. 2009 May 7;4(5):e5459. doi: 10.1371/journal.pone.0005459

Table 3. A list of SNPs initially identified by GWAS and re-examined in CMAS.

M	CHR	RS	NT	GI	Combined samples					Independent samples
					GCR	MA:MAF	HWE	ULR-NOMINAL	ULR-ORDINAL	GCR	MA:MAF	HWE	ULR-NOMINAL	ULR-ORDINAL
P	2	rs9308945	A/G	Hypothetical	99.8	A: 0.393	1.0000	0.0007	0.0002	99.8	A: 0.394	0.6162	0.0539	0.0215
P	2	rs6711736	A/G	Hypothetical	97.3	G: 0.392	0.3921	0.0004	0.0001	96.8	G: 0.393	0.1690	0.0226	0.0130
P	2	rs6729869	A/T	Hypothetical	99.7	T: 0.363	0.5964	0.0017	0.0011	99.6	T: 0.362	0.2330	0.0345	0.0589
P	2	rs10495809	A/G	Intergenic	99.4	A: 0.453	0.9480	0.0260	0.0076	99.3	A: 0.453	0.5784	0.3715	0.1607
P	4	rs10517739	C/T	Intergenic	99.6	C: 0.316	0.5590	0.6727	0.9571	99.5	C: 0.311	0.3964	0.0489	0.0368
P	4	rs1444280	C/G	FSTL5	97.5	C: 0.310	0.3669	0.5331	0.8619	97.8	C: 0.304	0.2256	0.0121	0.0127
P	4	rs10517740	G/T	Intergenic	91.4	T: 0.210	<0.0001	<0.0001	<0.0001	89.6	T: 0.200	<0.0001	<0.0001	<0.0001
I	7	rs1526555	A/C	KIAA0960	95.9	A: 0.130	0.0101	0.3549	0.1685	95.2	A: 0.128	0.0921	0.7118	0.4393
I	14	rs2331706	C/T	RAD51L1	99.9	T: 0.377	0.8912	0.4841	0.2285	99.9	T: 0.380	1.0000	0.3090	0.1298
I	14	rs765899	C/T	RAD51L1	98.7	T: 0.377	0.6309	0.4011	0.1873	99.5	T: 0.378	1.0000	0.3330	0.1383
I	11	rs7950640	C/G	LOC643652	99.7	C: 0.363	0.7408	0.9408	0.8137	99.6	C: 0.357	0.8203	0.7638	0.5403
I	7	rs2214310	C/T	xC7orf9	99.7	C: 0.482	0.6158	0.7633	0.6486	99.7	C: 0.488	0.8881	0.8882	0.9074
I	7	rs994531	A/G	xC7orf9	99.6	A: 0.478	0.4090	0.8472	0.6270	99.6	A: 0.485	0.8385	0.9398	0.7262
I	12	rs10506451	A/G	PPM1H	99.7	A: 0.362	0.8935	0.1134	0.0418	99.6	A: 0.363	0.3631	0.1468	0.0719
I	6	rs1115620	A/T	LOC643884	98.0	T: 0.482	0.5292	0.8051	0.5189	97.7	T: 0.477	0.5228	0.8794	0.8378
I	6	rs2502397	A/G	LOC7805441	99.9	A: 0.488	0.6640	0.2685	0.1465	99.9	A: 0.485	0.5768	0.5201	0.2660
I	6	rs1886985	A/G	IMPG1	99.9	G: 0.491	0.9494	0.8774	0.9232	99.8	G: 0.488	1.0000	0.9408	0.9257
I	20	rs6129969	C/T	Intergenic	99.9	T: 0.392	0.2834	0.3593	0.3800	99.9	T: 0.385	0.0386	0.0539	0.7652
I	20	rs2206416	C/T	Intergenic	98.7	C: 0.368	<0.0001	0.7193	0.9571	98.4	C: 0.337	<0.0001	0.0545	0.6498
I	11	rs10488767	A/G	ARGAP20	98.7	A: 0.285	0.4337	0.7580	0.4661	98.4	A: 0.278	0.9359	0.4576	0.3175
I	16	rs10500328	A/G	Intergenic	87.2	A: 0.158	0.0001	0.3558	0.2359	84.6	A: 0.096	0.0268	0.0407	0.0417
I	1	rs618171	A/G	LOC643717	99.5	A: 0.464	0.2786	0.2278	0.1167	99.3	A: 0.468	0.3009	0.4699	0.3065
I	7	rs7805441	C/T	MAGI2	99.7	T: 0.467	0.2573	0.1722	0.1993	99.6	T: 0.471	0.1860	0.3112	0.5076

For each SNP, the method used (M), chromosome (CHR), RS number (RS), nucleotide types (NT) and gene information (GI) are shown. The results for combined samples and independent samples are shown as follows: (1) genotyping call rate (GCR(%)), (2) minor allele and minor allele frequency (MA:MAF), (3) p values of the exact HWE test (HWE), (4) exact p value of the ULR-NOMINAL analysis [model: logit{Prob(Y = YOH|I₁₁,I₁₂,I_Gender,Z_Age} = a₀+a₁₁×I₁₁+a₁₂×I₁₂+a₂×I_Gender+a₃×Z_Age] and (5) exact p value of the ULR-ORDINAL analysis [model: logit{Prob(Y = YOH|X,I_Gender,Z_Age)} = a₀+a₁×X+a₂×I_Gender+a₃×Z_Age], where Y is YOH status, I_1j is an indicator of the three genotypes (j = 1, 2) of a SNP, I_Gender is an indicator of gender, Z_Age is a covariate for age, and X is a variable for the number of reference alleles.