SNP-h2 was estimated at 0.123 (SE = 0.025) in female individuals and 0.247 (SE = 0.021) in male individuals (Supplemental Figure S2 and Table S4). Downsampling male cases and controls randomly to match the female sample size and case-control ratio showed more similar SNP-h2 estimates (see Supplemental Figure S2 and Table S6). Results varying the relative population prevalence assumed are shown in Supplemental Table S7. Figure 2 summarizes these results, illustrating the impact of the assumed male:female ratio (which affects assumed sex-specific population prevalence rates) and sample size on SNP-h2 estimates; SNP-h2 estimates increased in male individuals and decreased in female individuals as the ratio was increased, and downsampling male cases and controls gave similar SNP-h2 estimates in both sexes.
