We used the tool CAVIARBF23,47 in a fine-mapping exercise to identify candidate causal SNPs. We used the 74 baseline annotations employed by stratified LD Score regression as well as 451 annotations from from Pickrell46. We applied a MAF filter of 0.01 and a sample-size filter of 400,000 and only considered SNPs within a 50-kb radius of a lead SNP. We computed exact Bayes factors by averaging over prior variances of 0.01, 0.1, and 0.5; we set the sample size to the mean sample size of our considered SNPs; and we added 0.2 to the main diagonal of the LD matrix because we used a reference panel for LD estimation. To incorporate annotations, we used the elastic net setting with parameters selected via 5-fold cross-validation. The resulting annotation effect sizes and list of candidate causal SNPs are given in Supplementary Tables 37 and 10. Regional association plots of four noteworthy candidates are shown in Supplementary Figure 9.
