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Dataset ID

NHA000164

Type of data
GWAS for 10 phenotypes
Access criteria
Unrestricted-access
Total data volume
10.4 GB
File formats
  • TXT
  • HTML
Research
hum0197
Date published
2021-12-21
Date modified
2021-12-21
Secondary ID
hum0197.v5.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0197.v5.gwas.AG.v1.txt.gzDisease name: Albumin/Globulin ratio / Abbreviation: AG591 MB
hum0197.v5.gwas.AID.v1.txt.gzDisease name: Autoimmune disease / Abbreviation: AID / ICD10: M351.6 GB
hum0197.v5.gwas.CAD.v1.txt.gz1.6 GB
hum0197.v5.gwas.MP.v1.txt.gzDisease name: Age at menopause / Abbreviation: Age_at_Menopause589 MB
hum0197.v5.gwas.MT.v1.txt.gzDisease name: Malignant tumor / Abbreviation: Malignant_Tumor / ICD10: C00-C971.6 GB
hum0197.v5.gwas.Men.v1.txt.gzDisease name: Age at menarche / Abbreviation: Age_at_Menarche591 MB
hum0197.v5.gwas.NAP.v1.txt.gzDisease name: Non-albumin protein / Abbreviation: NAP591 MB
hum0197.v5.gwas.P.v1.txt.gzDisease name: Phosphate / Abbreviation: P589 MB
hum0197.v5.gwas.cpd.v1.txt.gzDisease name: Cigarettes per day / Abbreviation: Smoking_CPD590 MB
hum0197.v5.gwas.eGFR.v1.txt.gzDisease name: Estimated glomerular filtration rate / Abbreviation: eGFR591 MB
hum0197.v5.gwas.ens.v1.txt.gzDisease name: Smoking (ever vs never) / Abbreviation: Smoking_Ever_Never1.6 GB
hum0197_v5_finemap_v1_header.htmlDictionary file36.5 KB

Analysis method

genome wide SNPs

Materials and participants
Biobank Japan (n = 179,000), no. Phenotypes: 79
  • Health status
    Mixed
  • Subject count
    179,000 (Individual)
  • Cohort
    BioBank Japan
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
HumanExome BeadChip Kit
HumanOmniExpress BeadChip Kit
HumanOmniExpressExome BeadChip Kit
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Reference genome
GRCh37
QC and filtering
GWAS: We included imputed variants with Rsq > 0.7. For binary traits, variants with MAC < 10 were additionally excluded.
Fine-mapping: We defined fine-mapping regions based on a 3 Mb window around each lead variant and merged regions if they overlapped. We excluded the major histocompatibility complex (MHC) region (chr 6: 25-36 Mb) from analysis due to extensive LD structure in the region. For each method, we only included variants from successfully fine-mapped regions while excluding those from failed regions (e.g., due to conversion failure or available memory restrictions).
Imputation
Eagle, Minimac3
Analysis method
GWAS: 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 was used with the same covariates.
Fine-mapping: FINEMAP and SuSiE were used with GWAS summary statistics and in-sample dosage LD, allowing up to 10 causal variants per region.
Variant count
13,531,752 variants
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)