COVID19-hg GWAS meta-analyses round 4

Release Date

October 20, 2020

Study Abbreviations
Full NameAbbreviation
Amsterdam UMC COVID study groupAmsterdam_UMC_COVID_study_group
AncestryAncestry
Genetic determinants of COVID-19 complications in the Brazilian populationBRACOVID
Genetic modifiers for COVID-19 related illnessBelCovid
Biobanque Quebec COVID19BQC19
deCODEDECODE
(Genetics of COVID-related Manifestation)Corea
Estonian BiobankEstBB
FinnGenFinnGen
GEN-COVID, reCOVIDGENCOVID
genomiCCgenomicc
Genes & HealthGNH
Generation ScotlandGS
COVID19-Host(a)geHOSTAGE
Helix Exome+ COVID-19 PhenotypesHelix
UK Blood Donors CohortINTERVAL
Michigan Genomics InitiativeMGI
Million Veterans ProgramMVP
Netherlands Twin RegisterNTR
Partners Healthcare BiobankPHBB
Penn Medicine BiobankPMBB
Qatar Genome ProgramQGP
Determining the Molecular Pathways and Genetic Predisposition of the Acute Inflammatory Process Caused by SARS-CoV-2SPGRX
Genomic epidemiology of SARS-Cov-2 and host genetics in Coronavirus Disease 2019 (COVID-19)Stanford
The genetic predisposition to severe COVID-19SweCovid
UK BiobankUKBB
Bonn Study of COVID19 geneticsBoSCO
23andMe23ANDME
Italy COVID19-Host(a)geItaly_HOSTAGE
Spain COVID19-Host(a)geSpain_HOSTAGE
Genomics Englandgenomicsengland100kgp
LifelinesLifelines
Gene RiskGeneRISK
Rotterdam StudyRS
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_het_pp-value from Cochran's Q heterogeneity test
all_meta_sample_Ntotal sample size
all_meta_AFallele frequency in the meta-analysis
rsidrisd
AF_fccalculated based on each study's ancestry in gnomAD or all populations if the ancestry is not present in gnomAD
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. 1000G EUR phase 3 samples were used as a panel for pruning. Nine genome-wide significant SNPs from C2 and B2 analyses AND SNPs +/-100kb with P<0.01 around these top SNPs selected (no r2 threshold) coming to total 461 SNPs (MAF max 0.1%). Excluding the regions above, the top 9539 SNPs from clumps using MAF 1% variants, r2=0.1, kb=250.

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

A1_ALL
Phenotype

Very severe respiratory confirmed covid vs. not hospitalized covid

Population

all

Total Cases

269

Total Controls

688

Contributing Studies
Namen_casesn_controls
BoSCO_EUR59262
FinnGen_FIN54224
SPGRX_EUR10151
BQC19_EUR55151
Downloads

GRCh37 liftover: COVID19_HGI_A1_ALL_20201020.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_A1_ALL_20201020.b37.txt.gz.tbi

GRCh37 (filtered): COVID19_HGI_A1_ALL_20201020.b37_1.0E-5.txt

GRCh38: COVID19_HGI_A1_ALL_20201020.txt.gz

GRCh38 (.tbi): COVID19_HGI_A1_ALL_20201020.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_A1_ALL_20201020.txt.gz_1.0E-5.txt

A2_ALL

Please note: the plots shown here display results from an analysis with the 23andMe study included. However, due to privacy, the downloadable gz files do not include the 23andMe study. A limited version of the analysis that includes the 23andMe study is available in the file labeled "10K".

Phenotype

Very severe respiratory confirmed covid vs. population

Population

All

Total Cases

4933

Total Controls

1398672

Contributing Studies
Namen_casesn_controls
Amsterdam_UMC_COVID_study_group_EUR661413
BRACOVID_AMR4501637
GENCOVID_EUR4682472
SweCovid_EUR783778
FinnGen_FIN54238657
genomicc_EUR16768380
SPGRX_EUR101302
BQC19_EUR55480
UKBB_EUR329364341
23ANDME_EUR495680440
23ANDME_HIS10294330
Italy_HOSTAGE_EUR6981255
Spain_HOSTAGE_EUR302925
BoSCO_EUR59262
Downloads

