COVID19-hg GWAS meta-analyses round 6

Release Date

June 15, 2021

Study Abbreviations
Full NameAbbreviation
23andMe23ANDME
24Geneticsidipaz24genetics
ACCOuNTACCOuNT
Amsterdam UMC COVID study groupAmsterdam_UMC_COVID_study_group
Ancestry Freeze FourANCESTRY_Freeze_Four
Biobanque Quebec COVID19BQC19
Bonn Study of COVID19 geneticsBoSCO
CCHC COVID-19 GWASCCHC_AMR
CHOP CAGCHOP_CAG
CHULACOVIDCHULACOVID
Columbia University COVID19 BiobankCU
CoronagenesCoronagenes
COVID19-Host(a)geHOSTAGE
deCODEDECODE
Determining the Molecular Pathways and Genetic Predisposition of the Acute Inflammatory Process Caused by SARS-CoV-2SPGRX
Egypt hgCOVID hubEgypt_hgCOVID_hub
EraCoreEraCORE
Estonian BiobankEstBB
EXCEEDEXCEED
FHoGIDFHoGID
FinnGenFinnGen
Geisinger Health SystemGHS_Freeze_145
GEN-COVID, reCOVIDGENCOVID
Generation ScotlandGeneration_Scotland
Genes & HealthGNH
Genes for GoodGFG
Genetic determinants of COVID-19 complications in the Brazilian populationBRACOVID
Genetic influences on severity of COVID-19 illness in KoreaGenetics_COVID19_Korea
Genetic modifiers for COVID-19 related illnessBelCovid
Genetics of COVID-related ManifestationCorea
Genomes for LifeGCAT
Genomic epidemiology of SARS-Cov-2 and host genetics in Coronavirus Disease 2019 (COVID-19)Stanford
genomiCCgenomicc
Genomics Englandgenomicsengland100kgp
Genotek COVID-19 studyGenotek
Helix Exome+ COVID-19 PhenotypesHelix
Host genetic factors in COVID-19 patients in relation to disease susceptibility, disease severity and pharmacogenomicsthaicovid
HUNTHUNT
Iran CovidIranCovid
Japan Coronavirus TaskforceJapanTaskForce
Latvia COVID-19 research platformLGDB
LifelinesLifelines
Michigan Genomics InitiativeMGI
Million Veterans ProgramMVP
Mount Sinai Health System COVID-19 Genomics InitiativeSINAI_COVID
Netherlands Twin RegisterNTR
Penn Medicine BiobankPMBB
Qatar Genome ProgramQGP
Saudi Human Genome ProgramSaudiHumanGenomeProgram
The Colorado Center for Personalized MedicineCCPM
The genetic predisposition to severe COVID-19SweCovid
The Norwegian Mother, Father and Child Cohort StudyMOBA
TOPMed CHRISTOPMed_CHRIS10K
TOPMed GardenaTOPMed_Gardena
TwinsUKTwinsUK
UK BiobankUKBB
UK Blood Donors CohortINTERVAL
Vanda COVIDVanda
Vanderbilt BiobankBioVU
Variability in immune response genes and severity of SARS-CoV-2 infection (INMUNGEN-CoV2 study)INMUNGEN_CoV2
Women's Health Genome StudyWGHS
Data Columns
Column NameDescription
#CHRchromosome
POSchromosome position
REFreference and non-effect allele
ALTalternative and effect allele (beta is for this allele)
SNP#CHR:POS:REF:ALT
all_meta_Nnumber of studies that had the variant after AF and INFO filtering and as such were used for the meta
all_inv_var_meta_betaeffect size on log(OR) scale
all_inv_var_meta_sebetastandard error of effect size
all_inv_var_meta_pp-value
all_inv_var_meta_casestotal number of cases
all_inv_var_meta_controlstotal number of controls
all_inv_var_meta_effectiveeffective sample size
all_inv_var_het_pp-value from Cochran's Q heterogeneity test
all_meta_AFallele frequency in the meta-analysis
rsidrisd
Release Notes

Meta-analysis was done with fixed effects inverse variance weighting. Results are available in genome builds 38 and 37. An AF filter of 0.001 and an INFO filter of 0.6 was applied to each study before meta.

Extras

**Note** a summary table of top results can be found here.

**Note** the full download files do not contain the 23andMe samples, but the plots display results from analyses that include the 23andMe.

