Motivated by differences in the magnitude of genetic effects associated with rheumatoid arthritis (RA) observed at genes PTPN22, CTLA4, and PADI4 across samples of common ancestry [1], we concentrate on interactions between each of these genes and a genome-wide subset of markers selected to be in approximate linkage equilibrium using the genome-wide data provided by Genetic Analysis Workshop 16 (GAW16) Problem 1. This evidence concerns the gene CTLA4 and rheumatoid arthritis.