Table 2.

Characteristics of minimum-p SNPs in the second simulation study

	cis-eQTL	TReC		MLE			IMP			TRUE
Gene	MAF	LD	MAP	LD	MAF	Rsq	LD	MAP	Rsq	LD	MAP
EIF3I	0.23	0.72	0.24	0.87	0.25	0.45	0.59	0.27	0.54	0.99	0.23
PIGV	0.15	0.41	0.20	0.61	0.21	0.52	0.44	0.24	0.45	0.88	0.17
EIF2C1	0.10	0.58	0.20	0.64	0.21	0.64	0.53	0.24	0.65	0.83	0.15
MAP7D1	0.11	0.38	0.22	0.71	0.16	0.80	0.65	0.17	0.73	0.78	0.15

NOTE: cis-eQTL is a randomly selected causal SNP for each gene. TReC is the TReC model. MLE, IMP and TRUE are the maximum-likelihood method, the two-stage method, and the method using the true phase, respectively, with the TReCASE model. LD is the average Pearson correlation coefficient between the genotypes of the minimum-p SNP and the cis-eQTL. MAF is the average minor allele frequency. Rsq is the average phasing accuracy. Each entry is based on β_A = β_T = 0.5 and 1,000 replicates.