CLOCK is suggested to associate with comorbid alcohol use and depressive disorders

Table 5 SNP allele and genotype frequency association analysis for the three Sample sets.

Gene	Function	SNP	Alleles	Sample set	MAF A/U	OR (95% CI)*	P-values allele		P-values genotype
							*	Empirical	Cochran- Armitage trend*	Dominant model*	Recessive model*
CLOCK	Intron	rs11240	G/C	1.	0.44/0.33	1.65 (1.14-2.38)	0.0077	0.0072	0.0077	0.055	0.013
				2.	0.33/0.33	1.02 (0.85-1.24)	Ns	Ns	Ns	Ns	Ns
				3.	0.44/0.33	1.59 (1.13-2.26)	0.0084	0.0068	0.0082	0.048	0.016
ARNTL2	Intron	rs2306074	C/T	1.	0.30/0.35	0.77 (0.53-1.12)	Ns	Ns	Ns	0.043	Ns
				2.	0.33/0.35	0.90 (0.74-1.09)	Ns	Ns	Ns	Ns	Ns
				3.	0.30/0.34	0.80 (0.55-1.15)	Ns	Ns	Ns	0.056	Ns
ACADS	Mis-sense mutation	rs1799958	A/G	1.	0.34/0.26	1.47 (1.01-2.15)	0.045	0.044	0.045	0.097	Ns
				2.	0.28/0.26	1.11 (0.91-1.37)	Ns	Ns	Ns	Ns	Ns
				3.	0.34/0.27	1.44 (1.01-2.07)	0.046	0.040	0.046	0.097	Ns

SNPs which showed nominal association (allelic or genotypic) P < 0.05 for Sample set 1 are displayed as are the p-values P < 0.1. Ns = non significant. Analysis in Sample set 2 and 3 were then performed for these SNPs. Alleles: the minor allele first. Odds ratio (OR): the proportion of minor versus major allele in the affected (A) divided by the proportion of minor versus major allele in the non-affected (U) individuals. Empirical P is the point-wise P-value after 10,000 permutations.* gender was used as covariate.