We also found that the combination of HLA-DRB1*12:01 and *09:01, the diplotype that was most strongly associated with susceptibility to ACPA-negative RA in the previous study, was especially strongly associated with ACPA-negative RF-positive RA (p = 5.0×10−6, OR: 4.97 for ACPA-negative RF-positive RA; p = 0.040, OR: 2.46 for ACPA-negative RF-negative RA). This evidence concerns the gene PRTN3 and rheumatoid arthritis.