. Author manuscript; available in PMC: 2012 Jul 1.

Published in final edited form as: Arthritis Rheum. 2011 Jul;63(7):2049–2057. doi: 10.1002/art.30356

Table 2.

Most significant replicated SNPs in Set 1.

Marker¹	Ch	Position (Mb)	Locus	MA	Stage 1 P-value²	Stage 2 P-value²	Joint-analysis
Marker¹	Ch	Position (Mb)	Locus	MA	Stage 1 P-value²	Stage 2 P-value²	Case MAF	Control MAF	P-value²	OR [95% CI]
rs4659444*	1	26.698	RPS6KA1	T	1.48E-02	5.97E-03^D	0.24	0.21	1.14E-03^D	1.29 [1.11–1.50]
rs4970514^S2*	1	26.719	RPS6KA1	T	2.36E-02	6.43E-03^D	0.24	0.20	3.61E-03^D	1.26 [1.08–1.47]
rs2285210^S2	1	173.218	RABGAP1L	C	3.11E-03^R	3.35E-02^R	0.32	0.29	2.71E-04^R	1.64 [1.26–2.14]
rs10971259^S2*	9	32.969	DNAJA1	T	8.66E-03	3.14E-02	0.12	0.15	4.89E-03	0.81 [0.69–0.94]
rs10124051^S2	9	32.997	DNAJA1	C	2.87E-04	4.53E-02	0.08	0.11	1.12E-04	0.72 [0.60–0.85]
rs366078^S2	16	84.522	IRF8	C	1.15E-02	4.20E-03^D	0.10	0.13	2.41E-04	0.74 [0.63–0.87]

Table excludes MHC, IRF5-TNPO3, ITGAM-ITGAX, TNFAIP3 and STAT4 loci. The reported P-values are not adjusted for the number of comparisons, but except for the markers denoted with *, all met a FDR-adjusted threshold of significance in the joint-analysis, as described in the Methods. The smallest P-value is presented and, unless noted otherwise, it is under the additive model. OR and CI calculated under the model presented. Ch – chromosome; Mb – Megabases; MA –minor allele; MAF – Minor allele frequency; OR – odds ratio; CI – 95% confidence interval;

The superscript after the marker denotes if it was imputed in any cohort: ^S1Stage 1, ^S2Stage 2;

The superscript after the P-value denotes its genetic model, when other than the additive: ^Ddominant, ^Rrecessive.