Our analysis of transcriptional variations between SLE patients with and without the DAP1 risk allele detected increased expression of FCRLA, HLA-DPB1, CD1C, CD88, and PTPRCAP (CD45) and decreased expression of FOXO3, CASP1, CASP3, CASP7, and CASP8AP2, which supports the hypothesis that low DAP1 underlies increased autophagy, activated antigen presentation, B and T cell pathways, and decreased apoptosis of immune cell lineages in some SLE patients. Here, HLA-DPB1 is linked to systemic lupus erythematosus.