We used LDSC (Bulik-Sullivan et al., 2015a, Bulik-Sullivan et al., 2015b) to evaluate SNP-based rg between samples. This method uses the linkage disequilibrium (LD) structure of the genome to estimate the distribution of effect sizes for individual SNPs as a function of their LD score. Under a polygenic model, causal SNPs are likely to be overrepresented in higher LD score bins (i.e., including additional SNPs in high LD) such that associations with SNPs in these LD bins will make stronger contributions to the phenotype under study. This polygenic distribution of effect sizes across LD score bins provides an estimate of SNP-based heritability, i.e., the proportion of phenotypic variance that is attributable to the aggregate effects of genome-wide SNPs. The correlation between distributions of effect sizes across LD bins between two phenotypes then provides an estimate of SNP-based rg.
