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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)
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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

JGAD000791

Type of data
SNP array data of 2680 patients with inflammatory bowel diseases
Access criteria
Controlled-access (Type I)
Total data volume
76.8 GB
File formats
  • CEL
Research
hum0166
Date published
2024-01-11
Date modified
2024-01-11
DDBJ Search
JGAD000791 (opens in a new tab)
JGA Study
JGAS000661 (opens in a new tab)

Analysis method

Genotyping by array

Materials and participants
inflammatory bowel diseases: 1221 + 2680 cases
Crohn's disease (ICD10: K509): 516 + 1175 cases
Ulcerative Colitis (ICD10: K519): 674 + 1459 cases
Gastrointestinal Behçet's disease (ICD10: M352): 16 >+ 43 cases
other inflammatory bowel diseases (ICD10: K523): 15 + 3 cases
  • Health status
    Affected
  • Subject count
    3901 (Individual)
Disease
Crohn's disease (K509)
Ulcerative Colitis (K519)
Gastrointestinal Behçet's disease (M352)
other inflammatory bowel diseases (K523)
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 Japonica Array
Reference genome
GRCh37
QC and filtering
・SNVs with low imputation quality
(with a posterior genotype probability of < 0.8 for each genotype or with info score < 0.5 for each variant)
・call rate < 0.97
・minor allele frequency (MAF) < 0.01 or 0.05
(0.01 for GWASs of > 50 cases, 0.05 for GWASs of low-frequency adverse events or conditional GWASs on rs116855232)
・Hardy-Weinberg equilibrium (HWE) p < 1 × 10^−6
Imputation
・EAGLE (v 2.4) for prephasing
・IMPUTE4 (v 1.0) ＋ 2KJPN (reference panel)
Analysis method
Affymetrix Power Tools (version 1.16.1, Affymetrix)
Variant count
5,831,032 SNPs
Data use policy
NBDC data sharing policy (JGAP000001)