We partitioned all autosomal chromosomes into 2,763 overlapping 3Mb-long loci with a 1Mb spacing between the start points of consecutive loci. We computed a PIP for each SNP based on the locus whose center was closest to the SNP (excluding SNPs >1Mb away from the closest center and loci wherein all SNPs had squared marginal effect sizes smaller than 0.00005). We excluded the MHC region (chr6 25.5M-33.5M) and two other long-range LD regions (chr8 8M-12M, chr11 46M-57M)62 from all analyses, following our observations that both FINEMAP and SuSiE tend to produce spurious results in these regions, finding many PIP=1 SNPs across many traits regardless of their BOLT-LMM p-values. We verified that other previously reported long-range LD regions62 do not harbor a disproportionate number of PIP>0.95 SNPs. We specified per-locus causal effect variances for SuSiE and PolyFun + SuSiE via our modified HESS approach. For all S-LDSC and fine-mapping analyses we specified a sample size corresponding to the BOLT-LMM effective sample size31 (given by the true sample size multiplied by the median ratio between χ2 statistics of BOLT-LMM and linear regression across SNPs having BOLT-LMM χ2>30).
