The allele frequency of each SNP was determined in cases and controls as described in the Methods and 1438 SNPs were significantly associated with RA using an allelic test (P<0.05); 88 of these SNPs mapped to chr 6p21 between HLA-F and HLA-DPB1 within the major histocompatibility complex (MHC). Here, HLA-F is linked to rheumatoid arthritis.