There are additional not listed here available at this storage bucket:

gs://covid19-hg-public/20210415/results/20210607

You will need gsutil to list and download these files.

Included are ancestry-specific (AFR, EUR, HIS/AMR) and admixed (AFR/HIS/AMR) results for hospitalization and susceptibility scans are now available. Also the top 10k variants including 23andMe, as well as leave UKBB out results for all ancestries and EUR only are available.

Note: variants with heterogeneity p-value less than 0.001 across studies are in green.

A2_ALL_leave_23andme
Phenotype

Very severe respiratory confirmed covid vs. population

Population

All

Total Cases

8779

Total Controls

1001875

Contributing Studies
Namen_casesn_controls
ANCESTRY_Freeze_Four_EUR667113882
BQC19_EUR165743
BelCovid_EUR1841477
CHULACOVID_EAS137326
Egypt_hgCOVID_hub_AFR167180
FinnGen_FIN190278193
GENCOVID_EUR10772443
GHS_Freeze_145_EUR321108168
GNH_SAS15134013
HOSTAGE_EUR17799116
PMBB_AFR558622
SaudiHumanGenomeProgram_ARAB147768
SweCovid_EUR1133748
UKBB_EUR417420114
Amsterdam_UMC_COVID_study_group_EUR661413
SPGRX_EUR101302
genomicc_EUR16768380
BRACOVID_AMR5391149
CU_AFR1332610
CU_EUR2032149
JapanTaskForce_EAS1551705
genomicc_EAS149745
idipaz24genetics_EUR5975
INMUNGEN_CoV2_EUR70654
Vanda_EUR58900
Downloads

GRCh37 liftover: COVID19_HGI_A2_ALL_leave_23andme_20210607.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_A2_ALL_leave_23andme_20210607.b37.txt.gz.tbi

GRCh38: COVID19_HGI_A2_ALL_leave_23andme_20210607.txt.gz

GRCh38 (.tbi): COVID19_HGI_A2_ALL_leave_23andme_20210607.txt.gz.tbi

B1_ALL_leave_23andme
Phenotype

Hospitalized covid vs. not hospitalized covid

Population

All

Total Cases

14480

Total Controls

73191

Contributing Studies
Namen_casesn_controls
ANCESTRY_Freeze_Four_AFR1351494
ANCESTRY_Freeze_Four_AMR1993553
ANCESTRY_Freeze_Four_EUR148423869
BelCovid_EUR365121
CHOP_CAG_AFR147412
EstBB_EUR2712335
FHoGID_EUR470280
GENCOVID_EUR1267331
GHS_Freeze_145_EUR7734503
GNH_SAS3394812
Generation_Scotland_EUR5543674
IranCovid_MID210183
MVP_AFR13003573
MVP_AMR5171962
MVP_EUR24179251
UKBB_AFR101291
UKBB_CSA126489
UKBB_EUR30678947
DECODE_EUR891808
PMBB_AFR66100
QGP_ARAB60640
SPGRX_EUR31151
BoSCO_EUR212512
Downloads

GRCh37 liftover: COVID19_HGI_B1_ALL_leave_23andme_20210607.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_B1_ALL_leave_23andme_20210607.b37.txt.gz.tbi

GRCh38: COVID19_HGI_B1_ALL_leave_23andme_20210607.txt.gz

GRCh38 (.tbi): COVID19_HGI_B1_ALL_leave_23andme_20210607.txt.gz.tbi

B2_ALL_leave_23andme
Phenotype

Hospitalized covid vs. population

Population

All

Total Cases

24274

Total Controls

2061529

Contributing Studies
Namen_casesn_controls
ANCESTRY_Freeze_Four_AFR1355688
ANCESTRY_Freeze_Four_AMR19912323
ANCESTRY_Freeze_Four_EUR1484113882
BQC19_EUR378530
BelCovid_EUR3671477
EstBB_EUR352196455
FinnGen_FIN273278193
GENCOVID_EUR12872443
GHS_Freeze_145_EUR773108168
GNH_SAS33933825
Generation_Scotland_EUR55418683
HOSTAGE_EUR315112483
MVP_AFR130098129
MVP_AMR51743062
MVP_EUR2417366449
PMBB_AFR1268551
UKBB_AFR1016535
UKBB_CSA1268750
UKBB_EUR3067417464
Amsterdam_UMC_COVID_study_group_EUR1081413
Corea_EAS696500
DECODE_EUR89274322
QGP_ARAB6013360
SPGRX_EUR311302
BRACOVID_AMR853835
CU_AFR3042610
CU_EUR4532149
Genetics_COVID19_Korea_EAS6246549
JapanTaskForce_EAS5721705
LGDB_EUR571531
idipaz24genetics_EUR10675
INMUNGEN_CoV2_EUR236654
CHOP_CAG_AFR147412
FHoGID_EUR470280
IranCovid_MID210183
BoSCO_EUR212512
CHULACOVID_EAS137326
Egypt_hgCOVID_hub_AFR167180
SaudiHumanGenomeProgram_ARAB147768
SweCovid_EUR1133748
genomicc_EUR16768380
genomicc_EAS149745
Vanda_EUR58900
Downloads

