Table 4.

Summary results of significant individual haplotypes associated with alcohol dependence comorbid with drug dependence (AD+DD) in the TTC12 region.

SNP#		T1	T2	T3	T4	T5	T6	T7	T8	T9	# of famb	Hap-freqc				t-stat/Zd	I-hap pe	Global p
Allelesa		G/A	A/G	A/G	T/G	A/C	A/G	A/G	G/T	A/G		pooled	control	case	diff
Case-Control	3-SNP				G	A	A				---	0.18	0.16	0.26	0.10	3.43	0.00065	0.00055
						A	A	G			---	0.12	0.11	0.15	0.04	3.56	0.00040	0.011
							A	G	T		---	0.15	0.14	0.18	0.04	3.10	0.0020	0.0032
					T	C	G				---	0.14	0.12	0.23	0.11	3.26	0.0012	0.00055
						C	G	A			---	0.18	0.16	0.25	0.09	3.51	0.00048	0.011
							G	A	G		---	0.35	0.33	0.41	0.08	2.72	0.0068	0.0032
	4-SNP		G	A	G	A					---	0.11	0.09	0.16	0.07	2.83	0.0049	0.021
				A	G	A	A				---	0.11	0.08	0.17	0.09	4.27	0.000023	0.017
				G	G	A	G				---	0.11	0.09	0.17	0.08	3.08	0.0022	0.017
					G	A	A	G			---	0.10	0.08	0.14	0.06	4.24	0.000027	0.0039
						A	A	G	T		---	0.12	0.11	0.15	0.04	3.65	0.00028	0.0032
							A	G	T	A	---	0.14	0.13	0.16	0.03	2.68	0.0076	0.019
				A	T	C	G				---	0.15	0.12	0.23	0.11	3.29	0.0011	0.017
					T	C	G	A			---	0.15	0.12	0.23	0.11	3.80	0.00016	0.0039
						C	G	A	G		---	0.18	0.16	0.25	0.09	3.81	0.00016	0.0032
	5-SNP		G	A	G	A	A				---	0.09	0.07	0.15	0.08	4.25	0.000025	0.019
			G	G	G	A	G				---	0.11	0.09	0.16	0.07	3.11	0.0019	0.019
				A	G	A	A	G			---	0.07	0.05	0.12	0.07	4.37	0.000015	0.013
				G	G	A	G	A			---	0.11	0.09	0.16	0.07	3.58	0.00038	0.013
					G	A	A	A	G		---	0.10	0.09	0.12	0.03	2.61	0.0094	0.0011
					G	A	A	G	T		---	0.10	0.08	0.14	0.06	3.95	0.000087	0.0011
						A	A	G	T	A	---	0.11	0.11	0.14	0.03	3.00	0.0028	0.0051
			A	A	T	C	G				---	0.14	0.12	0.23	0.11	3.24	0.0013	0.019
				A	T	C	G	A			---	0.15	0.12	0.23	0.11	3.56	0.00040	0.013
					T	C	G	A	G		---	0.15	0.12	0.23	0.11	3.71	0.00023	0.0011
						C	G	A	G	A	---	0.10	0.08	0.16	0.08	3.81	0.00015	0.0051
Family				G	G	A					33	0.26	---	---	---	2.80	0.0051	0.024
		G	G	G	G						32	0.24	---	---	---	2.60	0.0094	0.019
			G	G	G	A					32	0.25	---	---	---	2.68	0.0075	0.016
		G	G	G	G	A					30	0.24	---	---	---	2.93	0.0034	0.012

^aThe allele listed on top is the common allele. Black square with white allele denotes risk haplotypes.

^bNumber of informative families.

^cHaplotype frequency for the pooled (combined the case and control samples for the case-control design, but representing overall estimates of haplotype frequency for the family design), control, case, and the difference between cases and controls.

^d“t-stat” is the t-statistic calculated for the case-control sample, and “Z” for the family sample.

^eIndividual haplotype p-value.