Table 1.
Results for linkage disequilibrium (LD) clumping in the HKDC1–HK1–NK2R–TSPAN15 region (10:70929740–71367422)
| Variant | Base-pair location | A1 | A0 | AFR MAF | AMR MAF | EAS MAF | EUR MAF | SAS MAF | Beta | s.e. | P | Closest gene (consequence) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs143849423 | 10:70969723 | G | T | 0.0008 | 0.0140 | 0.0000 | 0.0159 | 0.0050 | 0.0363 | 0.0064 | 1.74 × 10−8 | HKDC1 (downstream gene variant) |
| rs72814215 | 10:70998703 | G | A | 0.0008 | 0.0060 | 0.0000 | 0.0139 | 0.0070 | 0.0580 | 0.0090 | 1.21 × 10−10 | HKDC1 (intron variant) |
| 10:71002040 | 10:71002040 | T | TG | NA | NA | NA | 0.4105 | NA | 0.0653 | 0.0019 | 7.52 × 10−257 | HKDC1 (intron variant) |
| 10:71069872 | 10:71069872 | T | TA | NA | NA | NA | 0.1777 | NA | 0.0204 | 0.0027 | 8.62 × 10−14 | HK1 (NA) |
| rs5030918 | 10:71078526 | A | C | 0.000 | 0.0010 | 0.0000 | 0.0149 | 0.0020 | 0.2872 | 0.0063 | 0 | HK1 (intron variant) |
| rs2015803 | 10:71081399 | T | C | 0.4675 | 0.4860 | 0.2480 | 0.2664 | 0.2700 | 0.0455 | 0.0021 | 6.32 × 10−101 | HK1 (intron variant) |
| 10:71118821 | 10:71118821 | AAG | A | NA | NA | NA | 0.0401 | NA | 0.3077 | 0.0049 | 0 | HK1 (NA) |
| rs9299503 | 10:71136050 | A | G | 0.3109 | 0.4510 | 0.1935 | 0.4930 | 0.1935 | 0.0533 | 0.0020 | 1.87 × 10−157 | HK1 (intron variant) |
| rs4745984 | 10:71143488 | C | A | 0.0144 | 0.3520 | 0.3254 | 0.0984 | 0.0700 | 0.0472 | 0.0031 | 1.79 × 10−53 | HK1 (intron variant) |
| 10:71144995 | 10:71144995 | C | CTT | NA | NA | NA | 0.0635 | NA | 0.0418 | 0.0039 | 1.20 × 10−26 | HK1 (NA) |
| rs117056999 | 10:71154564 | T | C | 0.0030 | 0.0100 | 0.0000 | 0.0288 | 0.0030 | 0.0400 | 0.0054 | 1.22 × 10−13 | HK1 (intron variant) |
| rs1236903 | 10:71198994 | C | G | 0.0030 | 0.0320 | 0.0000 | 0.0795 | 0.0150 | 0.0269 | 0.0040 | 1.77 × 10−11 | TSPAN15 (intergenic) |
| rs77356330 | 10:71205544 | C | T | 0.0030 | 0.0320 | 0.000 | 0.0378 | 0.0060 | 0.0308 | 0.0042 | 2.48 × 10−13 | TSPAN15 (regulatory region variant) |
| rs72811732 | 10:71227549 | A | T | 0.0008 | 0.0190 | 0.0000 | 0.0368 | 0.0030 | 0.0444 | 0.0053 | 7.96 × 10−17 | TSPAN15 (intron variant) |
| rs11598811 | 10:71288098 | A | G | 0.0023 | 0.0760 | 0.0000 | 0.0716 | 0.0150 | 0.0307 | 0.0037 | 1.46 × 10−16 | NEUROG3 (upstream gene variant) |
Results for the 16 independent variants (r2 < 0.01 in 1,000 kb) in the region with minor allele frequencies from 5 genetic ancestries: African (AFR), admixed American (AMR), East Asian (EAS), European (EUR) and South Asian (SAS). The variant ID is from dbSNP, the base-pair locations are in build 37 and the annotations are from Variant Effect Predictor. The association tests were two-sided without multiple corrections. A1, effect allele; A0, other allele; s.e., standard error; NA, variant not found in the reference panel.