GRCh37 liftover: COVID19_HGI_B2_ALL_leave_23andme_20210607.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_B2_ALL_leave_23andme_20210607.b37.txt.gz.tbi

GRCh38: COVID19_HGI_B2_ALL_leave_23andme_20210607.txt.gz

GRCh38 (.tbi): COVID19_HGI_B2_ALL_leave_23andme_20210607.txt.gz.tbi

C2_ALL_leave_23andme
Phenotype

Covid vs. population

Population

All

Total Cases

112612

Total Controls

2474079

Contributing Studies
Namen_casesn_controls
ANCESTRY_Freeze_Four_AFR16295688
ANCESTRY_Freeze_Four_AMR375212323
ANCESTRY_Freeze_Four_EAS120570
ANCESTRY_Freeze_Four_EUR25353113882
BQC19_EUR477431
BelCovid_EUR4881477
CCHC_AMR_HIS953140
CCPM_AMR2203111
CCPM_EUR89624851
Coronagenes_EUR181734
EXCEED_EUR2361083
EstBB_EUR4070189406
FinnGen_FIN2695278193
GCAT_EUR4474541
GENCOVID_EUR16972443
GFG_EUR1364978
GHS_Freeze_145_AFR1283050
GHS_Freeze_145_AMR881307
GHS_Freeze_145_EUR5276108168
GNH_SAS515129013
Generation_Scotland_EUR171217525
HUNT_EUR28352072
INTERVAL_EUR209839733
Lifelines_EUR89526600
MGI_AFR1112989
MOBA_EUR39156038
MVP_AFR489394556
MVP_AMR249741100
MVP_EUR11778357198
NTR_EUR2285265
PMBB_AFR3798298
PMBB_EUR609702
SINAI_COVID_EUR9423784
TwinsUK_EUR2472320
UKBB_AFR4266210
UKBB_AMR51929
UKBB_CSA6958181
UKBB_EAS1042605
UKBB_EUR13256407275
UKBB_MID891510
WGHS_EUR22511887
genomicsengland100kgp_EUR82244369
genomicsengland100kgp_SAS2354205
thaicovid_EAS191113
Corea_EAS1086500
Helix_EUR1785441
MGI_EUR12251458
QGP_ARAB70013360
SPGRX_EUR362302
ACCOuNT_AFR57799
BioVU_EUR14170615
CU_AFR3322610
CU_EUR5082149
DECODE_EUR4256270934
Genotek_EUR67612317
JapanTaskForce_EAS6141705
LGDB_EUR2751313
Stanford_EUR169190
TOPMed_CHRIS10K_EUR922373
TOPMed_Gardena_EUR452458
EraCORE_EUR3021646
HOSTAGE_EUR315112483
Amsterdam_UMC_COVID_study_group_EUR1081413
BRACOVID_AMR853835
Genetics_COVID19_Korea_EAS6246549
idipaz24genetics_EUR10675
INMUNGEN_CoV2_EUR236654
CHULACOVID_EAS137326
Egypt_hgCOVID_hub_AFR167180
SaudiHumanGenomeProgram_ARAB147768
SweCovid_EUR1133748
genomicc_EUR16768380
genomicc_EAS149745
Vanda_EUR58900
Downloads

GRCh37 liftover: COVID19_HGI_C2_ALL_leave_23andme_20210607.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_C2_ALL_leave_23andme_20210607.b37.txt.gz.tbi

GRCh38: COVID19_HGI_C2_ALL_leave_23andme_20210607.txt.gz

GRCh38 (.tbi): COVID19_HGI_C2_ALL_leave_23andme_20210607.txt.gz.tbi

Contributing studies