The proportion of variance in phenotypic liability that could be explained by the aggregated effect of all SNPs (h2-SNP) was estimated using LD-Score Regression analysis (online Supplemental Methods) (Bulik-Sullivan et al., 2015b). For this analysis, we included in the regression 1 217 311 SNPs that were present in the HapMap 3 reference panel. Analyses were performed using pre-computed LD scores based on 1000 Genomes Project reference data on individuals of European ancestry. The h2-SNP estimates for the two binary traits were converted to the liability scale, using sample prevalence of 0.159 for AD and 0.15 for MD.
