We do not directly use ∑j:i∈Sjτ^j as the empirical variance prior because it is estimated in the context where all SNPs in the 1000 Genomes Project database are included in the model [18]. Such per-SNP heritability estimates cannot be extrapolated to the risk prediction context where many fewer SNPs are analyzed [23]. Therefore, we rescale the heritability estimates to better quantify each SNP’s contribution toward chip heritability. Following [24], we use a summary statistics-based heritability estimator that approximates the Haseman-Elston estimator: H^2=(χ¯2−1)Nl− where χ¯2 and l¯ denote the mean Nβ^i2 and mean non-stratified LD score, respectively.
