Table 2.
The top five probes identified in the SMR analysis for blood.
| Phenotype* | CHR | Probe ID | Gene | Top eQTL | PeQTL | PGWAS | Beta | SE | PSMR | PHEIDI | NSNP |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Severe COVID-19 | 7 | ILMN_1,751,051 | C7orf25 | rs630191 | 2.00 × 10−112 | 1.36 × 10−04 | −0.39 | 0.10 | 1.68 × 10−04 | 1.55 × 10−01 | 20 |
| 5 | ILMN_1,654,685 | MCTP1 | rs306578 | 1.11 × 10−168 | 1.89 × 10−04 | 0.35 | 0.09 | 2.16 × 10−04 | 2.72 × 10−01 | 20 | |
| 15 | ILMN_1,778,734 | FAN1 | rs2240101 | 3.65 × 10−122 | 1.85 × 10−04 | 0.42 | 0.11 | 2.23 × 10−04 | 6.54 × 10−02 | 20 | |
| 7 | ILMN_1,749,432 | MRPL32 | rs601057 | 1.82 × 10−33 | 1.60 × 10−04 | −0.75 | 0.21 | 3.14 × 10−04 | 1.24 × 10−01 | 20 | |
| 15 | ILMN_2,152,178 | FAN1 | rs11070620 | 7.48 × 10−65 | 3.86 × 10−04 | 0.55 | 0.16 | 5.12 × 10−04 | 7.02 × 10−02 | 20 | |
| Severe COVID-19 NEJM# | 21 | ILMN_1,765,146 | IFNAR2 | rs2252639 | 5.57 × 10−44 | 4.23 × 10−05 | 0.69 | 0.18 | 8.54 × 10−05 | 7.52 × 10−02 | 15 |
| 21 | ILMN_1,791,057 | IFNAR2 | rs2252639 | 5.21 × 10−34 | 4.23 × 10−05 | −0.78 | 0.20 | 1.04 × 10−04 | 1.61 × 10−01 | 16 | |
| 11 | ILMN_1,704,972 | TRIM5 | rs35253098 | 5.68 × 10−85 | 7.93 × 10−05 | −0.45 | 0.12 | 1.09 × 10−04 | 7.86 × 10−01 | 20 | |
| 16 | ILMN_1,716,704 | NLRC5 | rs1684577 | 2.30 × 10−35 | 3.80 × 10−04 | 0.71 | 0.21 | 6.38 × 10−04 | 5.00 × 10−02 | 20 | |
| 11 | ILMN_2,404,665 | TRIM5 | rs34080219 | 3.47 × 10−17 | 2.32 × 10−04 | −1.03 | 0.30 | 7.44 × 10−04 | 1.15 × 10−01 | 20 | |
| COVID-19 | 20 | ILMN_1,681,591 | PTPN1 | rs117437913 | 4.76 × 10−56 | 1.29 × 10−04 | −0.21 | 0.06 | 1.99 × 10−04 | 6.23 × 10−03 | 20 |
| 21 | ILMN_1,765,146 | IFNAR2 | rs2252639 | 5.57 × 10−44 | 2.68 × 10−04 | 0.20 | 0.06 | 4.23 × 10−04 | 1.19 × 10−01 | 15 | |
| 21 | ILMN_1,791,057 | IFNAR2 | rs2252639 | 5.21 × 10−34 | 2.68 × 10−04 | −0.23 | 0.07 | 4.81 × 10−04 | 1.67 × 10−01 | 17 | |
| 5 | ILMN_1,757,106 | MARCH6 | rs2589667 | 4.49 × 10−155 | 5.08 × 10−04 | −0.10 | 0.03 | 5.66 × 10−04 | 6.97 × 10−01 | 20 | |
| 16 | ILMN_1,681,945 | ITGAD | rs2454911 | 6.71 × 10−13 | 8.85 × 10−05 | 0.41 | 0.12 | 5.79 × 10−04 | 1.10 × 10−01 | 20 | |
| COVID-19 negative¶ | 1 | ILMN_2,123,743 | FCER1G | rs2070901 | 1.89 × 10−230 | 2.16 × 10−05 | −0.15 | 0.04 | 2.54 × 10−05 | 5.43 × 10−01 | 20 |
| 15 | ILMN_1,783,956 | ATP8B4 | rs7172615 | 9.53 × 10−92 | 1.86 × 10−04 | −0.20 | 0.05 | 2.37 × 10−04 | 3.06 × 10−01 | 20 | |
| 3 | ILMN_1,654,612 | ZNF589 | rs11720622 | 2.51 × 10−52 | 3.24 × 10−04 | −0.27 | 0.08 | 4.66 × 10−04 | 9.38 × 10−02 | 20 | |
| 19 | ILMN_1,760,858 | RAB8A | rs35848422 | 1.99 × 10−89 | 4.38 × 10−04 | −0.19 | 0.05 | 5.33 × 10−04 | 6.88 × 10−01 | 15 | |
