Fig. 2.

Identification of risk and protective alleles for 135 phenotypes. a–c Manhattan plots for logistic regression for all PTVs and all phenotypes stratified by minor allele frequency a > 1%, b between 0.1% and 1%, and c between 0.01% and 0.1%. Scatter points are colored according to phenotype. Fourteen associations with -log₁₀ p values> 20 were plotted at 20. PTVs in genes near or in the MHC region have smaller scatter points. d Effect size “cascade plot” for all associations outside the MHC with BY-adjusted p < 0.05. Error bars represent 95% confidence intervals. e–f Manhattan plots for PTVs in or near the MHC with minor allele frequency e > 1% and f between 0.1 and 1%. The p values for gray points are the same as in a and b, respectively. The p values for the color points have been re-calculated conditional on HLA alleles