Table 3.
The top five probes identified in the SMR analysis for lung.
| Phenotype* | CHR | Probe ID | Gene | Top eQTL | PeQTL | PGWAS | BETA | SE | PSMR | PHEIDI | NSNP |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Severe COVID-19 | 7 | ENSG00000136197.8 | C7orf25 | rs583301 | 1.53 × 10−33 | 1.59 × 10−04 | −0.82 | 0.23 | 3.13 × 10−04 | 1.62 × 10−01 | 20 |
| 11 | ENSG00000110756.13 | HPS5 | rs4150641 | 3.15 × 10−16 | 9.23 × 10−05 | −1.02 | 0.29 | 4.21 × 10−04 | 3.88 × 10−01 | 20 | |
| 15 | ENSG00000244879.3 | GABPB1-AS1 | rs504781 | 1.55 × 10−91 | 4.23 × 10−04 | −0.27 | 0.08 | 5.14 × 10−04 | 5.49 × 10−02 | 20 | |
| 15 | ENSG00000259715.1 | CTD-3110H11.1 | rs504781 | 2.39 × 10−72 | 4.23 × 10−04 | −0.29 | 0.08 | 5.41 × 10−04 | 1.29 × 10−01 | 20 | |
| 15 | ENSG00000259845.1 | HERC2P10 | rs75874589 | 8.76 × 10−39 | 3.43 × 10−04 | 0.35 | 0.10 | 5.56 × 10−04 | 8.18 × 10−01 | 20 | |
| Severe COVID-19 NEJM# | 11 | ENSG00000177236.3 | AP006621.1 | rs4963156 | 2.04 × 10−84 | 1.88 × 10−05 | 0.32 | 0.08 | 2.90 × 10−05 | 1.33 × 10−01 | 20 |
| 11 | ENSG00000255284.1 | AP006621.5 | rs4963156 | 1.31 × 10−71 | 1.88 × 10−05 | 0.42 | 0.10 | 3.14 × 10−05 | 1.93 × 10−01 | 20 | |
| 11 | ENSG00000255142.1 | AP006621.6 | rs4963156 | 1.51 × 10−33 | 1.88 × 10−05 | 0.47 | 0.12 | 5.47 × 10−05 | 2.92 × 10−01 | 20 | |
| 22 | ENSG00000100299.13 | ARSA | rs6151429 | 6.98 × 10−42 | 5.22 × 10−04 | 0.32 | 0.10 | 7.74 × 10−04 | 7.45 × 10−01 | 20 | |
| 20 | ENSG00000231742.1 | RP11–112L6.4 | rs6122883 | 9.14 × 10−29 | 4.94 × 10−04 | 0.36 | 0.11 | 8.83 × 10−04 | 2.47 × 10−01 | 20 | |
| COVID-19 | 21 | ENSG00000241837.2 | ATP5O | rs12627646 | 8.98 × 10−36 | 3.78 × 10−05 | 0.26 | 0.07 | 9.11 × 10−05 | 2.68 × 10−01 | 20 |
| 10 | ENSG00000214435.3 | AS3MT | rs4919690 | 7.09 × 10−41 | 4.30 × 10−04 | −0.11 | 0.03 | 6.61 × 10−04 | 1.35 × 10−01 | 20 | |
| 10 | ENSG00000166275.11 | C10orf32 | rs9527 | 1.76 × 10−37 | 6.56 × 10−04 | −0.13 | 0.04 | 9.93 × 10−04 | 4.25 × 10−01 | 20 | |
| 16 | ENSG00000156886.11 | ITGAD | rs2454911 | 1.41 × 10−09 | 8.85 × 10−05 | 0.19 | 0.06 | 1.00 × 10−03 | 6.30 × 10−01 | 9 | |
| 16 | ENSG00000223496.1 | EXOSC6 | rs4985407 | 8.47 × 10−57 | 8.08 × 10−04 | −0.13 | 0.04 | 1.05 × 10−03 | 3.14 × 10−01 | 20 | |
