Table 2.

Power comparison under the scenario that both phenotypes are associated with the causal locus.

Residual Correlation	Window-Size = 1			Window-Size = 3			Window-Size = 5
	UHTR	PCHTR	BHTR	UHTR	PCHTR	BHTR	UHTR	PCHTR	BHTR
0.90	31.0	35.3	25.5	42.7	48.1	35.1	55.1	58.4	47.7
0.60	38.2	42.2	31.8	37.9	50.0	43.2	54.5	57.6	49.2
0.30	37.3	50.5	37.6	51.9	63.2	51.4	63.7	73.2	62.0
0.00	38.8	41.9	51.7	59.7	55.3	66.5	73.3	67.6	76.4
−0.30	38.9	5.0	70.1	53.8	3.9	86.1	66.0	4.0	92.3
−0.60	39.6	4.7	97.2	54.9	4.3	99.5	64.5	3.9	99.9
−0.90	41.1	4.1	100.0	54.7	3.9	100.0	65.1	4.4	100.0

Note: 1000 individuals were simulated under each parameter setting. Power was estimated based on 5000 replications. ‘UHTR’ denotes the univariate haplotype trend regression testing, ‘PCHTR’ denotes the principle component based univariate haplotype trend regression testing and ‘BHTR’ denotes the bivatiate haplotype trend regression testing.