. Author manuscript; available in PMC: 2011 Mar 5.

Published in final edited form as: Am J Med Genet B Neuropsychiatr Genet. 2010 Mar 5;153B(2):418–427. doi: 10.1002/ajmg.b.30995

Table 2. Association analyses of GABRR1 and GABRR2 and their flanking regions.

Gene	SNP number	SNP_ID	Chromosome position¹	SNP location²	MAF³	Minor nucleotide⁴	DSM- IV⁵	Early onset⁵	COGA⁵
*PNRC1*	1	rs1130809	89,850,613	exon 2, Thr321	0.18	C	0.70	0.18^*	0.77
	2	rs11961455	89,852,007	downstream	0.42	C	0.66	0.23^*	0.39

*SRrp35*	3	rs6938490	89,862,949	3′UTR	0.29	A	0.90	0.47	0.33
	4	rs423516	89,884,774	promoter	0.29	T	0.57	0.15	0.72

*PM20D2*	5	rs4707518	89,907,725	upstream	0.29	C	0.69	0.22	0.98
	6	rs1929635	89,923,709	intron 4	0.28	G	0.49	0.13	0.73

*GABRR1*	7	rs1331100	89,935,180	downstream	0.29	G	0.72	0.18	0.81
	8	rs416115	89,941,956	downstream	0.30	C	0.17	0.014^*	0.08^*
	9	rs3734201	89,945,162	3′UTR	0.42	C	0.58	0.04	0.55
	10	rs1796743	89,945,463	exon 10, Ala389	0.35	T	0.40	0.12^*	0.27
	11	rs407221	89,947,094	intron 8	0.27	C	0.21	0.23	0.37
	12	rs368873	89,949,881	intron 7	0.29	G	0.43	0.03^*	0.14^*
	13	rs407206	89,951,687	intron 7	0.32	A	0.13	0.12	0.15
	14	rs423463	89,955,427	intron 6	0.19	A	0.68	0.41^*	0.97
	15	rs453503	89,957,318	intron 5	0.19	T	0.64	0.38^*	0.66
	16	rs452667	89,960,039	intron 5	0.19	T	0.62	1.00	0.45
	17	rs439912	89,963,734	intron 5	0.45	C	0.13	0.56	0.32
	18	rs422751	89,964,592	exon 5, Asp140	0.16	G	0.97	0.86	0.8
	19	rs11967322	89,966,483	intron 3	0.43	T	0.19	0.45	0.58
	20	rs7741132	89,969,614	intron 2	0.33	A	0.14	0.06	0.13
	21	rs7758893	89,973,360	intron 1	0.19	C	0.79	0.51^*	0.76
	22	rs881293	89,974,522	intron 1	0.32	C	0.63	0.29^*	0.71
	23	rs1029057	89,979,273	intron 1	0.28	T	1.00	0.87	0.44
	24	rs6902106	89,982,459	intron 1	0.28	C	0.34	0.14^*	0.09^*
	25	rs17504587	89,982,921	intron 1	0.19	T	0.04	0.03	0.01
	26	rs1186902	89,983,681	exon 1, Arg21His	0.28	C	0.81	0.97	0.36
	27	rs12200969	89,983,685	exon 1, Val20Met	0.34	C	0.20	0.09^*	0.11^*
	28	rs1186903	89,984,290	promoter	0.35	A	0.11^*	0.048^*	0.10^*
	29	rs914479	89,986,927	upstream	0.35	C	0.08^*	0.028^*	0.04^*
	30	rs914478	89,987,638	upstream	0.34	C	0.12^*	0.06^*	0.07^*
	31	rs9342188	90,002,245	intergenic	0.09	C	0.83	0.27^*	0.59
	32	rs1321355	90,007,632	intergenic	0.27	G	0.10^*	0.10^*	0.08^*
	33	rs282135	90,008,949	intergenic	0.28	G	0.74	0.93	0.24
	34	rs6914006	90,014,480	intergenic	0.44	A	0.46	0.47	0.73

