Table 3.

Newly identified SNPs associated with rheumatoid arthritis susceptibility

SNP						Meta-analysis				Replication				Joint		Breslow-Day test
ID	Chr.	Position	Locus	Allele		Frequency				Frequency
				Major	Minor	Control	Case	p	OR	Control	Case	p	OR	p	OR	p
rs3890745	1p36	2585786	MMEL1-TNFRSF14	T	C	0.329	0.295	4.3 × 10−6	0.86	0.321	0.301	0.0035	0.92	1.1 × 10−7	0.89	0.31
rs42041	7q21	91891395	CDK6	C	G	0.243	0.274	5.5 × 10−5	1.15	0.261	0.277	0.010	1.08	4.0 × 10−6	1.11	0.43
rs2812378	9p13	34700260	CCL21	A	G	0.339	0.364	6.9 × 10−5	1.13	0.334	0.355	0.00097	1.10	2.8 × 10−7	1.12	0.67
rs4750316	10p15	6433266	PRKCQ	G	C	0.194	0.171	9.9 × 10−5	0.86	0.197	0.183	0.0078	0.91	4.4 × 10−6	0.88	0.77
rs1678542	12q13	56254982	KIF5A-PIP4K2C	C	G	0.373	0.352	5.4 × 10−6	0.87	0.366	0.351	0.0026	0.92	8.8 × 10−8	0.89	0.62
rs4810485	20q13	44181354	CD40	G	T	0.254	0.221	2.4 × 10−7	0.83	0.246	0.231	0.0032	0.91	8.2 × 10−9	0.87	0.37

We list results of 6 SNPs (out of 31 tested) that replicated with P ≤ 0.01. The first six columns list SNP characteristics. The next four columns list GWA meta-analysis results including allele frequencies, a two-tailed P value for SNP association, and an odds ratio. The next four columns list similar results for replication genotyping; significance is reported on the basis of a stratified one-tailed CMH statistic. The next two columns summarize joint (overall) analysis results. Significance is reported on the basis of a stratified two-tailed CMH statistic across all 11 sample collections. The final column lists the Breslow-Day test for heterogeneity of odds ratios across all 11 collections.