In each of these simulations, stratified LD score regression gave unbiased estimates of heritability and of the heritability of the CNS cell-type group (Supplementary Figures 2a,b, 3a,b). While in theory the ratio of these two unbiased estimators could be a biased estimator of the proportion of heritability (and therefore the estimates that we report here), in practice we saw only negligible bias in our estimates of proportion of heritability (Supplementary Figures 2c, 3c). Using out-of-sample LD caused some downward attenuation bias in estimates of total SNP-heritability and heritability of the CNS cell-type group, but also gave unbiased estimates of proportion of heritability and properly calibrated type 1 error (Supplementary Figure 4).
