Two-stage joint selection method to identify candidate markers from genome-wide association studies

BMC Proceedings

Table 1 WTCCC-data-validated SNPs and SNP pairs (epistases) associated with RA

Chr	SNP	Location	Gene Code	± kbp^a	OR^b	p-Value^c	Marg. Rank^d
1	rs3811019	114183625	PTPN22	0	1.46	6.93 × 10^-7	1150
6	rs1265777	32381136	C6orf10	0	1.01	9.84 × 10^-1	436
6	rs574710	32396168	C6orf10	0	0.89	7.44 × 10^-1	488
6	rs539703	32396440	C6orf10	0	1.05	9.34 × 10^-1	440
6	rs2894249	32433813	C6orf10	0	0.79	3.76 × 10^-4	245
6	rs2076533	32471505	BTNL2	0	2.03	2.00 × 10^-16	630
6	rs3763308	32482618	BTNL2	0	0.42	1.91 × 10^-8	959
6	rs9268645	32516505	HLA-DRA	0	0.85	2.90 × 10^-2	278
6	rs7194	32520458	HLA-DRA	0	1.02	7.96 × 10^-1	110
6	rs9273363	32734250	HLA-DQB1	5	0.73	4.14 × 10^-9	709
6	rs6908943	32743274	HLA-DQB1	5	0.69	2.92 × 10^-7	1131
8	SNP_A-4193342	97922693	PGCP	0	1.38	1.68 × 10^-7	416671
22	rs16981203	24729414	MYO18B	0	1.3	1.08 × 10^-5	501

^a± kbp, location of the SNPs. "0" indicates the SNP is physically located within the corresponding gene; "5" indicates the SNP is located outside the gene but is less than 5 kbp away.
^bOR, the joint odds ratios and p-values in the full model containing all of the selected variables.
^cp-value, for the full model containing all of the selected variables.
^dMarg. Rank, marginal ranks of the SNPs by single-marker analysis in the WTCCC data. The rank >1015 corresponds to the Bonferroni p-value > 0.1 in a single-marker study.

ISSN: 1753-6561