cis-eQTL analysis, we considered all genes 50 kb upstream or downstream of the lead SNP. Fourteen of the risk-associated SNPs are represented directly on the Affymetrix SNP array. For an additional 23, we were able to select proxies on the basis of maximum LD with minimum r2 of 0.5. In case of equal LD, we used proximity on the genome to break the tie. LD estimates were extracted from the HapMap data for the CEU population. eQTL analysis was performed by regressing the gene expression of selected candidate genes on the genotype followed by a significance test of the t statistic for the genotype covariate. For both the normal and tumor analyses, the linear regression was adjusted for potential batch effects by including indicator variables for the plate identifier component of the TCGA sample barcode. In addition, the first principal component of the complete gene expression matrix was added as a covariate to adjust for other global, typically non-genetic contributions to the gene expression signal. To prevent spurious associations due to confounding by nearby eQTLs, we corrected the model for the most strongly associated eQTL SNP in the region. For the tumor analysis only, we also added the copy number
