Table 2.

Parameter settings of variance components and genetic effects in simulations

Scenario	${\sigma }_e^2$	${\sigma }_a^2$	R/P/N under Ha	Settings of γ under Ha
I, III	10	0	45/45/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.2)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.2,-0.05)$
			50/40/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.175)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.23,-0.05)$
			55/35/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.155)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.271,-0.05)$
			60/30/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.138)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.325,-0.05)$
II	10	0	45/45/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.5)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.5,-0.05)$
			50/40/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.445)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.569,-0.05)$
			55/35/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.4)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.657,-0.05)$
			60/30/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.363)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.775,-0.05)$
IV, VI, VII, IX	2	2	45/45/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.2)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.2,-0.05)$
			50/40/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.175)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.23,-0.05)$
			55/35/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.155)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.271,-0.05)$
			60/30/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.138)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.325,-0.05)$
V, VIII	2	2	45/45/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.5)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.5,-0.05)$
			50/40/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.445)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.569,-0.05)$
			55/35/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.4)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.657,-0.05)$
			60/30/10	${\mathit{\gamma }}_R\stackrel{\mathit{iid}}{\sim }\mathit{unif}(0.05,0.363)$,	${\mathit{\gamma }}_P\stackrel{\mathit{iid}}{\sim }\mathit{unif}(-0.775,-0.05)$

Note: Variance components ${\sigma }_e^2$ and ${\sigma }_a^2$ represent variances attributed to random measurement error and additive polygenic random effects in the phenotypic model. Under H_a, each scenario contains four settings of genetic variants depending on the number of risk, protective, and neutral variants (R/P/N). The genetic effects of risk and protective variants are denoted by γ_R and γ_P respectively.