Finally, we examined cis-pQTLs of the HLA-pGenes identified from the flagship pQTL study, and found that the cis-pQTLs of five HLA-pGenes—CD5, CD6, IL7R, SLAMF8, and TNFSF11—are themselves associated with autoimmune diseases with HLA risk (Supplementary Fig. 10a). This evidence concerns the gene CD6 and autoimmune disease.