We created lists of candidate SNPs for PRSs by filtering variants based on these measures (pe, pa, pm, rm) and with varying thresholds. We considered the p-value thresholds 5 × 10−8, 1 × 10−7, 1×10−6, 1×10−5, 1×10−4, 1×10−3, 0.01, 0.05, 0.5 and r-value thresholds 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 0.99. For generalization analysis, we initially took all variants with p-value < 10−6 in the EA GWAS, then performed generalization analysis using these SNPs to compute r-values. Therefore, by construction, smaller lists of SNPs are considered using this approach. Finally, we clumped the SNPs using PLINK (Purcell et al., 2007) to generate a list of SNPs in no or low LD (ρ2 < 0.2), where LD was evaluated using the 1000 Genomes EA population panel (1000 Genomes Project Consortium, 2012).
