Table 3.

Power for the CLR and Mantel statistic using 500 case-control pairs

						Model 3e		Model 4f		Mantel
	MAFa	D'b	r2b	Model 1c	Model 2d	Main	Interaction	Main	Interaction	M(0) (main effect)	M(1) (joint effect)
SNP1	0.32	1	0.16	1	1	0.28	0	0.02	0.01	1.00	1.00
SNP2	0.12	1	0.04	0.99	0.99	0.06	0	0.01	0.01	1.00	1.00
SNP3	0.37	0.95	0.17	1	1	0.48	0.01	0.02	0.01	1.00	1.00
SNP4	0.49	1	0.34	1	1	0.37	0	0.02	0.01	1.00	1.00
SNP5	0.05	0.21	0	0.01	0.01	0	0.01	0.01	0.01	1.00	1.00
SNP6	0.13	1	0.05	1	1	0.08	0	0.01	0.01	1.00	1.00
SNP7	0.13	1	0.05	1	1	0.08	0	0.01	0	1.00	1.00
SNP8	0.23	1	0.1	1	1	0.36	0	0.02	0.02	1.00	1.00
SNP9	0.23	1	0.1	1	1	0.36	0	0	0	1.00	1.00
SNP10	0.41	0.94	0.41	1	1	0.51	0.01	0.05	0.01	1.00	1.00
DR locus	0.25	1	1	1	1	0.44	0.01	0.14	0.01	1.00	1.00
Locus C	0.42	1	0.45	1	1	0.2	0.01	0.04	0.01	1.00	1.00
SNP13	0.4	1	0.22	1	1	0.42	0.01	0.09	0.02	1.00	1.00
SNP14	0.33	0.99	0.65	1	1	0.4	0.03	0.03	0.01	1.00	1.00
SNP15	0.48	0.93	0.3	0.15	0.07	0	0	0.01	0.01	1.00	1.00
SNP16	0	0.92	0	1	1	0.56	0	0.02	0.01	1.00	1.00
SNP17	0.24	0.98	0.92	1	0.99	0.03	0	0.01	0.01	1.00	1.00
SNP18	0.1	1	0.04	1	0.99	0.07	0	0.01	0.01	1.00	1.00
SNP19	0.12	1	0.05	1	1	0.12	0	0.01	0.01	1.00	1.00
SNP20	0.39	0.56	0.07	1	1	0.52	0	0.01	0.01	1.00	1.00
SNP21	0.47	0.94	0.26	1	1	0	0.02	0.01	0.01	1.00	1.00
SNP22	0.1	0.71	0.02	1	1	0.33	0	0.07	0.01	1.00	1.00

Power is the percentage of replicates in which the main or interaction effect of the respective marker had an adjusted p-value ≤ 0.05.

^aMinor allele frequency among controls

^bLD values calculated using the control population in Replicate 1

^cModel 1, main effect of one SNP at a time

^dModel 2, interaction term with sex of one SNP at a time

^eModel 3, main and interaction with sex of one SNP at a time

^fModel 4, stepwise model with main and interaction effects of all SNPs