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Dataset ID

NHA000194

Type of data
GWAS for POP
Access criteria
Unrestricted-access
Total data volume
163 MB
File formats
  • XLSX
  • ZIP
Research
hum0467
Date published
2024-10-02
Date modified
2024-10-02
Secondary ID
hum0467.v1.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0467.v1.gwas.v1.zip162 MB
hum0467_header_definition.xlsxDictionary file9.5 KB

Analysis method

Genotyping by array (GWAS)

Materials and participants
[GWAS-1]
POP (ICD-10: N81): BBJ_Hondo n = 418, Controls: BBJ_Hondo n = 68,040
[GWAS-2]
POP: POP_Hondo n = 128, Controls: OBi_Hondo n = 387
[GWAS-3]
POP: BBJ_Ryukyu n = 29, Controls: BBJ_Ryukyu n = 5,852
[GWAS-4]
POP: POP_Ryukyu n = 196, Controls: OBi_Ryukyu n = 2,346
  • Health status
    Mixed
  • Subject count
    77,396 (Individual)
  • Cohort
    BioBank Japan, Okinawa Biobank
  • Population
    Hondo, Ryukyu
Disease
POP (N81)
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
N/A
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
Illumina Infinium Asian Screening Array
QC and filtering
Sample QC: sample call rates ≧ 0.98
Genotyping QC: SNP call rate ≧ 0.98 (OBi, POP) or 0.99 (BBJ), MAF ≧ 0.01, p-values for Hardy-Weinberg equilibrium (HWE) test ≧ 1×10⁻⁶
Imputation QC: MAF ≥ 0.005 and imputation score (Rsq) ≥ 0.7
Imputation
minimac4
Imputation: reference 1KGP3+JEWEL_3K
Variant count
9,862,117 variants
Data use policy
NBDC data sharing policy (JGAP000001)