Fig. 4

Colorectal cancer case study. a Demonstration of a specific gene-phenotype association: MUTYH and colorectal cancer. Variants that affect the protein sequence are shown on top of the gene’s exons. As expected, variants within domains tend to be more damaging. While none of the variants that affect the protein is close to the exome-wide significance threshold (p < 5E−07), the association is very significant by PWAS (FDR q value = 2.3E−6). The full summary statistics of the 47 variants are presented in Additional file 2: Table S1. b PWAS QQ plot of all 18,053 genes tested for association with colorectal cancer