Table 2 Variant candidate analysis for COVID-19 severity. This table presents the data summary for the variants analysed in the present study.
Variant | Ref/Alt | Genomic coordinates | Closer gene | Minor allele | Allele frequency controls | Allele frequency cases | Genotype frequency controls | Genotype frequency cases | HWE | p-value | OR | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
WT | Alt | WT | Alt | WT/WT | WT/Alt | Alt/Alt | WT/WT | WT/Alt | Alt/Alt | ||||||||
rs114301457 | C/T | 1:155,066,988 | EFNA4 | C | 1.00 | 0.00 | 0.99 | 0.01 | 0.99 | 0.01 | 0.00 | 0.98 | 0.02 | 0.00 | 1.00 | 0.32 | NA |
rs7528026 | G/A | 1:155,175,305 | TRIM46 | G | 1.00 | 0.00 | 0.98 | 0.02 | 1.00 | 0.00 | 0.00 | 0.91 | 0.09 | 0.00 | 1.00 | 0.02* | NA |
rs41264915 | A/G | 1:155,197,995 | THBS3 | A | 0.97 | 0.03 | 0.98 | 0.02 | 0.96 | 0.02 | 0.02 | 0.98 | 0.0 | 0.02 | < 0.01* | 0.76 | 0.82 |
rs1123573 | A/G | 2:60,480,453 | BCL11A | A | 0.79 | 0.21 | 0.76 | 0.24 | 0.62 | 0.34 | 0.04 | 0.54 | 0.45 | 0.02 | 0.27 | 0.52 | 1.22 |
rs2232354 | T/G | 2:113,129,758 | IL1RN | T | 0.86 | 0.14 | 0.72 | 0.28 | 0.04 | 0.21 | 0.75 | 0.14 | 0.27 | 0.59 | 0.01* | 0.01* | 2.29 |
rs147509469 | G/A | 2:191,909,428 | CAVIN2, TMEFF2 | A | 0.97 | 0.03 | 1.00 | 0.00 | 0.02 | 0.02 | 0.96 | 0.00 | 0.00 | 1.00 | 0.01* | 0.08 | 0.00 |
rs73062389 | A/G | 3:45,793,925 | SLC6A20 | G | 0.95 | 0.05 | 0.95 | 0.05 | 0.02 | 0.07 | 0.91 | 0.00 | 0.11 | 0.89 | 0.27 | 1.00 | 1.00 |
rs2271616 | G/T | 3:45,796,521 | SLC6A20 | T | 0.87 | 0.13 | 0.89 | 0.11 | 0.75 | 0.23 | 0.02 | 0.82 | 0.14 | 0.04 | 0.19 | 0.54 | 0.77 |
rs2531743 | G/A | 3:45,796,808 | SLC6A20, LZTFL1 | A | 0.71 | 0.29 | 0.77 | 0.23 | 0.46 | 0.48 | 0.05 | 0.55 | 0.43 | 0.02 | 0.89 | 0.29 | 0.72 |
rs72893671 | T/A | 3:45,809,291 | SLC6A20, LZTFL1 | T | 0.96 | 0.04 | 0.91 | 0.09 | 0.91 | 0.09 | 0.00 | 0.82 | 0.18 | 0.00 | 1.00 | 0.18 | 2.09 |
rs17713054 | G/A | 3:45,818,159 | SLC6A20, LZTFL1 | G | 0.99 | 0.01 | 0.92 | 0.08 | 0.98 | 0.02 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | < 0.01* | 9.69 |
