 ⬤  ⬤ - ⬤ ◒ - ◓ ⬤ - ◒ ◒ - ◒ - ◓ ◒ - ◒ - ◓ - ◓ 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.05 0.10 0.15 0.20 0.05 0.10 0.15 0.20 0.05 0.10 0.15 0.20 Total trait variation explained Power/Type 1 error Test BMA 2 SNP models BMA 3 SNP models PCs Figure 4: Effect of more than two causal variants. Each plot reflects simulations in which causal variants in total explain a fixed proportion of variance of two quantitative traits, shown on the x axis, each available in a sample of 1,000 individuals. The total number of causal variants is shown by the number of circles above each plot, with full circles indicating a causal variant shared by both traits and half shaded a causal variant associated with one trait or the other. Analysis was conducted by proportional testing using either a PC approach with number of principal components selected to capture 90% of genetic variation or a BMA approach, averaging over the space of either all possible two SNP or three SNP models. We considered only tagging genotype scenarios. 29