LD score regression (Bulik‐Sullivan et al., 2015b) uses the natural experiment present in the genome due to variable amounts of Linkage Disequilibrium (LD) between SNPs. Causal variants will cause straight slope decline in test statistics of nearby SNPs with decreasing levels of LD to the causal variant in the case of additive genetic variation. The slope of the regression line of the chi‐square statistic against LD scores across the genome reflects the heritability of the trait (Bulik‐Sullivan et al., 2015b). SNP heritability estimation using LD score regression has the advantage of being insensitive to population stratification effects, as these will result in an upward shift across all LD score bins, thus affecting the intercept and not the slope of the LD‐dependent regression.
