A principal-components-based clustering method to identify multiple variants associated with rheumatoid arthritis and arthritis-related autoantibodies

Table 3 Cluster associations with rheumatoid arthritis case-control status

Cluster No.	SNP	Position^a	MAF	R_O^2b	R_N^2c	(1-R_O²)/(1-R_N²) Ratio	p-Value^d
1	rs3130544	31,166,319	0.125	0.805	0.682	0.612	0.0002
	rs2442749	31,460,019	0.288	0.346	0.231	0.850
	rs3099844	31,556,955	0.113	0.897	0.570	0.240
	rs9267444	31,591,437	0.328	0.332	0.193	0.828
	rs2734583	31,613,459	0.110	0.917	0.565	0.192
	rs2857595	31,676,448	0.165	0.648	0.334	0.529
	rs3131379	31,829,012	0.097	0.906	0.660	0.277
	rs1270942	32,026,839	0.096	0.885	0.697	0.381
	rs389884	32,048,876	0.094	0.878	0.707	0.415
23	rs6910071	32,390,832	0.350	0.675	0.504	0.656	0.0008
	rs3817963	32,476,065	0.402	0.880	0.558	0.271
	rs3806156	32,481,676	0.453	0.787	0.534	0.458
	rs3763309	32,483,951	0.358	0.898	0.566	0.235
	rs2395163	32,495,787	0.355	0.901	0.574	0.232
	rs2395175	32,513,004	0.312	0.841	0.485	0.308
	rs2395185	32,541,145	0.444	0.773	0.446	0.411
	rs2516049	32,678,378	0.429	0.825	0.423	0.303
	rs660895	32,685,358	0.361	0.832	0.515	0.346
	rs532098	32,686,030	0.489	0.701	0.312	0.434

^aBased on HapMap Data Release 23a (Phase II), NCBI Build 36, dbSNP Build 126
^bSquared correlation coefficient between a given SNP and its own cluster
^cThe next highest squared correlation coefficient between a given SNP and any other cluster
^dp-Value from 1 df Wald χ² for association with outcome, adjusted for all other clusters in the model

ISSN: 1753-6561