GRCh37 (filtered): COVID19_HGI_A2_ALL_20201020.b37_1.0E-5.txt

GRCh38 (filtered): COVID19_HGI_A2_ALL_20201020.txt.gz_1.0E-5.txt

GRCh38 with 23andMe 10K: COVID19_HGI_A2_ALL_20201020.10k.txt.gz

GRCh37 with 23andMe 10K: COVID19_HGI_A2_ALL_20201020.10k.b37.txt.gz

GRCh38 leave out 23andMe: COVID19_HGI_A2_ALL_leave_23andme_20201020.txt.gz

GRCh38 leave out 23andMe (.tbi): COVID19_HGI_A2_ALL_leave_23andme_20201020.txt.gz.tbi

GRCh37 leave out 23andMe: COVID19_HGI_A2_ALL_leave_23andme_20201020.b37.txt.gz

GRCh37 leave out 23andMe (.tbi): COVID19_HGI_A2_ALL_leave_23andme_20201020.b37.txt.gz.tbi

B1_ALL
Phenotype

Hospitalized covid vs. not hospitalized covid

Population

All

Total Cases

2430

Total Controls

8478

Contributing Studies
Namen_casesn_controls
UKBB_EUR413897
BoSCO_EUR139262
DECODE_EUR891808
FinnGen_FIN83224
SPGRX_EUR31151
GNH_SAS6241
PMBB_AFR66100
QGP_ARAB60640
MVP_AFR349862
MVP_EUR4361083
MVP_HIS117392
Ancestry_EUR2501967
BQC19_EUR55151
Downloads

GRCh37 liftover: COVID19_HGI_B1_ALL_20201020.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_B1_ALL_20201020.b37.txt.gz.tbi

GRCh37 (filtered): COVID19_HGI_B1_ALL_20201020.b37_1.0E-5.txt

GRCh38: COVID19_HGI_B1_ALL_20201020.txt.gz

GRCh38 (.tbi): COVID19_HGI_B1_ALL_20201020.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_B1_ALL_20201020.txt.gz_1.0E-5.txt

B2_ALL_eur_leave_23andme
Phenotype

Hospitalized covid vs. population, leave out 23andMe

Population

Eur

Total Cases

6406

Total Controls

902088

Contributing Studies
Namen_casesn_controls
Amsterdam_UMC_COVID_study_group_EUR1081413
DECODE_EUR89274322
BelCovid_EUR1091484
GENCOVID_EUR5712472
FinnGen_FIN83238628
SPGRX_EUR311302
HOSTAGE_EUR16102205
BQC19_EUR181354
UKBB_EUR765364341
MVP_EUR4362180
BoSCO_EUR139262
Ancestry_EUR2501967
SweCovid_EUR783778
genomicc_EUR16768380
Downloads

GRCh37 liftover: COVID19_HGI_B2_ALL_eur_leave_23andme_20201020.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_B2_ALL_eur_leave_23andme_20201020.b37.txt.gz.tbi

GRCh37 (filtered): COVID19_HGI_B2_ALL_eur_leave_23andme_20201020.b37_1.0E-5.txt

GRCh38: COVID19_HGI_B2_ALL_eur_leave_23andme_20201020.txt.gz

GRCh38 (.tbi): COVID19_HGI_B2_ALL_eur_leave_23andme_20201020.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_B2_ALL_eur_leave_23andme_20201020.txt.gz_1.0E-5.txt

B2_ALL

Please note: the plots shown here display results from an analysis with the 23andMe study included. However, due to privacy, the downloadable gz files do not include the 23andMe study. A limited version of the analysis that includes the 23andMe study is available in the file labeled "10K".

Phenotype

Hospitalized covid vs. population

Population

All

Total Cases

8638

Total Controls

1736547

Contributing Studies
Namen_casesn_controls
Amsterdam_UMC_COVID_study_group_EUR1081413
DECODE_EUR89274322
BRACOVID_AMR7561637
BelCovid_EUR1091484
GENCOVID_EUR5712472
FinnGen_FIN83238628
SPGRX_EUR311302
GNH_SAS6227353
HOSTAGE_EUR16102205
Corea_EAS696500
PMBB_AFR668536
QGP_ARAB6013360
BQC19_EUR181354
UKBB_EUR765364341
23ANDME_EUR613680416
23ANDME_HIS14094327
MVP_AFR3491745
MVP_EUR4362180
MVP_HIS117585
BoSCO_EUR139262
Ancestry_EUR2501967
SweCovid_EUR783778
genomicc_EUR16768380
Downloads