rs71325088 | T/C | 3:45,821,460 | SLC6A20, LZTFL1 | T | 0.99 | 0.01 | 0.92 | 0.08 | 0.98 | 0.02 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | < 0.01* | 9.69 |
rs10490770 | T/C | 3:45,823,240 | SLC6A20, LZTFL1 | T | 0.99 | 0.01 | 0.92 | 0.08 | 0.98 | 0.02 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | < 0.01* | 9.69 |
rs11385942 | Del/A | 3:45,834,968 | LZTFL1 | Del | 0.99 | 0.01 | 0.91 | 0.09 | 0.98 | 0.02 | 0.00 | 0.82 | 0.18 | 0.00 | 1.00 | < 0.01* | 10.88 |
rs35081325 | A/T | 3:45,848,429 | LZTFL1 | A | 0.99 | 0.01 | 0.92 | 0.08 | 0.98 | 0.02 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | < 0.01* | 9.69 |
rs73064425 | C/T | 3:45,859,597 | LZTFL1 | C | 0.99 | 0.01 | 0.92 | 0.08 | 0.98 | 0.02 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | < 0.01* | 9.69 |
rs71325091 | G/A | 3:45,890,915 | LZTFL1 | G | 0.96 | 0.04 | 0.92 | 0.08 | 0.93 | 0.07 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | 0.15 | 2.35 |
rs13433997 | T/C | 3:46,008,273 | FYCO1, XCR1 | T | 0.92 | 0.08 | 0.88 | 0.12 | 0.84 | 0.16 | 0.00 | 0.77 | 0.23 | 0.00 | 0.60 | 0.27 | 1.67 |
rs34438204 | T/C | 3:46,039,814 | XCR1 | T | 0.96 | 0.04 | 0.92 | 0.08 | 0.91 | 0.09 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | 0.27 | 1.87 |
rs7642320 | A/G | 3:46,049,130 | XCR1 | A | 0.88 | 0.12 | 0.86 | 0.14 | 0.77 | 0.23 | 0.00 | 0.71 | 0.29 | 0.00 | 0.21 | 0.55 | 1.26 |
rs9877748 | A/G | 3:46,069,589 | XCR1 | A | 0.91 | 0.09 | 0.88 | 0.12 | 0.84 | 0.14 | 0.02 | 0.77 | 0.23 | 0.00 | 1.00 | 0.51 | 1.33 |
rs13069742 | A/G | 3:46,072,724 | XCR1 | A | 0.91 | 0.09 | 0.88 | 0.12 | 0.84 | 0.14 | 0.02 | 0.77 | 0.23 | 0.00 | 1.00 | 0.51 | 1.33 |
rs35110864 | G/A | 3:46,112,965 | XCR1, CCR1 | G | 0.96 | 0.04 | 0.92 | 0.08 | 0.91 | 0.09 | 0.00 | 0.84 | 0.16 | 0.00 | 1.00 | 0.27 | 1.87 |
rs13085367 | T/C | 3:46,131,332 | XCR1, CCR1 | T | 0.96 | 0.04 | 0.92 | 0.08 | 0.093 | 0.07 | 0.00 | 0.86 | 0.12 | 0.02 | 0.31 | 0.15 | 2.35 |
rs4443214 | T/C | 3:46,136,372 | XCR1, CCR1 | T | 0.94 | 0.06 | 0.91 | 0.09 | 0.88 | 0.12 | 0.00 | 0.84 | 0.14 | 0.03 | 0.48 | 0.62 | 1.27 |
rs35775079 | C/T | 3:46,220,620 | CCR3 | C | 0.99 | 0.01 | 0.96 | 0.04 | 0.98 | 0.02 | 0.00 | 0.91 | 0.09 | 0.00 | 1.00 | 0.02* | 8.53 |
