Our matching strategy consists of three steps. First, we calibrated a statistical model to predict the probability for a given HM3 SNP to be GWS in any of our non-EUR GWAS meta-analyses as a function of their annotation. For that, we used a logistic regression of the non-EUR GWS status (1 = if the SNP is GWS in any of the non-EUR GWAS; 0 = otherwise) onto the 24 annotations as regressors. Second, we used that model to predict the probability to be GWS in non-EUR. Thirdly, we used the predicted probability to sample (with replacement) 1,000 random sets of 2,747 SNPs. Finally, we estimated the proportion of EUR GWS SNPs within 100 kb of SNPs in each sampled SNP set. We report in the main text the mean and s.d. over these 1,000 proportions.
