Using Beagle 4.1, we successfully imputed the SNV, CNV, two–digit and four–digit alleles of HLA genes (HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1, HLA-DRB1) and amino acids of 2810 vitiligo subjects (1117 cases, 1693 controls) and 2739 SLE subjects (1,693 controls and 1,046 cases). Here, HLA-B is linked to vitiligo.