# Table 2 Parameter choices for the simulation scenarios

Simulation scenario (μ 1,μ 2) (σ 1,σ 2) σ jk ρ α (0) α (1)α (0) a
1 Distinct differences (−0.05,0.5) (0.05, 0.75) Unif(0.1, 2) 100 $$\left [\begin {array}{c} 0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08\end {array}\right ]$$
2 No confounding (0.25, 0.25) (0.5, 0.5) 0.1 100 $$\left [\begin {array}{c} 0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]$$
3 Opposite effects (−0.75,0.75) (0.1, 0.1) 0.1 100 $$\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]$$
4 High precision (0.3, 0.1) (0.1, 0.1) 0.1 200 $$\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]$$
5 Low precision (0.3, 0.1) (0.1, 0.1) 0.1 10 $$\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]$$
6 Continuous phenotype (−0.05,0.25) (0.05, 0.15) 0.1 100 $$\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.03 \\[-5pt] -0.03 \end {array}\right ]$$
7 Few assoc. sites (1, 0.95) (0.05, 0.05) Unif(0.1, 2) 100 $$\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]$$
8 Many assoc. sites block 1 b (0.1,0.4) (0.01, 0.01) Unif(0.1, 2) 100 $$\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]$$
Many assoc. sites block 2 c (0.2,0.7) (0.01, 0.01) Unif(0.1, 2) 100 $$\left [\begin {array}{c}0.57 \\[-5pt] 0.43 \end {array}\right ]$$ $$\left [\begin {array}{r}0.08 \\[-5pt] -0.08 \end {array}\right ]$$
1. k=1 corresponds to monocytes, and k=2 corresponds to CD4 + T cells
2. aAverage change in cell-type proportion for unit increase in phenotype
3. bBackground correlation for block 1 was 0.4
4. cBackground correlation for block 2 was 0.5