*GABRR2*	35	rs3734198	90,021,011	downstream	0.43	G	0.62	0.84	0.92
	36	rs282129	90,024,217	exon 9, Met430Thr	0.28	A	0.03^*	0.08^*	0.02^*
	37	rs13211104	90,027,125	intron 8	0.30	A	0.03^*	0.07^*	0.03^*
	38	rs9451191	90,029,831	intron 8	0.26	A	0.021	0.002	0.17
	39	rs723041	90,030,782	intron 8	0.13	T	0.79	0.86	0.83
	40	rs9294426	90,031,297	intron 7	0.29	A	0.55	0.38	1.00
	41	rs12206367	90,031,345	intron 7	0.12	A	0.43	0.38	0.84
	42	rs2273507	90,031,964	intron 7	0.20	G	0.70	0.55	0.52
	43	rs2273508	90,034,567	intron 4	0.11	T	0.97	0.63	0.46
	44	rs282121	90,036,802	intron 3	0.41	T	0.025	0.02	0.05
	45	rs282117	90,038,132	exon 3, Val83	0.42	T	0.07	0.017	0.12
	46	rs282115	90,038,431	intron 2	0.07	A	0.78	0.20^*	0.96
	47	rs9451194	90,042,098	intron 2	0.45	A	0.91	0.53	0.65
	48	rs9362632	90,051,417	intron 2	0.29	G	0.87	0.88	0.36
	49	rs3798256	90,053,124	intron 2	0.45	G	0.22	0.06	0.36
	50	rs964626	90,056,015	intron 2	0.21	C	0.13^*	0.16^*	0.13^*
	51	rs9451196	90,057,273	intron 2	0.12	T	0.07^*	0.21^*	0.30^*
	52	rs6454750	90,057,490	intron 2	0.45	T	1.00	0.65	0.80
	53	rs2148174	90,062,644	intron 2	0.33	T	0.41	0.78	0.85
	54	rs7742664	90,065,463	intron 2	0.22	T	0.20^*	0.03^*	0.25^*
	55	rs2325202	90,068,229	intron 1	0.36	G	0.22	0.04^*	0.16
	56	rs1570028	90,069,154	intron 1	0.49	A	0.34	0.07^*	0.08
	57	rs6942204	90,072,687	intron 1	0.27	C	0.04	0.005	0.016
	58	rs6454752	90,075,080	intron 1	0.23	T	0.43	0.21^*	0.07^*
	59	rs9294432	90,076,686	intron 1	0.47	T	0.51	0.14^*	0.04^*
	60	rs10944441	90,078,260	intron 1	0.18	A	0.08^*	0.012^*	0.005^*
	61	rs7764923	90,079,640	intron 1	0.24	T	0.08^*	0.02^*	0.007^*
	62	rs2236204	90,081,831	promoter	0.19	T	0.09^*	0.015^*	0.006^*
	63	rs9362636	90,083,516	promoter	0.06	G	0.86	0.88	0.91
	64	rs2064831	90,089,661	upstream	0.18	C	0.09^*	0.01^*	0.009^*

*UBE2J1*	65	rs13215418	90,093,230	downstream	0.17	T	0.56	0.93	0.73
	66	rs10502	90,096,389	exon 8, Val229Leu	0.40	C	0.34	0.11^*	0.07^*
	67	rs12189673	90,103,123	intron 5	0.30	C	0.62	0.25	0.05
	68	rs7760851	90,109,323	intron 2	0.50	G	0.40	0.48	0.009
	69	rs7743444	90,112,800	intron 1	0.24	T	0.88	0.97	0.52

Chromosome positions are based on NCBI Human Genome Assembly v36.3.

PNRC1 and PM20D2 are transcribed in forward direction; SRrp35, GABRR1, GABRR2 and UBE2J1 are transcribed in the opposite direction.

Minor Allele Frequency in this sample of European Americans.

⁴

Nucleotides are shown on the human genome strand.

⁵

P-value of UNPHASED PDT_sum statistic for association between the SNP and alcohol dependence. P ≤ 0.05 is in bold.

Minor allele is preferentially transmitted to affected individuals.