Table 1.

Contribution of HW disequilibrium to p value distribution, evaluated by regression analysis. Significant F tests (p < 0.05) demonstrating evidence of the contribution of HW disequilibrium to the p value distributions are shown in bold font

	Allb, c			Sequenceda, c			Nuclearb, c
Method	TDT	PDT	FBAT	TDT	PDT	FBAT	TDT	PDT	FBAT
Regression model of - log10 p values at all SNPs
R 2 full –R 2 reduced	4.4 × ${10}^{-4}$	3.6 × ${10}^{-7}$	1.5 × ${10}^{-6}$	0.0018	3.6 × ${10}^{-8}$	2 × ${10}^7$	2.9 × ${10}^{-6}$	8.26 × ${10}^{-9}$	3.5 × ${10}^{-7}$
# SNPse	6.1 × ${10}^6$	5.6 × ${10}^6$	2.1 × ${10}^6$	3.2 × ${10}^6$	3 × ${10}^6$	8 × ${10}^5$	3.6 × ${10}^6$	2.1 × ${10}^6$	5 × ${10}^5$
Regression models of - log10 p values greater than 3 only
R 2 full –R 2 reduced	0.002	8.4 × ${10}^{-5}$	8.8 × ${10}^{-4}$	0.0015	${\mathrm{N}\mathrm{A}}^f$	0.006	0.014	0.01	0.01
# SNPse	8 × ${10}^4$	517	870	1777	11	19	3.3 × ${10}^4$	53	54
F-test p-valuesd
All SNPs	0.00	0.16	0.07	0.00	0.74	0.69	0.00	0.89	0.68
P< ${10}^{-3}$	0.00	0.84	0.38	0.10	NAf	0.82	0.00	0.49	0.50

^aFull model is given by Eq. (1)

^bFull model is given by Eq. (2)

^cReduced model excludes $-{log}_{10}\left({\mathrm{H}\mathrm{W}\mathrm{E}}_{p\mathrm{value}}\right)$

^dTest to see if there is a significant difference between the full model and the reduced model. Numbers presented correspond to pvalues of the F test where the null hypothesis is ${\beta }_{\mathrm{H}\mathrm{W}\mathrm{E}}=0$

^eThe number of informative SNPs

^fNot enough data points to fit the model