Each PVE analysis considered a single combination of (1) trait, (2) the analysis from which P values were derived (GIANT, GIANT + PAGE or GIANT + UKB50k) and (3) the target population in which PVE was calculated (either PAGE or UKB50k). To avoid overweighting any single region owing to linkage disequilibrium between multiple associated SNPs, we first defined a ‘locus’ as a contiguous series of genome-wide significant tag SNPs with genome-wide significance, for which each tag SNP was less than 500 kb from the next. Then we selected the single SNP within each locus with the smallest P value in the given analysis (the best tag SNP) and calculated the PVE for that SNP in the target population. The meta-analysis was effectively limited to allele frequencies greater than 5%, so we used the standard P < 5 × 10−8 threshold for significance to define loci.
