Table 3

Top 20 SNPs and the landmark SNP2140 in Stage 1 allelic and genotypic association tests
						Stage 1					Stage 2					Stage 1 + Stage 2

	SNP Marker	rs#	Gene symbol	Position	Allele 1/2	Allele 1 frequency case	Allele 1 frequency control	p value of allele frequency	p value of genotype frequency	p value of Armitage trend test^a)	Allele 1 frequency case	Allele 1 frequency control	p value of allele frequency	p value of genotype frequency	p value of Armitage trend test^a)	Allele 1 frequency case	Allele 1 frequency control	p value of allele frequency	p value of genotype frequency	p value of Armitage trend test^a)

1	SNP2248	-	ATP8B4	48175632	G/T	0.23	0.31	0.00053	0.0024	0.00052	0.29	0.28	0.59	0.61	0.59	0.27	0.30	0.075	0.19	0.075
2	SNP2372	rs4261468	RAB27A	53342894	A/G	0.49	0.41	0.00091	0.0034	0.00078	0.47	0.48	0.67	0.80	0.66	0.48	0.45	0.076	0.20	0.072
3	SNP3295	rs12443171	intergenic	48225107	C/T	0.34	0.43	0.00091	0.0030	0.00099	0.38	0.40	0.49	0.66	0.49	0.37	0.41	0.0079	0.018	0.0081
4	SNP3347	rs1386166	intergenic	51376772	A/G	0.35	0.44	0.0014	0.0013	0.0016	0.37	0.40	0.15	0.23	0.16	0.36	0.42	0.0017	0.0080	0.0021
5	SNP1439	rs9972478	RAB27A	53347024	A/C	0.30	0.23	0.0017	0.0068	0.0016	0.27	0.29	0.28	0.34	0.27	0.28	0.26	0.25	0.37	0.25
6	SNP3391	rs2414351	intergenic	52746565	C/G	0.24	0.18	0.0019	0.0066	0.0017	0.19	0.21	0.16	0.39	0.17	0.21	0.20	0.34	0.64	0.35
7	SNP2373	rs2305424	RAB27A	53368640	C/T	0.47	0.55	0.0037	0.011	0.0032	0.48	0.48	0.97	0.86	0.96	0.48	0.51	0.061	0.11	0.058
8	SNP1441	rs2414409	PIGB	53419009	C/T	0.47	0.55	0.0039	0.013	0.0034	0.48	0.48	0.93	0.91	0.93	0.48	0.51	0.077	0.16	0.074
9	SNP1280	rs2278167	SLC27A2	48285140	G/T	0.61	0.54	0.0050	0.014	0.0047	0.59	0.56	0.20	0.095	0.19	0.60	0.55	0.0054	0.013	0.0047
10	SNP2039	rs2412424	FSIP1	37765425	C/T	0.65	0.59	0.0075	0.022	0.0061	0.62	0.62	0.91	0.62	0.91	0.64	0.61	0.072	0.16	0.067
11	SNP2098	rs4924524	CHAC1	39042673	C/T	0.76	0.70	0.0060	0.022	0.0064	0.73	0.76	0.21	0.082	0.21	0.75	0.73	0.42	0.15	0.42
12	SNP1440	rs7183960	PIGB	53409987	C/T	0.47	0.54	0.0074	0.022	0.0067	0.48	0.48	0.80	0.93	0.79	0.48	0.50	0.13	0.26	0.13
13	SNP2249	rs11638841	ATP8B4	48203899	C/G	0.73	0.66	0.0062	0.026	0.0069	0.67	0.68	0.72	0.89	0.72	0.70	0.67	0.15	0.33	0.15
14	SNP3176	rs996215	intergenic	44577114	A/G	0.23	0.30	0.0067	0.027	0.0073	0.28	0.27	0.51	0.74	0.50	0.26	0.28	0.22	0.46	0.22
15	SNP2097	rs4924523	CHAC1	39042662	A/T	0.24	0.30	0.0072	0.025	0.0076	0.27	0.24	0.22	0.085	0.22	0.26	0.27	0.43	0.15	0.43
16	SNP2072	rs936216	PAK6	38344560	A/C	0.75	0.81	0.0092	0.0075	0.0084	0.75	0.78	0.093	0.14	0.10	0.75	0.79	0.0032	0.015	0.0038
17	SNP1438	rs12910930	RAB27A	53332998	C/G	0.33	0.27	0.0095	0.016	0.0084	0.28	0.31	0.20	0.25	0.20	0.30	0.29	0.49	0.24	0.49
18	SNP2041	rs2254829	FSIP1	37779957	C/T	0.66	0.59	0.0099	0.030	0.0085	0.63	0.62	0.84	0.67	0.84	0.64	0.61	0.071	0.17	0.068
19	SNP1444	rs3743203	CCPG1	53436254	C/T	0.47	0.53	0.010	0.037	0.010	0.47	0.47	0.98	0.83	0.98	0.47	0.49	0.11	0.22	0.10
20	SNP3096	rs156787	FLJ39531	37335619	A/G	0.18	0.23	0.0092	0.038	0.011	0.18	0.21	0.065	0.065	0.062	0.18	0.22	0.0020	0.0041	0.0022

*	SNP2140	rs2412747	*UBR1*	41074095	C/T	0.81	0.77	0.049	0.11	0.049	0.79	0.75	0.039	0.072	0.039	0.80	0.76	0.0043	0.0081	0.0045

Significant results (p < 0.05) and () SNP2140 (rs2412747) in the UBR1* are shown in bold type. a)Armitage trend test was performed by using the DeFinetti program http://ijg.gsf.de/cgi-bin/hw/hwal.pl. The positions of top 20 SNPs with their p values in the increasing order in Armitage trend test are almost the same as those in allelic test, except for SNP 2039, 1440, and 3096 of which p values were underlined.
Yamaguchi et al. BMC Medical Genetics 2008 9:22 doi:10.1186/1471-2350-9-22