| 22 | ILMN_1,672,128 | ATF4 | rs710192 | 5.43 × 10−59 | 6.49 × 10−04 | −0.24 | 0.07 | 8.46 × 10−04 | 3.05 × 10−01 | 20 | |
| Hospitalized COVID-19 | 21 | ILMN_1,765,146 | IFNAR2 | rs2252639 | 5.57 × 10−44 | 1.26 × 10−06 | 0.42 | 0.09 | 4.75 × 10−06 | 1.48 × 10−03 | 15 |
| 21 | ILMN_1,791,057 | IFNAR2 | rs2252639 | 5.21 × 10−34 | 1.26 × 10−06 | −0.48 | 0.11 | 6.76 × 10−06 | 1.68 × 10−01 | 17 | |
| 7 | ILMN_1,770,030 | C7orf43 | rs6975031 | 1.96 × 10−34 | 1.58 × 10−04 | 0.40 | 0.11 | 3.06 × 10−04 | 3.52 × 10−02 | 20 | |
| 14 | ILMN_1,675,391 | SLC24A4 | rs61977314 | 1.84 × 10−69 | 4.57 × 10−04 | 0.23 | 0.07 | 5.87 × 10−04 | 1.78 × 10−01 | 20 | |
| 11 | ILMN_1,704,972 | TRIM5 | rs35253098 | 5.68 × 10−85 | 6.14 × 10−04 | −0.21 | 0.06 | 7.41 × 10−04 | 8.73 × 10−01 | 20 | |
| COVID-19 without hospitalization§ | 11 | ILMN_2,060,652 | BET1L | rs4980320 | 2.50 × 10−16 | 9.91 × 10−06 | 1.55 | 0.40 | 1.00 × 10−04 | 6.34 × 10−01 | 20 |
| 18 | ILMN_1,671,693 | C18orf10 | rs3909692 | 3.43 × 10−55 | 2.80 × 10−04 | −0.66 | 0.19 | 4.02 × 10−04 | 4.58 × 10−01 | 20 | |
| 1 | ILMN_1,741,801 | CDC7 | rs13447526 | 1.13 × 10−83 | 6.07 × 10−04 | 0.50 | 0.15 | 7.36 × 10−04 | 3.71 × 10−01 | 20 | |
| 7 | ILMN_1,714,158 | PON2 | rs2374993 | 1.45 × 10−44 | 5.20 × 10−04 | −0.71 | 0.21 | 7.56 × 10−04 | 2.09 × 10−01 | 20 | |
| 14 | ILMN_1,675,391 | SLC24A4 | rs61977314 | 1.84 × 10−69 | 6.03 × 10−04 | 0.54 | 0.16 | 7.61 × 10−04 | 1.73 × 10−01 | 20 | |
The GWAS summarized data were provided by the COVID-19 host genetics initiative6 and the control is the population unless otherwise noted. The eQTL data for blood14 can be downloaded at https://cnsgenomics.com/data/SMR/#eQTLsummarydata.
Summary data were provided by the Severe Covid-19 GWAS Group.5
The control is the non-predicted and non-self-reported COVID-19.
The control is COVID-19 without hospitalization, including laboratory confirmed or self-reported COVID-19.
PeQTL is the P value of the top associated cis-eQTL in the eQTL analysis, and PGWAS is the P value for the top associated cis-eQTL in the GWAS analysis. Beta is the estimated effect size in SMR analysis, SE is the corresponding standard error, PSMR is the P value for SMR analysis, PHEIDI is the P value for the HEIDI test and Nsnp is the number of SNPs involved in the HEIDI test.
CHR, chromosome; COVID-19, coronavirus disease 2019; HEIDI, heterogeneity in dependent instruments; SNP, single-nucleotide polymorphism; SMR, summary data-based Mendelian randomization; QTL, quantitative trait loci.
Bold font means statistical significance after correction for multiple testing using false discovery rate.