Table 2.
Significant genes associated with COVID-19 identified by MAGMA gene-based association analysis
| Gene | CHR | Start position | Stop position | Loci | MAGMA on COVID_I | MAGMA on ANA5 | MAGMA on meta-analysis data | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Z score | P-value | Z score | P-value | Z score | P-value | FDR | |||||
| LZTFL1 | 3 | 45 844 808 | 45 977 216 | 3p21.31 | 5.71 | 5.61 × 10−9 | 4.51 | 3.29 × 10−6 | 7.05 | 8.83 × 10−13 | 1.69 × 10−8 |
| XCR1 | 3 | 46 042 291 | 46 088 979 | 3p21.31 | 4.82 | 7.13 × 10−7 | 4.14 | 1.71 × 10−5 | 6.03 | 8.41 × 10−10 | 8.03 × 10−6 |
| CCR9 | 3 | 45 907 996 | 45 964 667 | 3p21.31 | 4.81 | 7.70 × 10−7 | 3.61 | 1.54 × 10−4 | 5.96 | 1.28 × 10−9 | 8.14 × 10−6 |
| FYCO1 | 3 | 45 939 391 | 46 057 316 | 3p21.31 | 4.28 | 9.55 × 10−6 | 3.32 | 4.49 × 10−4 | 5.50 | 1.95 × 10−8 | 9.31 × 10−5 |
| SLC6A20 | 3 | 45 776 941 | 45 858 039 | 3p21.31 | 4.05 | 2.60 × 10−5 | 2.72 | 3.26 × 10−3 | 5.11 | 1.58 × 10−7 | 6.03 × 10−4 |
| IFNAR2 | 21 | 34 582 231 | 34 656 831 | 21q22.11 | 3.53 | 2.10 × 10−4 | 3.50 | 2.31 × 10−4 | 5.02 | 2.58 × 10−7 | 7.58 × 10−4 |
| CXCR6 | 3 | 45 964 973 | 46 009 845 | 3p21.31 | 3.85 | 5.99 × 10−5 | 3.13 | 8.83 × 10−4 | 5.01 | 2.78 × 10−7 | 7.58 × 10−4 |
| HNRNPK | 9 | 86 562 998 | 86 615 692 | 9q21.32 | 2.02 | 2.16 × 10−2 | 3.18 | 7.42 × 10−4 | 4.18 | 1.46 × 10−5 | 3.48 × 10−2 |
| RMI1 | 9 | 86 575 321 | 86 638 989 | 9q21.32 | 2.09 | 1.84 × 10−2 | 3.15 | 8.29 × 10−4 | 4.12 | 1.86 × 10−5 | 3.94 × 10−2 |
| ABO | 9 | 136 110 563 | 136 170 630 | 9q34.2 | 4.85 | 6.28 × 10−7 | 0.10 | 0.46 | 3.21 | 6.55 × 10−4 | 0.43 |
Note: CHR = chromosome, FDR = False discovery rate, COVID_I = COVID_I GWAS summary statistics (Dataset #1), ANA5 = ANA5 GWAS summary statistics (Dataset #2). The meta-analysis data were based on the combination of COVID_I GWAS summary data (controlled for potential population stratification) with ANA5 GWAS summary data.