GRCh37 (filtered): COVID19_HGI_B2_ALL_20201020.b37_1.0E-5.txt

GRCh38 (filtered): COVID19_HGI_B2_ALL_20201020.txt.gz_1.0E-5.txt

GRCh38 with 23andMe 10K: COVID19_HGI_B2_ALL_20201020.10k.txt.gz

GRCh37 with 23andMe 10K: COVID19_HGI_B2_ALL_20201020.10k.b37.txt.gz

GRCh38 leave out 23andMe: COVID19_HGI_B2_ALL_leave_23andme_20201020.txt.gz

GRCh38 leave out 23andMe (.tbi): COVID19_HGI_B2_ALL_leave_23andme_20201020.txt.gz.tbi

GRCh37 leave out 23andMe: COVID19_HGI_B2_ALL_leave_23andme_20201020.b37.txt.gz

GRCh37 leave out 23andMe (.tbi): COVID19_HGI_B2_ALL_leave_23andme_20201020.b37.txt.gz.tbi

C1_ALL

Please note: the plots shown here display results from an analysis with the 23andMe study included. However, due to privacy, the downloadable gz files do not include the 23andMe study. A limited version of the analysis that includes the 23andMe study is available in the file labeled "10K".

Phenotype

Covid vs. lab/self-reported negative

Population

All

Total Cases

24057

Total Controls

218062

Contributing Studies
Namen_casesn_controls
UKBB_AFR68268
UKBB_CSA66350
UKBB_EUR131013646
DECODE_EUR189729014
EstBB_EUR31312019
genomicsengland100kgp_EUR2181617
GNH_SAS114256
Lifelines_EUR3581253
MGI_EUR122508
MVP_AFR12179204
MVP_EUR152024135
MVP_HIS5103325
NTR_EUR145117
PHBB_AFR60375
PHBB_EUR1513118
PHBB_HIS66276
PMBB_AFR166934
BQC19_EUR206327
INTERVAL_EUR1611119
23ANDME_AFR5063110
23ANDME_EUR991385072
23ANDME_HIS255313086
Ancestry_EUR241714933
Downloads

GRCh37 (filtered): COVID19_HGI_C1_ALL_20201020.b37_1.0E-5.txt

GRCh38 (filtered): COVID19_HGI_C1_ALL_20201020.txt.gz_1.0E-5.txt

GRCh38 with 23andMe 10K: COVID19_HGI_C1_ALL_20201020.10k.txt.gz

GRCh37 with 23andMe 10K: COVID19_HGI_C1_ALL_20201020.10k.b37.txt.gz

GRCh38 leave out 23andMe: COVID19_HGI_C1_ALL_leave_23andme_20201020.txt.gz

GRCh38 leave out 23andMe (.tbi): COVID19_HGI_C1_ALL_leave_23andme_20201020.txt.gz.tbi

GRCh37 leave out 23andMe: COVID19_HGI_C1_ALL_leave_23andme_20201020.b37.txt.gz

GRCh37 leave out 23andMe (.tbi): COVID19_HGI_C1_ALL_leave_23andme_20201020.b37.txt.gz.tbi

C2_ALL

Please note: the plots shown here display results from an analysis with the 23andMe study included. However, due to privacy, the downloadable gz files do not include the 23andMe study. A limited version of the analysis that includes the 23andMe study is available in the file labeled "10K".

