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COVID-19 is an emerging, rapdily evolving situation


Get the latest public health information from CDC: https://www.coronavirus.gov

Get the latest research information from NIH: https://www.nih.gov/coronavirus

Get the latest COVID-19 GWAS Results from GRASP: https://grasp.nhlbi.nh.gov/COVID19GWASResults.aspx

 

COVID-19 GWAS Results -- for public download/use

This site compiles COVID-19 genetic scan results for immediate public download and use from any source permitting such use.
The use of the term “positive” below denotes a positive or assumed positive COVID-19 case based on study definitions. “Negative” indicates someone who has tested negative or presumed negative based on study definitions for COVID-19. “Unknown” indicates population control samples who may not have been tested or may not yet have results.
After each COVID-19 release of UK Biobank data (https://www.ukbiobank.ac.uk/2020/04/covid/) we are calculating GWAS summary statistics and releasing them to this site.

  • GWAS were conducted with SAIGE (https://github.com/weizhouUMICH/SAIGE) adjusted for baseline age, sex and 10 principal components
  • European ancestry (EA) only case/controls (as sample N increases for other groups additional analyses will be considered)
  • Two analyses:
    • Positive COVID-19 tests vs. Negative only COVID-19 tests (files with name whites)
    • Positive COVID-19 tests vs. All UK BioBank EA with either Negative tests or no known tests (files with name “ALLwhites”)

Summary statistics are for UK Biobank (v.3) imputed genome-wide association (GWAS) studies of COVID-19 test positives with variant filters of imputation quality INFO score >0.3, minor allele count (MAC) > 2, minor allele frequency > 0.0001. Note allele2 is coded allele. See SAIGE output description here: https://github.com/weizhouUMICH/SAIGE/wiki/Genetic-association-tests-using-SAIGE.


Annotation of all top results P<1E-5 was done from several sources:

All files are in compressed Gzip format.
Send questions, comments or requests to add data or analysis to: ming-huei.chen@nih.gov, florian.thibord@nih.gov, and johnsonad2@nih.gov


Analysis date: 06/05/2020
1,221 positive cases vs. 4,117 negative controls; ~27.26 million variants: UKBB_covid19_whites_060520.SAIGE.bgen.txt.gz
1,221 positive cases vs. 458,029 negative/unknown UKBB controls; ~38.06 million variants: UKBB_covid19_ALLwhites_060520.SAIGE.bgen.txt.gz

Annotated top results (only variants with P<1E-5):
1,221 positive cases vs. 4,117 negative controls; 244 variants:
top_UKBB_covid19_whites_060520.txt.gz
top_UKBB_covid19_whites_060520_grasp.txt.gz
top_UKBB_covid19_whites_060520_ebi.txt.gz
top_UKBB_covid19_whites_060520_GTeX.txt.gz
top_UKBB_covid19_whites_060520_eQTLdb.txt.gz

1,221 positive cases vs. 458,029 negative/unknown UKBB controls; 406 variants:
top_UKBB_covid19_ALLwhites_060520.txt.gz
top_UKBB_covid19_ALLwhites_060520_grasp.txt.gz
top_UKBB_covid19_ALLwhites_060520_ebi.txt.gz
top_UKBB_covid19_ALLwhites_060520_GTeX.txt.gz
top_UKBB_covid19_ALLwhites_060520_eQTLdb.txt.gz

Analysis date: 05/25/2020
1,095 positive cases vs. 2,797 negative controls; ~24.33 million variants: UKBB_covid19_whites_052520.txt.gz
1,095 positive cases vs. 458,155 negative/unknown UKBB controls; ~38.06 million variants: UKBB_covid19_ALLwhites_052520.txt.gz

Annotated top results (only variants with P<1E-5):
1,095 positive cases vs. 2,797 negative controls; 172 variants:
top_UKBB_covid19_whites_052520.txt.gz
top_UKBB_covid19_whites_052520_grasp.txt.gz
top_UKBB_covid19_whites_052520_ebi.txt.gz
top_UKBB_covid19_whites_052520_GTeX.txt.gz
top_UKBB_covid19_whites_052520_eQTLdb.txt.gz

1,095 positive cases vs. 458,155 negative/unknown UKBB controls; 448 variants:
top_UKBB_covid19_ALLwhites_052520.txt.gz
top_UKBB_covid19_ALLwhites_052520_grasp.txt.gz
top_UKBB_covid19_ALLwhites_052520_ebi.txt.gz
top_UKBB_covid19_ALLwhites_052520_GTeX.txt.gz
top_UKBB_covid19_ALLwhites_052520_eQTLdb.txt.gz

