Table 1. Type I error and power of different simulation scenarios in association analysis.

Scenarios	Important parameters			Binary trait					Continuous trait
	Eg	Vgp	Vge	AllVar	IsoeQTL	GeneQTL	Gen3eQTL	Gen6eQTL	AllVar	IsoeQTL	GeneQTL	Gen3eQTL	Gen6eQTL
				Type I error
1	0	0	0.05	0	0	0	0	0.002	0	0	0.001	0.002	0.003
2	0	0	0.15	0	0.002	0.001	0	0	0	0	0	0.001	0
3	0	0	0.3	0	0	0	0.002	0	0	0.001	0.001	0.002	0.002
				Power
4	0	0.005	0.05	0.251	0.036	0.022	0.034	0.031	0.246	0.032	0.019	0.032	0.038
5	0	0.005	0.15	0.219	0.021	0.013	0.023	0.032	0.301	0.025	0.017	0.037	0.043
6	0	0.005	0.3	0.229	0.028	0.017	0.021	0.034	0.282	0.024	0.017	0.025	0.039
7	0.1	0	0.05	0	0.017	0.019	0.006	0.001	0	0.017	0.027	0.009	0.001
8	0.1	0	0.15	0	0.213	0.221	0.113	0.054	0.002	0.245	0.245	0.132	0.068
9	0.1	0	0.3	0.018	0.704	0.659	0.581	0.388	0.027	0.72	0.686	0.607	0.446
10	0.1	0.005	0.05	0.288	0.052	0.076	0.043	0.043	0.313	0.063	0.091	0.05	0.041
11	0.1	0.005	0.15	0.403	0.33	0.302	0.199	0.134	0.46	0.357	0.334	0.229	0.136
12	0.1	0.005	0.3	0.569	0.778	0.738	0.677	0.485	0.62	0.805	0.774	0.712	0.512

Eg denotes the effect size of gene expression on phenotype. Vgp denotes phenotype variance explained by all variants. Vge denotes gene expression variance explained by all variants.