COVID19-hg GWAS meta-analyses round 3

Release Date

July 2, 2020

Study Abbreviations
Full NameAbbreviation
Genetic determinants of COVID-19 complications in the Brazilian populationBRACOVID
Genetic modifiers for COVID-19 related illnessBelCovid
deCODEDECODE
FinnGenFinnGen
GEN-COVID, reCOVIDGENCOVID
UK 100,000 Genomes Projectgenomicsengland100kgp_EUR
Genes & HealthGNH
Generation ScotlandGS
COVID19-Host(a)geHOSTAGE
Helix Exome+ COVID-19 PhenotypesHelix
UK Blood Donors CohortINTERVAL
LifeLines CytoSNPLifelinesCyto
LifeLines Global Screening ArrayLifelinesGsa
Netherlands Twin RegisterNTR
Partners Healthcare BiobankPHBB
Qatar Genome ProgramQGP
UK BiobankUKBB
Data Columns
Column NameDescription
#CHRchromosome
POSchromosome position in build 37
REFnon-effect allele
ALTeffect allele (beta is for this allele)
SNP#CHR:POS:REF:ALT
{STUDY}_AF_Allele2allele frequency in {STUDY}
{STUDY}_AF_fcallele frequency in {STUDY} / allele frequency in gnomAD v3 (1000000 if frequency in gnomAD is 0). Calculated based on each study's ancestry in gnomAD
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
Release Notes

Meta-analysis was done with inverse variance weighting. Analysis carried out on GRCh38; results also available through GRCh37 liftover. An AF filter of 0.0001 and an INFO filter of 0.6 was applied to each study prior to meta-analysis.

ANA_A2_V2
Phenotype

very severe respiratory confirmed covid vs. population

Population

All

Total Cases

536

Total Controls

329391

Contributing Studies
Namen_casesn_controls
GENCOVID_EUR3272461
UKBB_EUR108325397
BRACOVID_AMR1011533
Downloads

GRCh37 liftover: COVID19_HGI_ANA_A2_V2_20200701.b37.txt.gz

GRCh37 liftover (.tbi): COVID19_HGI_ANA_A2_V2_20200701.b37.txt.gz.tbi

GRCh37 liftover (filtered): COVID19_HGI_ANA_A2_V2_20200701.b37_1.0E-5.txt

GRCh38: COVID19_HGI_ANA_A2_V2_20200701.txt.gz

GRCh38 (.tbi): COVID19_HGI_ANA_A2_V2_20200701.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_ANA_A2_V2_20200701.txt.gz_1.0E-5.txt

ANA_B1_V2
Phenotype

hospitalized covid vs. not hospitalized covid

Population

All

Total Cases

928

Total Controls

2028

Contributing Studies
Namen_casesn_controls
UKBB_EUR784406
DECODE_EUR861462
FinnGen_FIN58160
Downloads

GRCh37 liftover: COVID19_HGI_ANA_B1_V2_20200701.b37.txt.gz

GRCh37 liftover (.tbi): COVID19_HGI_ANA_B1_V2_20200701.b37.txt.gz.tbi

GRCh37 liftover (filtered): COVID19_HGI_ANA_B1_V2_20200701.b37_1.0E-5.txt

GRCh38: COVID19_HGI_ANA_B1_V2_20200701.txt.gz

GRCh38 (.tbi): COVID19_HGI_ANA_B1_V2_20200701.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_ANA_B1_V2_20200701.txt.gz_1.0E-5.txt

ANA_B2_V2
Phenotype

hospitalized covid vs. population

Population

All

Total Cases

3199

Total Controls

897488

Contributing Studies
Namen_casesn_controls
HOSTAGE_EUR16102205
UKBB_EUR784419747
GENCOVID_EUR3662461
BRACOVID_AMR1761533
DECODE_EUR86223971
GNH_SAS6227353
FinnGen_FIN58218734
BelCovid_EUR571484
Downloads

