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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

NHA000158

Type of data
GWAS for 1,920 PBCs and 1,770 healthy controls
Access criteria
Unrestricted-access
Total data volume
83.6 MB
File formats
  • XLSX
  • ZIP
Research
hum0261
Date published
2021-01-19
Date modified
2021-01-19
Secondary ID
hum0261.v2.gwas.v1

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
hum0261_GWAS2_dd.xlsxDictionary file10.7 KB
hum0261_v2_gwas_v1.zip83.6 MB

Analysis method

Genotyping by array

Materials and participants
1,920 PBCs (ICD10: K743) and 1,770 healthy controls
  • Health status
    Mixed
  • Subject count
    3690 (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
Reference genome
GRCh37
QC and filtering
Sample QCs: sample call rate < 0.97, closely related samples by PRIMUS (PI_HAT > 0.09375), outlier from Japanese cluster by PCA (Smirnov-Grubbs test with a Bonferroni corrected P < 0.05)
SNP QCs: SNP call rate < 0.99, HWE P < 0.0001, MAF < 0.05
Imputation
Eagle v2.3.2 for haplotype phasing
Analysis method
ASI: Genotyping Console ver. 4.2.0.26
Japonica: Affymetrix Power Tools ver. 1.18.2
IMPUTE4 v1.0 for genotype imputation with 2KJPN reference panel
Variant count
4,902,084 SNPs
Data use policy
NBDC data sharing policy (JGAP000001)