We computed enrichment of functional annotations among fine-mapped SNPs (Figure 4) as the ratio between the proportion of common SNPs with PIP above a given threshold having a specific annotation and the proportion of common SNPs having the annotation. We excluded continuous annotations and annotations constructed via windows around other annotations, and merged concordant annotations for common and low-frequency variants. We computed P-values using Fisher’s exact test (meta-analyzed across traits via Fisher’s method). We computed standard errors by (1) computing the standard error s of the log of the enrichment via the standard formula for the standard error of relative risk (exploiting the fact that enrichment and relative risk are both ratios of proportions); and (2) computing the standard error of the enrichment via r2(es2−1) (i.e., the standard deviation of the exponent of a normal random variable), where r is the original enrichment estimate (meta-analyzed across traits using a fixed-effects meta-analysis). We excluded traits having <10 PIP>0.95 SNPs from the meta-analysis. The annotations shown in Figure 4 are non-synonymous, Conserved_LindbladToh (denoted Conserved), Human_Promoter_Villar_ExAC (denoted Promoter-ExAC), H3K4me3_Trynka (denoted H3K4me3), and Repressed_Hoffman (denoted Repressed) (see Supplementary Table 1 for details).
