Table 3.

Pruned set of candidate gene SNPs at r² < 0.50

SNP	Status	Gene	COGA family study p-value	MAF Fam	MAF COGA	MAF SAGE	Risk Allele
rs10499934	In_sample	ACN9	0.003	0.23	0.22	0.23	A
rs12671685	In_sample	ACN9	0.027	0.11	0.12	0.11	A
rs7794886	In_sample	ACN9	0.006	0.35	0.36	0.35	T
rs4147531	In_sample	ADH1A	0.007	0.43	0.46	0.47	C
rs1229982	In_sample	ADH1B	0.048	0.22	0.20	0.19	T
rs1126672	In_sample	ADH4	0.010	0.29	0.28	0.29	C
rs17115439	In_sample	ANKK1	0.096	0.33	0.32	0.32	C
rs680244	In_sample	CHRNA5	0.114	0.42	0.41	0.42	G
rs1799978	In_sample	DRD2	0.168	0.06	0.05	0.05	G
rs279858	In_sample	GABRA2	0.010	0.38	0.42	0.42	A
rs1897356	In_sample	GABRB3	0.020	0.17	0.15	0.15	C
rs16918941	In_sample	OPRK1	0.023	0.06	0.06	0.07	G
rs6985606	In_sample	OPRK1	0.004	0.48	0.50	0.48	T
rs997917	In_sample	OPRK1	0.011	0.27	0.29	0.27	C
rs1997794	In_sample	PDYN	0.011	0.37	0.36	0.35	C
rs2235749	In_sample	PDYN	0.010	0.27	0.27	0.26	A
rs6045819	In_sample	PDYN	0.038	0.10	0.12	0.12	G
rs11722288	In_sample	TACR3	0.022	0.29	0.29	0.29	G
rs3762894	In_sample	ADH4	0.050	0.16	0.15	0.16	C
rs1391175	Use_proxy rs13120165	GABRG1	0.036	0.06	0.03	0.03	A
rs3097490	Use_proxy rs1571281	GABRG3	0.137	0.44	0.44	0.46	G
rs324640	Use_proxy rs324649	CHRM2	0.038	0.43	0.42	0.42	T

“Status” indicates whether or not the SNP was genotyped directly on the Illumina 1M SNP chip or a proxy SNP was used. The SNP numbers are SNPs from candidate gene studies, with proxy SNPs indicated as such in the “status” column. The COGA family-based association p-values from our re-run analyses are listed. “MAF Fam” shows the minor allele frequency of the SNP in the COGA family-based candidate gene association sample. “MAF COGA” and “MAF SAGE” correspond to the MAF in the COGA and SAGE GWAS samples, respectively. The risk allele corresponds to the GWAS alleles matched by allele frequency to the risk allele in the family-based candidate gene association sample.