Similar to ref. 16, we improve power by excluding large-effect variants when computing the LD score intercept; for this study, we chose to exclude variants with χ2 statistic 30 × the mean, exploiting the fact that genome-wide significant SNPs are not due to population stratification (these variants are not excluded in subsequent steps). Then, we divide the summary statistics by s=χavg2−χ02, where χavg2 is the weighted mean χ2 statistic and χ02 is the LD score intercept, obtaining estimates α^ of α. (We also divide the LD score intercept by s2.) We assess the significance of the heritability by performing a block jackknife on s, defining the significance Zh as s divided by its estimated standard error.
