Specifically we propose to compare case-only designs that test for single-nucleotide polymorphism (SNP)-by-SNP interactions in RA between alleles at loci in candidate genes PTPN22, PADI4, and CTLA4, each known to have a previous putative marginal association with RA, and alleles at a selected subset of markers in the GAW16 data from the North American Rheumatoid Arthritis Consortium (NARAC). Here, PADI4 is linked to rheumatoid arthritis.