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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

1–20 / 80

FileLabelSizeCopy URL
hum0197.v5.finemap.AD.v1.zipDisease name: Atopic dermatitis / Abbreviation: AD / ICD10: L2019.3 MB
hum0197.v5.finemap.AF.v1.zipDisease name: Atrial fibrillation / Abbreviation: AFib / ICD10: I4835.0 MB
hum0197.v5.finemap.AG.v1.zipDisease name: Albumin/Globulin ratio / Abbreviation: AG70.7 MB
hum0197.v5.finemap.AID.v1.zipDisease name: Autoimmune disease / Abbreviation: AID / ICD10: M3511.9 MB
hum0197.v5.finemap.ALP.v1.zipDisease name: Alkaline phosphatase / Abbreviation: ALP55.3 MB
hum0197.v5.finemap.ALT.v2.zipDisease name: Alanine aminotransferase / Abbreviation: ALT / v2: replaced with the fixed files43.9 MB
hum0197.v5.finemap.AST.v2.zipDisease name: Aspartate aminotransferase / Abbreviation: AST / v2: replaced with the fixed files49.2 MB
hum0197.v5.finemap.Alb.v1.zipDisease name: Albumin / Abbreviation: Alb32.1 MB
hum0197.v5.finemap.As.v1.zipDisease name: Asthma / Abbreviation: Asthma / ICD10: J4526.9 MB
hum0197.v5.finemap.BAS.v1.zipDisease name: Basophil / Abbreviation: Baso51.1 MB
hum0197.v5.finemap.BC.v1.zipDisease name: Breast cancer / Abbreviation: BrC / ICD10: C5011.4 MB
hum0197.v5.finemap.BMI.v1.zipDisease name: Body mass index / Abbreviation: BMI125 MB
hum0197.v5.finemap.BUN.v1.zipDisease name: Blood urea nitrogen / Abbreviation: BUN56.8 MB
hum0197.v5.finemap.BW.v1.zipDisease name: Body weight / Abbreviation: BW220 MB
hum0197.v5.finemap.CAD.v1.zipDisease name: Coronary artery disease / Abbreviation: CAD / ICD10: I200、I209、I21974.3 MB
hum0197.v5.finemap.CC.v1.zipDisease name: Colorectal cancer / Abbreviation: CRC / ICD10: C1820.4 MB
hum0197.v5.finemap.CL.v1.zipDisease name: Cholelithiasis / Abbreviation: Cholelithiasis / ICD10: K8020.6 MB
hum0197.v5.finemap.COPD.v1.zipDisease name: Chronic obstructive pulmonary disease / Abbreviation: COPD / ICD10: J447.6 MB
hum0197.v5.finemap.CRP.v1.zipDisease name: C-reactive protein / Abbreviation: CRP8.5 MB
hum0197.v5.finemap.Ca.v1.zipDisease name: Calcium / Abbreviation: Ca23.3 MB

1–20 / 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)