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Dataset ID

NHA000200

Type of data
GWAS for serum levels of ALT, AST and GGT
Access criteria
Unrestricted-access
Total data volume
532 MB
File formats
  • XLSX
  • ZIP
Research
hum0496
Date published
2025-02-27
Date modified
2025-02-27
Secondary ID
hum0496.v1.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0496.v1.gwas.v1.zip532 MB
hum0496_v1_gwas_v1.xlsxDictionary file9.5 KB

Analysis method

Genotyping by array (GWAS)

Materials and participants
ALT: n=15,224 (OBi-Ryukyu n=8,440, BBJ-Ryukyu n=6,784)
AST: n=15,203 (OBi-Ryukyu n=8,406, BBJ-Ryukyu n=6,797)
GGT: n=14,496 (OBi-Ryukyu n=8,434, BBJ-Ryukyu n=6,062)
  • Health status
    Healthy
  • Subject count
    15,224 (Individual)
  • Cohort
    BioBank Japan, Okinawa Biobank
Sample description
DNAs extracted from peripheral blood cells or saliva
  • Tissue
    Peripheral blood, Saliva
  • Tumor / normal
    Normal
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Reagent kit
N/A
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Illumina Infinium Asian Screening Array
QC and filtering
Sample QC: sample call rate ≧0.98
Genotyping QC: SNP call rate ≧ 0.98, MAF ≧ 0.01, p-values for Hardy-Weinberg equilibrium (HWE) test > 1×10−6
Imputation QC: MAF ≧ 0.005, Rsq ≧ 0.7
Imputation
minimac4
Imputation: reference 3,256 Japanese WGS from the BBJ and 2,504 individuals from the 1KGP (phase3v5)
Variant count
ALT: 9,224,376 variants
AST: 9,222,117 variants
GGT: 9,235,975 variants
Processed data type
GWAS summary statistics
Phenotype data
Included
Data use policy
NBDC data sharing policy (JGAP000001)