Table 1 Associations of the HLA variants with the T1D risk identified through trans-ethnic fine-mapping study.
From: A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes
Frequency (BBJ) | Frequency (UKB) | |||||||
|---|---|---|---|---|---|---|---|---|
Case | Control | Case | Control | OR (95% CI)a | Pa | |||
HLA variant | n = 831 | n = 61,556 | n = 732 | n = 353,727 | BBJ | UKB | BBJ | UKB |
HLA-DRβ1 amino acid position 71 | ||||||||
Alanine | 0.10 | 0.18 | 0.043 | 0.15 | 0.85 (0.66–1.10) | 1.34 (0.89–1.99) | 0.23 | 0.16 |
Arginine | 0.82 | 0.73 | 0.33 | 0.45 | (reference) | |||
Glutamic acid | 0.073 | 0.074 | 0.083 | 0.12 | 1.26 (0.89–1.77) | 0.72 (0.56–0.93) | 0.019 | 0.0013 |
Lysine | 0.0096 | 0.011 | 0.54 | 0.28 | 1.31 (0.71–2.24) | 2.11 (1.77–2.53) | 0.035 | 1.9 × 10−16 |
HLA-DQβ1 amino acid position 185 | ||||||||
Isoleucine | 0.39 | 0.57 | 0.68 | 0.83 | 2.74 (2.21–3.40) | 4.12 (3.49–4.99) | 3.5 × 10−20 | 7.0 × 10−55 |
Threonine | 0.61 | 0.43 | 0.32 | 0.17 | (reference) | |||
HLA-DQβ1 amino acid position 30 | ||||||||
Histidine | 0.16 | 0.19 | 0.18 | 0.23 | 1.36 (0.97–1.93) | 4.16 (2.86–5.96) | 0.0078 | 3.0 × 10−14 |
Serine | 0.0042 | 0.0038 | 0.34 | 0.25 | inf | 3.82 (2.53–5.87) | 0.079 | 3.8 × 10−10 |
Tyrosine | 0.83 | 0.80 | 0.48 | 0.52 | (reference) | |||
HLA-DRβ1 amino acid position 74 | ||||||||
Alanine | 0.56 | 0.59 | 0.59 | 0.65 | (reference) | |||
Arginine | 0.0018 | 0.00088 | 0.28 | 0.15 | 0 (0–0.05) | 0.64 (0.42–0.96) | 0.080 | 0.0036 |
Glutamic acid | 0.32 | 0.27 | 0.021 | 0.036 | 0.77 (0.64–0.93) | 0.57 (0.38–0.82) | 6.5 × 10−4 | 4.0 × 10−4 |
Glutamine | 0.0024 | 0.0030 | 0.079 | 0.15 | 0 (0–0.0029) | 0.31 (0.21–0.44) | 0.079 | 4.5 × 10−10 |
Leucine | 0.12 | 0.14 | 0.023 | 0.023 | 0.97 (0.81–1.16) | 2.20 (0.85–4.84) | 0.074 | 0.0077 |
HLA-DQβ1 amino acid position 70 | ||||||||
Arginine | 0.60 | 0.62 | 0.79 | 0.63 | (reference) | |||
Glutamic acid | 0.26 | 0.17 | 0.020 | 0.020 | 0.73 (0.59–0.90) | 0.27 (0.11–0.71) | 2.0 × 10−4 | 0.0052 |
Glycine | 0.14 | 0.20 | 0.19 | 0.35 | 0.95 (0.72–1.25) | 0.50 (0.36–0.70) | 0.073 | 3.1 × 10−5 |
HLA-A amino acid position 62 | ||||||||
Arginine | 0.19 | 0.20 | 0.064 | 0.086 | 1.25 (1.05–1.49) | 0.93 (0.74-1.16) | 0.0012 | 0.53 |
Glutamic acid | 0.39 | 0.37 | 0.094 | 0.093 | 1.40 (1.21–1.63) | 1.33 (1.10-1.60) | 9.2 × 10−6 | 0.0025 |
Glutamine | 0.15 | 0.19 | 0.46 | 0.49 | (reference) | |||
Glycine | 0.26 | 0.24 | 0.33 | 0.29 | 1.44 (1.23–1.68) | 1.27 (1.12-1.44) | 6.6 × 10−6 | 1.6 × 10−4 |
Leucine | 0 | 0 | 0.055 | 0.044 | – | 2.01 (1.57–2.55) | 1.5 × 10−12 | 1.9 × 10−8 |
HLA-B allele | ||||||||
HLA-B*54:01 | 0.14 | 0.073 | 0 | 0 | 1.78 (1.51–2.08) | – | – | – |
