Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

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

61–80 / 80

FileLabelSizeCopy URL
hum0197.v5.finemap.PP.v1.zipDisease name: Pulse pressure / Abbreviation: PP30.0 MB
hum0197.v5.finemap.PrC.v1.zipDisease name: Prostate cancer / Abbreviation: PrC / ICD10: C6133.4 MB
hum0197.v5.finemap.RA.v1.zipDisease name: Rheumatoid arthritis / Abbreviation: RA / ICD10: M068.3 MB
hum0197.v5.finemap.RBC.v1.zipDisease name: Red blood cell / Abbreviation: RBC125 MB
hum0197.v5.finemap.SBP.v1.zipDisease name: Systolic blood pressure / Abbreviation: SBP46.5 MB
hum0197.v5.finemap.T1D.v1.zipDisease name: Type 1 diabetes / Abbreviation: T1D / ICD10: E103.0 MB
hum0197.v5.finemap.T2D.v1.zipDisease name: Type 2 diabetes / Abbreviation: T2D / ICD10: E11135 MB
hum0197.v5.finemap.TBil.v1.zipDisease name: Total bilirubin / Abbreviation: Tbil19.1 MB
hum0197.v5.finemap.TC.v1.zipDisease name: Total cholesterol / Abbreviation: TC61.9 MB
hum0197.v5.finemap.TG.v1.zipDisease name: Triglycerides / Abbreviation: TG40.2 MB
hum0197.v5.finemap.TP.v1.zipDisease name: Total protein / Abbreviation: TP49.4 MB
hum0197.v5.finemap.UA.v1.zipDisease name: Uric acids / Abbreviation: UA55.5 MB
hum0197.v5.finemap.UF.v1.zipDisease name: Uterine fibroids / Abbreviation: UF / ICD10: D2527.9 MB
hum0197.v5.finemap.Uro.v1.zipDisease name: Urolithiasis / Abbreviation: Urolithiasis / ICD10: N20.0/N20.224.5 MB
hum0197.v5.finemap.WBC.v1.zipDisease name: White blood cell / Abbreviation: WBC107 MB
hum0197.v5.finemap.cpd.v1.zipDisease name: Cigarettes per day / Abbreviation: Smoking_CPD7.8 MB
hum0197.v5.finemap.eGFR.v1.zipDisease name: Estimated glomerular filtration rate / Abbreviation: eGFR69.4 MB
hum0197.v5.finemap.ens.v1.zipDisease name: Smoking (ever vs never) / Abbreviation: Smoking_Ever_Never1.6 MB
hum0197.v5.finemap.sCr.v1.zipDisease name: Serum creatinine / Abbreviation: sCr118 MB
hum0197_v5_finemap_v1_header.htmlDictionary file36.5 KB

61–80 / 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)