a pre-specified PVE of that phenotype (ranged from 0.5% to 5% in HMDP and 0.04% to 0.4% in NFBC1966), which was further scaled with a random factor draw from a uniform distribution U(0.8, 1). The simulated effects were added back to the original phenotypes to form the new simulated phenotypes. For the four-phenotype analysis, we calculated the p value for each SNP-phenotype pair and we calculated statistical power at the conventional 0.05 level after Bonferroni correction (p=4.6×10−7 for HDMP and p=1.6×10−7 for NFBC1966). For the two-phenotype analysis, we obtained the minimal p value from the six pair-wise analyses for each SNP, and calculated statistical power as the proportion of these p values exceeding either the same significance level (p=4.6×10−7 for HDMP and p=1.6×10−7 for NFBC1966), or a significance level that was further adjusted to account for the six tests performed (p=7.6×10−8 for HDMP and p= 2.6×10−8 for NFBC1966).