GRCh37 liftover: COVID19_HGI_ANA_B2_V2_20200701.b37.txt.gz

GRCh37 liftover (.tbi): COVID19_HGI_ANA_B2_V2_20200701.b37.txt.gz.tbi

GRCh37 liftover (filtered): COVID19_HGI_ANA_B2_V2_20200701.b37_1.0E-5.txt

GRCh38: COVID19_HGI_ANA_B2_V2_20200701.txt.gz

GRCh38 (.tbi): COVID19_HGI_ANA_B2_V2_20200701.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_ANA_B2_V2_20200701.txt.gz_1.0E-5.txt

ANA_C1_V2
Phenotype

covid vs. lab/self-reported negative

Population

All

Total Cases

3523

Total Controls

36634

Contributing Studies
Namen_casesn_controls
DECODE_EUR159729065
UKBB_EUR11905014
genomicsengland100kgp_EUR147562
INTERVAL_EUR137472
NTR_EUR121108
GNH_SAS114256
PHBB_EUR97904
UKBB_AFR63125
UKBB_CSA57128
Downloads

GRCh37 liftover: COVID19_HGI_ANA_C1_V2_20200701.b37.txt.gz

GRCh37 liftover (.tbi): COVID19_HGI_ANA_C1_V2_20200701.b37.txt.gz.tbi

GRCh37 liftover (filtered): COVID19_HGI_ANA_C1_V2_20200701.b37_1.0E-5.txt

GRCh38: COVID19_HGI_ANA_C1_V2_20200701.txt.gz

GRCh38 (.tbi): COVID19_HGI_ANA_C1_V2_20200701.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_ANA_C1_V2_20200701.txt.gz_1.0E-5.txt

ANA_C2_V2
Phenotype

covid vs. population

Population

All

Total Cases

6696

Total Controls

1073072

Contributing Studies
Namen_casesn_controls
HOSTAGE_EUR16102205
DECODE_EUR1597282150
UKBB_EUR1190419341
GENCOVID_EUR4072461
FinnGen_FIN264203376
LifelinesGsa_EUR24718403
QGP_ARAB19713698
BRACOVID_AMR1761533
genomicsengland100kgp_EUR147562
INTERVAL_EUR13741699
Helix_EUR1333404
NTR_EUR1214648
GNH_SAS11427301
PHBB_EUR9728927
LifelinesCyto_EUR826488
UKBB_AFR636573
UKBB_CSA578819
BelCovid_EUR571484
Downloads

GRCh37 liftover: COVID19_HGI_ANA_C2_V2_20200701.b37.txt.gz

GRCh37 liftover (.tbi): COVID19_HGI_ANA_C2_V2_20200701.b37.txt.gz.tbi

GRCh37 liftover (filtered): COVID19_HGI_ANA_C2_V2_20200701.b37_1.0E-5.txt

GRCh38: COVID19_HGI_ANA_C2_V2_20200701.txt.gz

GRCh38 (.tbi): COVID19_HGI_ANA_C2_V2_20200701.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_ANA_C2_V2_20200701.txt.gz_1.0E-5.txt

ANA_D1_V2
Phenotype

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

Population

All

Total Cases

1865

Total Controls

29174

Contributing Studies
Namen_casesn_controls
NTR_EUR6954284
LifelinesGsa_EUR45812836
Helix_EUR3983959
LifelinesCyto_EUR1824485
GS_EUR1323610
Downloads

GRCh37 liftover: COVID19_HGI_ANA_D1_V2_20200701.b37.txt.gz

GRCh37 liftover (.tbi): COVID19_HGI_ANA_D1_V2_20200701.b37.txt.gz.tbi

GRCh37 liftover (filtered): COVID19_HGI_ANA_D1_V2_20200701.b37_1.0E-5.txt

GRCh38: COVID19_HGI_ANA_D1_V2_20200701.txt.gz

GRCh38 (.tbi): COVID19_HGI_ANA_D1_V2_20200701.txt.gz.tbi

GRCh38 (filtered): COVID19_HGI_ANA_D1_V2_20200701.txt.gz_1.0E-5.txt

Contributing studies