rs11919389 | T/C | 3:101,705,614 | RPL24 | T | 0.79 | 0.21 | 0.81 | 0.19 | 0.61 | 0.36 | 0.04 | 0.66 | 0.30 | 0.04 | 1.00 | 0.52 | 0.80 |
rs343320 | G/A | 3:146,517,122 | PLSCR1 | G | 0.91 | 0.09 | 0.96 | 0.04 | 0.84 | 0.15 | 0.02 | 0.93 | 0.07 | 0.00 | 0.35 | 0.09 | 0.37 |
rs56162149 | C/T | 5:131,995,059 | ACSL6 | C | 0.83 | 0.17 | 0.79 | 0.21 | 0.68 | 0.30 | 0.02 | 0.64 | 0.29 | 0.07 | 0.55 | 0.40 | 1.33 |
rs9271609 | T/C | 6:32,623,820 | HLA-DRB1 | T | 0.66 | 0.34 | 0.65 | 0.35 | 0.36 | 0.61 | 0.04 | 0.46 | 0.38 | 0.16 | 0.41 | 0.78 | 1.08 |
rs2496644 | A/C | 6:41,515,007 | LINC01276 | C | 0.74 | 0.26 | 0.73 | 0.27 | 0.54 | 0.41 | 0.05 | 0.54 | 0.39 | 0.07 | 0.81 | 0.88 | 1.04 |
rs1886814 | A/C | 6:41,534,945 | FOXP4 | A | 0.77 | 0.23 | 0.77 | 0.23 | 0.59 | 0.36 | 0.05 | 0.59 | 0.36 | 0.05 | 1.00 | 1.00 | 1.00 |
rs28368148 | C/G | 9:21,206,606 | IFNA10 | C | 1.00 | 0.00 | 0.99 | 0.01 | 1.00 | 0.00 | 0.00 | 0.98 | 0.02 | 0.00 | 1.00 | 1.00 | 1.00 |
rs505922 | T/C | 9:133,273,813 | ABO | T | 0.84 | 0.16 | 0.82 | 0.18 | 0.70 | 0.29 | 0.02 | 0.68 | 0.29 | 0.04 | 1.00 | 0.72 | 1.13 |
rs529565 | T/C | 9:133,274,084 | ABO | T | 0.84 | 0.16 | 0.78 | 0.22 | 0.70 | 0.29 | 0.02 | 0.61 | 0.34 | 0.05 | 1.00 | 0.24 | 1.50 |
rs61882275 | G/A | 11:34,482,745 | ELF5 | G | 0.61 | 0.39 | 0.54 | 0.46 | 0.32 | 0.57 | 0.11 | 0.32 | 0.45 | 0.23 | 0.70 | 0.34 | 1.29 |
rs10774671 | G/A | 12:112,919,388 | OAS1 | A | 0.76 | 0.24 | 0.82 | 0.18 | 0.57 | 0.38 | 0.05 | 0.71 | 0.21 | 0.07 | 0.25 | 0.25 | 0.68 |
rs2660 | G/A | 12:112,919,637 | OAS1 | A | 0.82 | 0.18 | 0.85 | 0.15 | 0.66 | 0.32 | 0.20 | 0.77 | 0.16 | 0.07 | 0.18 | 0.59 | 0.82 |
rs10850097 | C/T | 12:112,923,312 | OAS1 | T | 0.79 | 0.21 | 0.84 | 0.16 | 0.61 | 0.36 | 0.04 | 0.75 | 0.18 | 0.07 | 0.21 | 0.40 | 0.74 |
rs6489867 | C/T | 12:112,925,745 | OAS1 | T | 0.77 | 0.23 | 0.82 | 0.18 | 0.57 | 0.39 | 0.04 | 0.73 | 0.18 | 0.09 | 0.24 | 0.32 | 0.71 |
rs7955267 | C/T | 12:112,941,234 | OAS3 | T | 0.79 | 0.21 | 0.80 | 0.20 | 0.59 | 0.39 | 0.02 | 0.71 | 0.18 | 0.11 | 0.24 | 0.74 | 0.89 |
