Table 2 Two marker haplotype frequencies, transmission, and association statistics for CARD4 (caspase recruitment domain family, member 4) in inflammatory bowel diseases.

Variation	Haplotype*	fcontrols†	fcases†	p Value‡	fT§	fNT§	p Value¶	D′**
rs2075822 + ND1+32656	1 – 1	0.771	0.762	0.846	0.455	0.486	0.094	0.91
	1 – 2	0.042	0.040		0.140	0.101
	2 – 1	0.013	0.015		0.026	0.057
	2 – 2	0.174	0.184		0.380	0.357
ND1+32656 + rs2907748	1 – 1	0.784	0.775	0.727	0.473	0.519	0.719	0.98
	1 – 2	0.002	0.002		0.011	0.011
	2 – 1††	0.006	0.004		0.014	0.008
	2 – 2	0.208	0.220		0.503	0.462

*Allele 1 is defined as the major allele.

†Frequencies of haplotypes in cases and controls estimated by the expectation maximisation algorithm using COCAPHASE.[6]

‡Global significance value obtained after 10 000 permutations with COCAPHASE.

§Frequencies of transmitted (f_T) and non‐transmitted (f_NT) haplotypes observed using TDTPHASE.[6]

¶Global significance value obtained after 10 000 permutations with TDTPHASE.

**D′ value as a measure of linkage disequilibrium in the control sample.

††Protective haplotype previously identified by McGovern and colleagues.[2]