TRAF1 and rheumatoid arthritis: There are no rare variants (MAF<5%) on the Illumina HumanHap 550 k beadchip passing our QC filters in PTPN22. Rare variants are represented in the other established RA loci (TRAF1-C5, IL2RA, and IL2RB), but our results do not indicate any evidence of rare variant effects within these genes.