rs56106917 | C/Del | 12:132,489,231 | FBRSL | C | 0.74 | 0.26 | 0.71 | 0.29 | 0.57 | 0.34 | 0.09 | 0.50 | 0.41 | 0.09 | 0.48 | 0.55 | 1.19 |
rs9577175 | C/T | 13:112,889,041 | ATP11A | C | 0.79 | 0.21 | 0.72 | 0.28 | 0.59 | 0.39 | 0.02 | 0.50 | 0.45 | 0.05 | 0.21 | 0.28 | 1.40 |
rs4424872 | T/A | 15:93,046,840 | RGMA | A | 0.96 | 0.04 | 0.97 | 0.03 | 0.95 | 0.02 | 0.04 | 0.96 | 0.02 | 0.02 | < 001* | 0.47 | 0.58 |
rs117169628 | G/A | 16:89,196,249 | SLC22A31 | G | 0.88 | 0.12 | 0.87 | 0.13 | 0.77 | 0.23 | 0.00 | 0.79 | 0.16 | 0.05 | 0.47 | 0.69 | 1.17 |
rs79600142 | T/C | 17:45,820,356 | CRHR1 | T | 0.87 | 0.13 | 0.94 | 0.05 | 0.73 | 0.27 | 0.00 | 0.89 | 0.09 | 0.02 | 1.00 | 0.07 | 0.43 |
rs62054835 | A/C | 17:45,857,306 | MAPT-AS1 | A | 0.87 | 0.13 | 0.95 | 0.05 | 0.73 | 0.27 | 0.00 | 0.91 | 0.07 | 0.02 | 1.00 | 0.04* | 0.36 |
rs112572874 | A/G | 17:45,995,618 | MAPT | A | 0.86 | 0.14 | 0.94 | 0.06 | 0.71 | 0.29 | 0.00 | 0.89 | 0.09 | 0.02 | 1.00 | 0.04* | 0.40 |
rs1819040 | T/A | 17:46,142,465 | KANSL1 | T | 0.85 | 0.15 | 0.94 | 0.06 | 0.73 | 0.23 | 0.04 | 0.89 | 0.09 | 0.02 | 0.11 | 0.03* | 0.37 |
rs2532300 | T/C | 17:46,152,620 | KANSL1 | T | 0.87 | 0.13 | 0.94 | 0.06 | 0.73 | 0.27 | 0.00 | 0.89 | 0.09 | 0.02 | 1.00 | 0.07 | 0.43 |
rs3848456 | C/A | 17:49,863,260 | TAC4 | C | 0.75 | 0.25 | 0.77 | 0.23 | 0.52 | 0.46 | 0.02 | 0.57 | 0.39 | 0.04 | 0.12 | 0.75 | 0.90 |
rs77534576 | C/T | 17:49,863,303 | TAC4 | C | 0.83 | 0.17 | 0.85 | 0.15 | 0.66 | 0.34 | 0.00 | 0.73 | 0.23 | 0.04 | 0.73 | 0.72 | 0.87 |
rs12610495 | A/G | 19:4,717,660 | DPP9 | A | 0.78 | 0.22 | 0.71 | 0.29 | 0.61 | 0.34 | 0.05 | 0.55 | 0.32 | 0.12 | 0.21 | 0.28 | 1.39 |
rs2109069 | G/A | 19:4,719,431 | DPP9 | G | 0.75 | 0.25 | 0.70 | 0.30 | 0.55 | 0.39 | 0.05 | 0.52 | 0.36 | 0.12 | 0.48 | 0.37 | 1.30 |
rs2277732 | C/A | 19:4,723,658 | DPP9 | C | 0.77 | 0.23 | 0.71 | 0.29 | 0.59 | 0.36 | 0.05 | 0.54 | 0.34 | 0.12 | 0.33 | 0.29 | 1.38 |
rs4804803 | A/G | 19:7,747,847 | CD209 | A | 0.82 | 0.18 | 0.85 | 0.15 | 0.68 | 0.29 | 0.04 | 0.75 | 0.20 | 0.05 | 0.18 | 0.59 | 0.82 |
rs73510898 | G/A | 19:10,305,768 | ZGLP1 | G | 0.96 | 0.04 | 0.96 | 0.04 | 0.91 | 0.09 | 0.00 | 0.95 | 0.02 | 0.04 | 0.01* | 1.00 | 1.00 |
