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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
We apologize for any inconvenience this may cause and appreciate your understanding.

We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

NHA000156

Type of data
GWAS for 1,953 PBCs and 3,690 healthy controls
Access criteria
Unrestricted-access
Total data volume
16.7 MB
File formats
  • XLSX
  • ZIP
Research
hum0261
Date published
2021-01-08
Date modified
2021-01-08
Secondary ID
hum0261.v1.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0261_GWAS_dd.xlsxDictionary file10.7 KB
hum0261_v1_gwas_v1.zip16.7 MB

Analysis method

Genotyping by array

Materials and participants
1,953 PBCs (ICD10: K743) and 3,690 healthy controls
  • Health status
    Mixed
  • Subject count
    5643 (Individual)
Disease
PBCs (K743)
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
Axiom 2.0 Reagent Kit
Platform
Affymetrix Axiom Genome-Wide ASI 1 Array
Affymetrix Japonica Array
QC and filtering
HWE: P≥10^-6, Imputation info score: ≥ 0.5
Individuals call rate ≥ 98%, SNPs call rate ≥ 98%, MAF ≥ 1%
Imputation
IMPUTE4 (with 2KJPN reference panel)
Analysis method
ASI: Genotyping Console ver. 4.2.0.26
Japonica: Affymetrix Power Tools ver. 1.18.2
Variant count
1,022,237 SNVs
Data use policy
NBDC data sharing policy (JGAP000001)