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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

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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
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
hum0197.v5.finemap.InH.v1.zipDisease name: Inguinal hernia / Abbreviation: Inguinal_Hernia / ICD10: K401.6 MB
hum0197.v5.finemap.Kel.v1.zipDisease name: Keloid / Abbreviation: Keloid / ICD10: L91.06.1 MB
hum0197.v5.finemap.LDLC.v1.zipDisease name: LDL-cholesterol / Abbreviation: LDLC44.1 MB
hum0197.v5.finemap.LOY.v1.zipDisease name: Mosaic loss of chromosome Y / Abbreviation: LOY / ICD10: Q99840.4 MB
hum0197.v5.finemap.LYM.v1.zipDisease name: Lymphocyte / Abbreviation: Lym37.6 MB
hum0197.v5.finemap.LuC.v1.zipDisease name: Lung cancer / Abbreviation: LuC / ICD10: C348.6 MB
hum0197.v5.finemap.MAP.v1.zipDisease name: Mean arterial pressure / Abbreviation: MAP45.7 MB
hum0197.v5.finemap.MCH.v1.zipDisease name: Mean corpuscular hemoglobin / Abbreviation: MCH161 MB
hum0197.v5.finemap.MCHC.v1.zipDisease name: Mean corpuscular hemoglobin concentration / Abbreviation: MCHC63.9 MB
hum0197.v5.finemap.MCV.v1.zipDisease name: Mean corpuscular volume / Abbreviation: MCV183 MB
hum0197.v5.finemap.MI.v1.zipDisease name: Myocardial infarction / Abbreviation: MI / ICD10: I21/I22/I23/I24/I2554.4 MB
hum0197.v5.finemap.MON.v1.zipDisease name: Monocyte / Abbreviation: Mono75.3 MB
hum0197.v5.finemap.MP.v1.zipDisease name: Age at menopause / Abbreviation: Age_at_Menopause24.6 MB
hum0197.v5.finemap.MT.v1.zipDisease name: Malignant tumor / Abbreviation: Malignant_Neoplasms / ICD10: C00-C9712.3 MB
hum0197.v5.finemap.Men.v1.zipDisease name: Age at menarche / Abbreviation: Age_at_Menarche18.6 MB
hum0197.v5.finemap.NAP.v1.zipDisease name: Non-albumin protein / Abbreviation: NAP83.3 MB
hum0197.v5.finemap.NEU.v1.zipDisease name: Neutrophil / Abbreviation: Neutro36.9 MB
hum0197.v5.finemap.P.v1.zipDisease name: Phosphate / Abbreviation: P8.5 MB
hum0197.v5.finemap.PAD.v1.zipDisease name: Peripheral arterial disease / Abbreviation: PAD / ICD10: I73.94.7 MB
hum0197.v5.finemap.PLT.v1.zipDisease name: Platelet / Abbreviation: Plt192 MB
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

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)