We invoked an alternative explanation to account for the observed protective effects in RA observed by us and Carlton et al [9]; that the protective effects are caused by a single allele in the PTPN22 haplotype block, but outside of the region encompassing PTPN22 that was assessed by Carlton et al [9] (Figure 1), and not due to the Arg620 allele. Here, PTPN22 is linked to rheumatoid arthritis.