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Dataset ID

NHA000162

Type of data
GWAS for 215 phenotypes
Access criteria
Unrestricted-access
Total data volume
567 GB
File formats
  • HTML
  • ZIP
Research
hum0197
Date published
2021-03-22
Date modified
2021-03-22
Secondary ID
hum0197.v3.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
Per page
20
2050100

341–360 / 601

FileLabelSizeCopy URL
hum0197.v3.EUR.PeD.v1.zipDisease name: Periodontal disease / Abbreviation: Periodontal_Disease / ICD10: K05/K061.6 GB
hum0197.v3.EUR.Per.v1.zipDisease name: Pericarditis / Abbreviation: Pericarditis / ICD10: I30527 MB
hum0197.v3.EUR.Pl.v1.zipDisease name: Pleurisy / Abbreviation: Pleurisy / ICD10: J90/J91520 MB
hum0197.v3.EUR.Pn.v1.zipDisease name: Pneumonia / Abbreviation: Pneumonia / ICD10: J15516 MB
hum0197.v3.EUR.Pne.v1.zipDisease name: Pneumoconiosis / Abbreviation: Pneumoconiosis / ICD10: J60/J61/J62/J63/J64532 MB
hum0197.v3.EUR.Pneu.v1.zipDisease name: Pneumothorax / Abbreviation: Pneumothorax / ICD10: J93527 MB
hum0197.v3.EUR.Pol.v1.zipDisease name: Pollinosis / Abbreviation: Pollinosis / ICD10: J30522 MB
hum0197.v3.EUR.PrC.v1.zipDisease name: Prostate cancer / Abbreviation: PrC / ICD10: C61516 MB
hum0197.v3.EUR.PsV.v1.zipDisease name: Psoriasis vulgaris / Abbreviation: PsV / ICD10: L40520 MB
hum0197.v3.EUR.Pye.v1.zipDisease name: Pyelonephritis / Abbreviation: Pyelonephritis / ICD10: N10517 MB
hum0197.v3.EUR.RA.v1.zipDisease name: Rheumatoid arthritis / Abbreviation: RA / ICD10: M06518 MB
hum0197.v3.EUR.RD.v1.zipDisease name: Retinal detachment / Abbreviation: Retinal_Detachment / ICD10: H33519 MB
hum0197.v3.EUR.RF.v1.zipDisease name: Rheumatic fever / Abbreviation: Rheumatic_fever / ICD10: I00/I01527 MB
hum0197.v3.EUR.RW.v1.zipDisease name: Ringworm / Abbreviation: Ringworm / ICD10: B351.5 GB
hum0197.v3.EUR.SAP.v1.zipDisease name: Stable angina pectoris / Abbreviation: SAP / ICD10: I20.91.6 GB
hum0197.v3.EUR.SAS.v1.zipDisease name: Sleep apnea syndrome / Abbreviation: SAS / ICD10: G47.3516 MB
hum0197.v3.EUR.SCS.v1.zipDisease name: Spinal canal stenosis / Abbreviation: Spinal_canal_stenosis / ICD10: M48.0518 MB
hum0197.v3.EUR.SD.v1.zipDisease name: Substance dependence / Abbreviation: Substance_Dependence / ICD10: F19526 MB
hum0197.v3.EUR.SH.v1.zipDisease name: Subarachnoid hemorrhage / Abbreviation: Subarachnoid_Hemorrhage / ICD10: I60525 MB
hum0197.v3.EUR.SLE.v1.zipDisease name: Systemic lupus erythematosus / Abbreviation: SLE / ICD10: M32530 MB

341–360 / 601

Analysis method

genome wide SNPs

Materials and participants
Biobank Japan (n = 179,000), UK biobank (n = 361,000), FinnGen (n = 136,000), no. Phenotypes: 220
  • Health status
    Mixed
  • Subject count
    676,000 (Individual)
  • Cohort
    BioBank Japan, FinnGen, UK Biobank
  • Population
    British, Finnish, Japanese
Sample description
DNAs extracted from peripheral blood cells
  • Tissue
    Peripheral blood
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
FinnGen1 ThermoFisher Array
HumanExome BeadChip Kit
HumanOmniExpress BeadChip Kit
HumanOmniExpressExome BeadChip Kit
UK BiLEVE Axiom Array
UK Biobank Axiom Array
Platform
Applied Biosystems UK BiLEVE Axiom Array
Applied Biosystems UK Biobank Axiom Array
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Thermo Fisher Scientific FinnGen1 ThermoFisher Array
QC and filtering
BBJ: We included imputed variants with Rsq > 0.7.
UK Biobank: We excluded the variants with (i) INFO score ≤ 0.8, (ii) MAF ≤ 0.0001 (except for missense and protein-truncating variants annotated by VEP, which were excluded if MAF ≤ 1 × 10-6), and (iii) PHWE ≤ 1 × 10-10.
FinnGen: We excluded variants with an imputation INFO score < 0.8 or MAF < 0.0001.
Imputation
BBJ: Eagle, Minimac3
UK Biobank: IMPUTE4
FinnGen: beagle4.1
Analysis method
For binary traits, SAIGE software was used with age, age2, sex, age×sex, age2×sex, and top 20 principal components as covariates. For quantitative traits (biomarkers), BOLT-LMM or plink software was used with the same covariates.
Variant count
BBJ: 13,530,797 variants
UK Biobank: 13,791,467 variants
FinnGen: 16,859,359 variants
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)