rs74956615 | T/A | 19:10,317,045 | RAVER1 | T | 0.94 | 0.06 | 0.98 | 0.02 | 0.88 | 0.12 | 0.00 | 0.96 | 0.04 | 0.00 | 1.00 | 0.09 | 0.27 |
rs34536443 | G/C | 19:10,352,442 | TYK2 | G | 0.96 | 0.04 | 0.98 | 0.02 | 0.93 | 0.07 | 0.00 | 0.96 | 0.04 | 0.00 | 1.00 | 0.41 | 0.49 |
rs429358 | T/C | 19:44,908,684 | APOE | T | 0.88 | 0.12 | 0.95 | 0.05 | 0.79 | 0.18 | 0.04 | 0.89 | 0.11 | 0.00 | 0.20 | 0.11 | 0.46 |
rs368565 | C/T | 19:48,697,960 | FUT2 | T | 0.66 | 0.34 | 0.51 | 0.49 | 0.48 | 0.36 | 0.16 | 0.36 | 0.29 | 0.35 | 0.04* | 0.02* | 1.87 |
rs4801778 | G/T | 19:48,867,352 | PLEKHA4 | G | 0.85 | 0.15 | 0.88 | 0.12 | 0.73 | 0.23 | 0.04 | 0.77 | 0.21 | 0.02 | 0.44 | 0.56 | 0.79 |
rs17860115 | C/A | 21:33,230,000 | IFNAR2 | C | 0.52 | 0.48 | 0.48 | 0.52 | 0.25 | 0.54 | 0.21 | 0.25 | 0.46 | 0.29 | 1.00 | 0.59 | 1.15 |
rs2300370 | G/A | 21:33,232,252 | IFNAR2 | G | 0.54 | 0.46 | 0.46 | 0.54 | 0.27 | 0.54 | 0.20 | 0.23 | 0.46 | 0.30 | 1.00 | 0.29 | 1.33 |
rs2252639 | A/G | 21:33,245,424 | IFNAR2 | A | 0.52 | 0.48 | 0.53 | 0.47 | 0.23 | 0.57 | 0.20 | 0.29 | 0.48 | 0.23 | 0.70 | 0.89 | 0.96 |
rs2236757 | A/G | 21:33,252,612 | IFNAR2 | G | 0.54 | 0.46 | 0.52 | 0.48 | 0.25 | 0.57 | 0.18 | 0.30 | 0.43 | 0.27 | 0.18 | 0.79 | 1.07 |
rs2300371 | C/T | 21:33,259,936 | IFNAR2 | C | 0.54 | 0.46 | 0.55 | 0.45 | 0.25 | 0.57 | 0.18 | 0.34 | 0.43 | 0.23 | 1.00 | 0.79 | 0.93 |
rs8178521 | C/T | 21:33,287,378 | IL10RB | C | 0.76 | 0.24 | 0.74 | 0.26 | 0.57 | 0.38 | 0.05 | 0.61 | 0.27 | 0.12 | 0.13 | 0.64 | 1.15 |
rs35370143 | Del/Ins | 21:33,959,663 | LINC00649 | Del | 0.83 | 0.17 | 0.79 | 0.21 | 0.66 | 0.34 | 0.00 | 0.62 | 0.34 | 0.02 | 0.35 | 0.49 | 1.26 |
rs2298660 | C/T | 21:41,473,706 | TMPRSS2 | C | 0.79 | 0.21 | 0.81 | 0.19 | 0.62 | 0.34 | 0.04 | 0.68 | 0.27 | 0.05 | 0.76 | 0.74 | 0.89 |
rs2298661 | C/A | 21:41,473,715 | TMPRSS2 | C | 0.78 | 0.22 | 0.82 | 0.18 | 0.61 | 0.34 | 0.05 | 0.70 | 0.25 | 0.05 | 0.38 | 0.40 | 0.75 |
rs3787946 | G/C | 21:41,475,808 | TMPRSS2 | C | 0.78 | 0.22 | 0.80 | 0.20 | 0.61 | 0.34 | 0.05 | 0.66 | 0.29 | 0.05 | 0.57 | 0.62 | 0.85 |
