Rheumatoid arthritis (RA) is a polygenic autoimmune disease primarily affecting 
the synovial joints. Numerous animal models show similarities to RA in humans; 
some of them not only mimic the clinical phenotypes but also demonstrate the 
involvement of homologous genomic regions in RA. This paper compares 
corresponding non-MHC genomic regions identified in rodent and human genome-wide 
association studies (GWAS). To date, over 30 non-MHC RA-associated loci have 
been identified in humans, and over 100 arthritis-associated loci have been 
identified in rodent models of RA. The genomic regions associated with the 
disease are designated by the name(s) of the gene having the most frequent and 
consistent RA-associated SNPs or a function suggesting their involvement in 
inflammatory or autoimmune processes. Animal studies on rats and mice 
preferentially have used single sequence length polymorphism (SSLP) markers to 
identify disease-associated qualitative and quantitative trait loci (QTLs) in 
the genome of F2 hybrids of arthritis-susceptible and arthritis-resistant rodent 
strains. Mouse GWAS appear to be far ahead of rat studies, and significantly 
more mouse QTLs correspond to human RA risk alleles.