The method presented here for estimating genetic correlation from summary statistics relies on the fact that the GWAS effect-size estimate for a given SNP incorporates the effects of all SNPs in linkage disequilibrium (LD) with that SNP [19, 20]. For a polygenic trait, SNPs with high LD will have higher χ2 statistics on average than SNPs with low LD [19]. A similar relationship holds if we replace χ2 statistics for a single study with the product of z-scores from two studies of traits with non-zero genetic correlation.
