DQA1*0103 (*0103) shows a negative (protective) association with many autoimmune disease, this association is apparent in Japanese studies in the *0103:DQB1*0601 haplotype, and in Europe with the *0103:DQB1*0603 haplotype, indicating the protective effect is influenced by the alpha chain of DQ. DQA1*0103 is protective against Behçet's disease, pemphigus vulgaris, juvenile diabetes, steroid-sensitive nephrotic syndrome, myasthenia gravis coeliac disease multiple sclerosis, chronic active hepatitis C, and Vogt-Koyanagi-Harada syndrome. However, it may predispose carriers to chronic infection such as leprosy, Helicobacter pylori-positive gastric lymphoma, and AIDS.
DQA1*0103:DQB1*0601 is part of a multigene haplotype (DRB1*1502:DRB5*0102:DQA1*0103:DQB1*0601:DPA1*02:DPB1*0901) linked to Takayasu arteritis in Japanese. Another haplotype, DR8-DQ1 which contains this haplotype may be associated with primary biliary cirrhosis, Grave's disease There is a negative association of this DR15-DQ1 haplotype in Japanese with inflammatory bowel disease.
DQA1*0103:DQB1*0603 is part of a DR-DQ haplotype (DR13-DQ1) that increases for primary sclerosing cholangitis The same haplotype shows a negative association with rheumatic heart disease,