Skip to content
NBDC Human Database

No datasets in the cart.

Go to the cart

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

JGAD001017

Type of data
Quantitative Trait Loci Phenotype Matrix
Access criteria
Controlled-access (Type I)
Total data volume
42.3 MB
File formats
  • TXT
  • GZIP
Research
hum0541
Date published
2026-06-03
Date modified
2026-06-03
DDBJ Search
JGAD001017 (opens in a new tab)
JGA Study
JGAS000874 (opens in a new tab)

Unrestricted-access files linked to this dataset

Download the URL list
FileLabelSizeCopy URL
63phenotypes.xlsx63 phenotypes11.7 KB

Analysis method

Genotyping by array

Materials and participants
BioBank Japan (BBJ) 1st cohort: 176,894 individuals
  • Subject count
    176,894
  • Cohort
    BioBank Japan
Sample description
DNA extracted from peripheral blood cells
  • Tissue
    Peripheral blood
Sample provider
N/A
Experimental method
Genotyping by array
Target
N/A
Platform
Illumina HumanExome
Illumina HumanOmniExpress
Illumina HumanOmniExpressExome
QC and filtering
Sample QC: We excluded samples with
(1) Sample call rate < 0.98
(2) Samples with sex mismatches
(3) non-East Asian ancestry
(4) Samples overlapping with those in the reference panels
Variant QC: We excluded variants with
(1) variant call rate < 0.99
(2) number of heterozygotes < 5
(3) Hardy-Weinberg equilibrium (P < 1 × 10-6)
(4) palindromic variants
Imputation
haplotype phasing: SHAPEIT2 (v.2.837)
imputation: Minimac4 (v.1.0.0)
Analysis method
genotyping: GenomeStudio (v2.0.5)
Variant count
15,907,072 SNVs
Data use policy
NBDC data sharing policy (JGAP000001)