Supplementary Figure S1. Description of the TCGA data. Supplementary Figure S2. Flow chart describing data preprocessing, association testing and validation testing stages of the study. Supplementary Figure S3. QQ-plots and genomic inflation (G.I.) estimates for germlines associations with tumor site of origin. Supplementary Figure S4. Odds ratios for published cancer-associated markers from the NHGRI GWAS Catalog were compared to odds ratios for the same markers when testing for associations with tumor site of origin. Supplementary Figure S5. Power analysis and comparison of effect sizes between discovery and validation phases. Supplementary Figure S6. QQ-plots for germline associations with somatic status of cancer genes with validated associations. Supplementary Figure S7. Western blots.