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Dataset ID

NHA000163

Type of data
Fine-mapping for 79 phenotypes
Access criteria
Unrestricted-access
Total data volume
4.1 GB
File formats
  • HTML
  • ZIP
Research
hum0197
Date published
2021-12-21
Date modified
2021-12-21
Secondary ID
hum0197.v5.finemap.v1

Unrestricted-access files linked to this dataset

Download the URL list
Per page
20
2050100

21–40 / 80

FileLabelSizeCopy URL
hum0197.v5.finemap.Cat.v1.zipDisease name: Cataract / Abbreviation: Cataract / ICD10: H25/H263.0 MB
hum0197.v5.finemap.CeAn.v1.zipDisease name: Cerebral aneurysm / Abbreviation: CeAn / ICD10: I67.14.9 MB
hum0197.v5.finemap.Cir.v1.zipDisease name: Cirrhosis / Abbreviation: Cirrhosis / ICD10: K74.65.3 MB
hum0197.v5.finemap.DBP.v1.zipDisease name: Diastolic blood pressure / Abbreviation: DBP31.4 MB
hum0197.v5.finemap.EC.v1.zipDisease name: Esophageal cancer / Abbreviation: EsC / ICD10: C153.7 MB
hum0197.v5.finemap.EM.v1.zipDisease name: Endometriosis / Abbreviation: Endometriosis / ICD10: N803.0 MB
hum0197.v5.finemap.EOS.v1.zipDisease name: Eosinophil / Abbreviation: Eosino56.8 MB
hum0197.v5.finemap.GC.v1.zipDisease name: Gastric cancer / Abbreviation: GaC / ICD10: C165.7 MB
hum0197.v5.finemap.GD.v1.zipDisease name: Graves' disease / Abbreviation: GD / ICD10: E05.014.3 MB
hum0197.v5.finemap.GGT.v1.zipDisease name: γ-glutamyl transpeptidase / Abbreviation: GGT79.5 MB
hum0197.v5.finemap.GU.v1.zipDisease name: Gastric ulcer / Abbreviation: Gastric_Ulcer / ICD10: K253.8 MB
hum0197.v5.finemap.Gla.v1.zipDisease name: Glaucoma / Abbreviation: Glaucoma / ICD10: H4011.1 MB
hum0197.v5.finemap.Glucose.v1.zipDisease name: Glucose / Abbreviation: Glucose19.4 MB
hum0197.v5.finemap.HDLC.v1.zipDisease name: HDL-cholesterol / Abbreviation: HDLC60.8 MB
hum0197.v5.finemap.Hb.v1.zipDisease name: Hemoglobin / Abbreviation: Hb54.6 MB
hum0197.v5.finemap.HbA1c.v1.zipDisease name: HbA1c / Abbreviation: HbA1c32.4 MB
hum0197.v5.finemap.Hei.v2.zipDisease name: Height / Abbreviation: Height / v2: replaced with the fixed files569 MB
hum0197.v5.finemap.Ht.v1.zipDisease name: Hematocrit / Abbreviation: Ht68.8 MB
hum0197.v5.finemap.ILD.v1.zipDisease name: Interstitial lung disease / Abbreviation: IPF / ICD10: J84.1/J84.8/J84.94.1 MB
hum0197.v5.finemap.IS.v1.zipDisease name: Ischemic stroke / Abbreviation: IS / ICD10: I636.3 MB

21–40 / 80

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)