Fig 3 shows contour plots for the power per truly associated SNP and R2 for a trait with hSNP2=50%, 1k causal SNPs, 100k SNPs in total, and a fixed total sample size of 250,000 individuals. In this figure, various combinations of the CGR and the number of studies are considered. Logically, when there is just one study for discovery, CGR does not affect power. However, even for two studies, the effect of CGR on power is quite pronounced. For instance, when CGR is a half, the power per causal SNP is 63% for one study, 58% for two studies, 51% for ten studies, and 50% for 100 studies. Thus, when the number of studies is low, increasing the number of studies makes the effect of CGR on power more pronounced rapidly. When the number of studies is large, further increases in the number of studies hardly make the effect of CGR on power more pronounced.