Analysis date: 05/07/2020
880 positive cases vs. 1,686 negative controls; ~21.03 million variants: UKBB_covid19_whites_050720.txt.gz
880 positive cases vs. 458,370 negative/unknown UKBB controls; ~38.06 million variants: UKBB_covid19_ALLwhites_050720.txt.gz

Annotated top results (only variants with P<1E-5):
880 positive cases vs. 1,686 negative controls; 205 variants:
top_UKBB_covid19_whites_050720.txt.gz
top_UKBB_covid19_whites_050720_grasp.txt.gz
top_UKBB_covid19_whites_050720_ebi.txt.gz
top_UKBB_covid19_whites_050720_GTeX.txt.gz
top_UKBB_covid19_whites_050720_eQTLdb.txt.gz

880 positive cases vs. 458,370 negative/unknown UKBB controls; 374 variants:
top_UKBB_covid19_ALLwhites_050720.txt.gz
top_UKBB_covid19_ALLwhites_050720_grasp.txt.gz
top_UKBB_covid19_ALLwhites_050720_ebi.txt.gz
top_UKBB_covid19_ALLwhites_050720_GTeX.txt.gz
top_UKBB_covid19_ALLwhites_050720_eQTLdb.txt.gz

Ellinghaus, Degenhardt et al.
Meta-analysis of Spanish and Italian COVID19 cases with respiratory failure.
NOTE: full GWAS files are GRCh38 build position whereas top results and annotated files have been Lifted Over to GRCh37.

1,610 COVID19 cases with respiratory failure vs. 2,205 controls (adjusted for 10 genomics PCs); ~8.58 million variants: EllinghausPCs_covid19.full.txt.gz

1,610 COVID19 cases with respiratory failure vs. 2,205 controls (adjusted for age, sex, 10 genomics PCs) ~8.58 million variants: EllinghausPCsAgeSex_covid19.full.txt.gz

Annotated top results (only variants with P<1E-5):
1,610 positive cases vs. 2,205 negative controls; PC adjusted, 391 variants:
top_EllinghausPCs_covid19.txt.gz
top_EllinghausPCs_covid19_grasp.txt.gz
top_EllinghausPCs_covid19_ebi.txt.gz
top_EllinghausPCs_covid19_GTeX.txt.gz
top_EllinghausPCs_covid19_eQTLdb.txt.gz

1,610 positive cases vs. 2,205 negative controls; PC adjusted, 317 variants:
top_EllinghausPCsAgeSex_covid19.txt.gz
top_EllinghausPCsAgeSex_covid19_grasp.txt.gz
top_EllinghausPCsAgeSex_covid19_ebi.txt.gz
top_EllinghausPCsAgeSex_covid19_GTeX.txt.gz
top_EllinghausPCsAgeSex_covid19_eQTLdb.txt.gz

COVID-19 Host Genetics initiative results provided under Creative Commons License.
This includes meta-analyses of international case/control samples with a larger sample size than UKBB alone.
These analyses may also have greater test/population ascertainment and genetic heterogeneity effects. If you have samples to contribute we urge you to consider joining.
See also https://www.covid19hg.org/blog/ and https://www.nature.com/articles/s41431-020-0636-6

Analysis date: 05/15/2020
716 positive hospitalized cases vs. 616 positive non-hospitalized controls; ~10.98 million variants: COVID19_HGI_ANA2_20200513.txt.gz
Top_COVID19_ANA2_051320_grasp.txt.gz
Top_COVID19_ANA2_051320_ebi.txt.gz
Top_COVID19_ANA2_051320_GTeX.txt.gz
Top_COVID19_ANA2_051320_eQTLdb.txt.gz

1678 positive cases vs. 674,635 negative/unknown controls; ~34.01 million variants:
COVID19_HGI_ANA5_20200513.txt.gz
Top_COVID19_ANA5_051320_grasp.txt.gz
Top_COVID19_ANA5_051320_ebi.txt.gz
Top_COVID19_ANA5_051320_GTeX.txt.gz
Top_COVID19_ANA5_051320_eQTLdb.txt.gz

1294 predicted positive by flu-like symptoms vs. 26,969 predicted negative; ~7.52 million variants: COVID19_HGI_ANA7_20200513.txt.gz
Top_COVID19_ANA7_051320_grasp.txt.gz
Top_COVID19_ANA7_051320_ebi.txt.gz
Top_COVID19_ANA7_051320_GTeX.txt.gz
Top_COVID19_ANA7_051320_eQTLdb.txt.gz



This work was supported by the NHLBI Intramural Research program and the NIH Biowulf high performance computing cluster (https://hpc.nih.gov/).