For hypothyroidism, the strongest 4-digit allelic associations were seen at the HLA-DQA1*0501, HLA-DQB1*0201, HLA-DRB1*0301 alleles (P<10−6 for each allele), which collectively comprise the HLA-DR3-DQ2 haplotype (Supplementary Table 3). This evidence concerns the gene HLA-DQA1 and hypothyroidism.