| COVID-19 negative¶ | 3 | ENSG00000164048.9 | ZNF589 | rs6787500 | 2.81 × 10−36 | 2.55 × 10−04 | −0.24 | 0.07 | 4.45 × 10−04 | 3.37 × 10−02 | 20 |
| 1 | ENSG00000158869.6 | FCER1G | rs2070901 | 1.54 × 10−09 | 2.16 × 10−05 | −1.03 | 0.30 | 5.12 × 10−04 | 1.11 × 10−01 | 9 | |
| 3 | ENSG00000229759.1 | MRPS18AP1 | rs11130163 | 1.66 × 10−47 | 5.76 × 10−04 | −0.13 | 0.04 | 8.11 × 10−04 | 1.80 × 10−01 | 20 | |
| 11 | ENSG00000242689.1 | CNTF | rs73470773 | 1.67 × 10−14 | 4.26 × 10−04 | 0.30 | 0.09 | 1.36 × 10−03 | 1.70 × 10−02 | 20 | |
| 17 | ENSG00000261996.1 | CTC-281F24.1 | rs745057 | 1.79 × 10−14 | 6.84 × 10−04 | 0.27 | 0.09 | 1.91 × 10−03 | 4.72 × 10−01 | 20 | |
| Hospitalized COVID-19 | 6 | ENSG00000175967.3 | RP11–544L8__B.4 | rs11965077 | 1.78 × 10−21 | 4.95 × 10−05 | 0.40 | 0.11 | 1.89 × 10−04 | 9.36 × 10−01 | 5 |
| 16 | ENSG00000103226.13 | NOMO3 | rs55709104 | 7.52 × 10−34 | 2.07 × 10−04 | −0.21 | 0.06 | 3.88 × 10−04 | 7.94 × 10−01 | 20 | |
| 11 | ENSG00000117983.13 | MUC5B | rs12802931 | 7.44 × 10−10 | 4.19 × 10−05 | −0.44 | 0.13 | 6.48 × 10−04 | 1.11 × 10−03 | 9 | |
| 11 | ENSG00000225101.3 | OR52K3P | rs890417 | 1.50 × 10−23 | 4.38 × 10−04 | 0.23 | 0.07 | 9.10 × 10−04 | 3.83 × 10−01 | 20 | |
| 4 | ENSG00000181381.9 | DDX60L | rs6845647 | 8.95 × 10−16 | 3.31 × 10−04 | 0.38 | 0.11 | 1.05 × 10−03 | 4.02 × 10−01 | 20 | |
| COVID-19 without hospitalization§ | 11 | ENSG00000185627.13 | PSMD13 | rs1533825 | 9.92 × 10−24 | 1.85 × 10−05 | −1.43 | 0.36 | 8.18 × 10−05 | 4.04 × 10−01 | 20 |
| 6 | ENSG00000204536.9 | CCHCR1 | rs1265087 | 5.16 × 10−35 | 9.10 × 10−05 | 0.72 | 0.19 | 1.91 × 10−04 | 1.47 × 10−01 | 20 | |
| 11 | ENSG00000142082.10 | SIRT3 | rs6421986 | 6.61 × 10−13 | 2.09 × 10−05 | 1.99 | 0.54 | 2.51 × 10−04 | 2.59 × 10−01 | 20 | |
| 18 | ENSG00000134779.10 | TPGS2 | rs80033842 | 1.24 × 10−29 | 4.25 × 10−04 | −0.69 | 0.20 | 7.67 × 10−04 | 2.13 × 10−01 | 20 | |
| 22 | ENSG00000100106.15 | TRIOBP | rs5750494 | 7.46 × 10−11 | 1.45 × 10−04 | 1.24 | 0.38 | 1.03 × 10−03 | 4.97 × 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 lung15 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.