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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

41–60 / 80

FileLabelSizeCopy URL
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

41–60 / 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)