None of the SNPs in the two regions that have been implicated in RA pathogenesis, the human leukocyte antigen (HLA) region (on 6p21) and the PTPN22 gene (on 1p13), showed any significant evidence of association with either of the two quantitative phenotypes at the overall FDR of 0.05 using any of the methods. This evidence concerns the gene PTPN22 and rheumatoid arthritis.