Comparison of the power of haplotype-based versus single- and multilocus association methods for gene × environment (gene × sex) interactions and application to gene × smoking and gene × sex interactions in rheumatoid arthritis

Table 5 Adjusted p-values for the haplotype-trait association test in PTPN22

			Model 2 (main effects and haplotype-sex interaction effects)		Model 2 (main effects and haplotype-smoking interaction effects)
Common haplotypes in the investigated regions^a	Frequency	Model 1 (main effects of haplotypes)	Main	Interaction w/sex	Main	Interaction w/smoking
3 3 1 1 1 1 1 2 3 4 4 2 2 3	0.19	0.25	0.67	0.58	0.97	1
4 1 1 1 1 1 3 2 3 4 2 2 2 1	0.09	0.2	0.89	0.98	0.91	0.78
4 1 1 1 1 1 3 2 3 4 4 2 2 1	0.09	0.44	0.07	0.04 ^b	0.91	0.93
4 1 3 1 3 1 1 2 1 4 4 2 4 3	0.12	<0.001	0.6	0.15	0.17	0.82
4 1 3 1 3 1 1 2 3 4 4 2 4 3	0.12	0.44	0.98	0.98	0.97	1
4 1 1 1 1 1 3 2 3 2 4 4 2 3	0.27
(reference haplotype)