Leveraging LD between DQA1 and DQB1, we inferred their empirical haplotypes and assessed their association with the onset of type 1 diabetes and found that DQA1*03:01:01-DQB1*03:02:01 (DQ8.1) and DQA1*05:01:01-DQB1*02:01:01 (DQ2.5) had significant associations (HR 1.25 and 1.19, p=3.47×10−3 and 0.044, respectively), while DQA1*03:03:01-DQB1*03:01:01 had the opposite association (HR 0.55, p=1.19×10−3) (ESM Table 3). Here, HLA-DQA1 is linked to type 1 diabetes mellitus.