any variant that achieved P < 5×10-8 was selected. To adjust for the effects of somatic factors, we performed multivariate linear regression of the tumor gene expression on somatic copy number and methylation and used the scaled residuals as adjusted measures of gene expression. Then a second regression of the adjusted gene expression on the germline genotypes of each of the 15 risk loci was performed.