Phenotype

Covid vs. population

Population

All

Total Cases

30937

Total Controls

1471815

Contributing Studies
Namen_casesn_controls
UKBB_AFR686465
UKBB_CSA668487
UKBB_EUR1305370602
DECODE_EUR1897273257
EstBB_EUR313138272
GENCOVID_EUR7342472
FinnGen_FIN357238354
genomicsengland100kgp_EUR21862302
SPGRX_EUR362302
GNH_SAS11427301
Helix_EUR1785441
Corea_EAS1086500
Lifelines_EUR35825213
MGI_EUR12251458
MVP_AFR12176085
MVP_EUR15207600
MVP_HIS5102550
NTR_EUR1455252
PHBB_AFR602445
PHBB_EUR15129966
PHBB_HIS662405
PMBB_AFR1668436
QGP_ARAB70013360
Stanford_EUR109191
INTERVAL_EUR16141674
BQC19_EUR206327
23ANDME_AFR5063110
23ANDME_EUR991385072
23ANDME_HIS255313086
Ancestry_EUR241714933
Amsterdam_UMC_COVID_study_group_EUR1081413
BRACOVID_AMR7561637
BelCovid_EUR1091484
HOSTAGE_EUR16102205
SweCovid_EUR783778
genomicc_EUR16768380
Downloads

GRCh37 (filtered): COVID19_HGI_C2_ALL_20201020.b37_1.0E-5.txt

GRCh38 (filtered): COVID19_HGI_C2_ALL_20201020.txt.gz_1.0E-5.txt

GRCh38 with 23andMe 10K: COVID19_HGI_C2_ALL_20201020.10k.txt.gz

GRCh37 with 23andMe 10K: COVID19_HGI_C2_ALL_20201020.10k.b37.txt.gz

GRCh38 leave out 23andMe: COVID19_HGI_C2_ALL_leave_23andme_20201020.txt.gz

GRCh38 leave out 23andMe (.tbi): COVID19_HGI_C2_ALL_leave_23andme_20201020.txt.gz.tbi

GRCh37 leave out 23andMe: COVID19_HGI_C2_ALL_leave_23andme_20201020.b37.txt.gz

GRCh37 leave out 23andMe (.tbi): COVID19_HGI_C2_ALL_leave_23andme_20201020.b37.txt.gz.tbi

C2_ALL_eur_leave_23andme
Phenotype

Covid vs. population, leave out 23andMe

Population

Eur

Total Cases

14134

Total Controls

1284876

Contributing Studies
Namen_casesn_controls
UKBB_EUR1305370602
DECODE_EUR1897273257
EstBB_EUR313138272
GENCOVID_EUR7342472
FinnGen_FIN357238354
genomicsengland100kgp_EUR21862302
SPGRX_EUR362302
Helix_EUR1785441
Lifelines_EUR35825213
MGI_EUR12251458
MVP_EUR15207600
NTR_EUR1455252
PHBB_EUR15129966
Stanford_EUR109191
INTERVAL_EUR16141674
BQC19_EUR206327
Ancestry_EUR241714933
Amsterdam_UMC_COVID_study_group_EUR1081413
BelCovid_EUR1091484
HOSTAGE_EUR16102205
SweCovid_EUR783778
genomicc_EUR16768380
Downloads

GRCh37 liftover: COVID19_HGI_C2_ALL_eur_leave_23andme_20201020.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_C2_ALL_eur_leave_23andme_20201020.b37.txt.gz.tbi

GRCh37 (filtered): COVID19_HGI_C2_ALL_eur_leave_23andme_20201020.b37_1.0E-5.txt

GRCh38: COVID19_HGI_C2_ALL_eur_leave_23andme_20201020.txt.gz

GRCh38 (.tbi): COVID19_HGI_C2_ALL_eur_leave_23andme_20201020.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_C2_ALL_eur_leave_23andme_20201020.txt.gz_1.0E-5.txt

D1_ALL
Phenotype

Predicted covid from self-reported symptoms vs. predicted or self-reported non-covid

Population

All

Total Cases

3204

Total Controls

35728

Contributing Studies
Namen_casesn_controls
GS_EUR1323610
GeneRISK_EUR1543451
Helix_EUR6054778
Lifelines_EUR142716833
NTR_EUR6034669
RS_EUR2832387
Downloads

GRCh37 liftover: COVID19_HGI_D1_ALL_20201020.b37.txt.gz

GRCh37 (.tbi): COVID19_HGI_D1_ALL_20201020.b37.txt.gz.tbi

GRCh37 (filtered): COVID19_HGI_D1_ALL_20201020.b37_1.0E-5.txt

GRCh38: COVID19_HGI_D1_ALL_20201020.txt.gz

GRCh38 (.tbi): COVID19_HGI_D1_ALL_20201020.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_D1_ALL_20201020.txt.gz_1.0E-5.txt

Contributing studies