Multiple SNPs were associated in the whole cohort or after stratification by the major SE allele, HLA-DRB1*04, but only few passed conservative corrections for multiple testing (P ≤0.0004, Additional file 1: Tables S1-S4), namely: SNP rs6457617 (HLA-DQB1 gene) for several specificities, for the whole cohort and also after stratification for HLA-DRB1*04, and rs2476601 (PTPN22 gene) for the HLA-DRB1*04-positive RA group with anti-CEP-1 autoantibody. This evidence concerns the gene HLA-DQB1 and rheumatoid arthritis.