The serotype is determined by the antibody recognition of β6 subset of DQ β-chains.

DQ6 β-chains combine with α-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms.

DQB1*0604 is found at higher frequencies in parts Africa and Asia and is linked almost exclusively to DQA1*0102 as 6.4.

[3] Whereas DQ6 was protective against death (or need for liver transplantion) in primary sclerosing cholangitis.

It confers protection from narcolepsy,[5] juvenile diabetes,[6][7] Vogt-Koyanagi-Harada (VKH) syndrome,[8] pemphigus vulgaris,[9] multiple sclerosis,[10] myasthenia gravis.

[12][13] In multiple sclerosis DQA1*0102 was the most frequent allele and DQB1*0602 increased significantly in the MS patients.

[20] DQ6.3 (DQA1*0103 : DQB1*0603) is found in northcentral Europe at moderate frequencies, it is a protective against many autoimmune diseases.