Journal of Gastroenterology

, Volume 51, Issue 7, pp 672–681 | Cite as

Genetic characteristics of inflammatory bowel disease in a Japanese population

  • Yuta Fuyuno
  • Keiko Yamazaki
  • Atsushi Takahashi
  • Motohiro Esaki
  • Takaaki Kawaguchi
  • Masakazu Takazoe
  • Takayuki Matsumoto
  • Toshiyuki Matsui
  • Hiroki Tanaka
  • Satoshi Motoya
  • Yasuo Suzuki
  • Yutaka Kiyohara
  • Takanari Kitazono
  • Michiaki KuboEmail author
Original Article—Alimentary Tract



Crohn’s disease (CD) and ulcerative colitis (UC) are two major forms of inflammatory bowel disease (IBD). Meta-analyses of genome-wide association studies (GWAS) have identified 163 susceptibility loci for IBD among European populations; however, there is limited information for IBD susceptibility in a Japanese population.


We performed a GWAS using imputed genotypes of 743 IBD patients (372 with CD and 371 with UC) and 3321 controls. Using 100 tag single-nucleotide polymorphisms (SNPs) (P < 5 × 10−5), a replication study was conducted with an independent set of 1310 IBD patients (949 with CD and 361 with UC) and 4163 controls. In addition, 163 SNPs identified by a European IBD GWAS were genotyped, and genetic backgrounds were compared between the Japanese and European populations.


In the IBD GWAS, two East Asia-specific IBD susceptibility loci were identified in the Japanese population: ATG16L2FCHSD2 and SLC25A15ELF1WBP4. Among 163 reported SNPs in European IBD patients, significant associations were confirmed in 18 (8 CD-specific, 4 UC-specific, and 6 IBD-shared). In Japanese CD patients, genes in the Th17–IL23 pathway showed stronger genetic effects, whereas the association of genes in the autophagy pathway was limited. The association of genes in the epithelial barrier and the Th17–IL23R pathways were similar in the Japanese and European UC populations.


We confirmed two IBD susceptibility loci as common for CD and UC, and East Asian-specific. The genetic architecture in UC appeared to be similar between Europeans and East Asians, but may have some differences in CD.


Crohn’s disease Ulcerative colitis Genome-wide association study Inflammatory bowel disease Ethnic difference 



The authors would like to thank all the patients and their families for their contribution to this project; we also thank the residents of Hisayama for their participation, all the members of the Division of Health and Welfare of Hisayama for their cooperation, and the many members of the Hisayama study for their assistance. In addition, we express our gratitude to the members of the Pharma SNP Consortium, the members of the BioBank Japan project, the Rotary Club of Osaka-Midosuji District 2660 Rotary International in Japan, and Mikiko Endo, Kyota Ashikawa, and other members of the Laboratory for Genotyping Development for their technical assistance. This work was supported by a grant from the BioBank Japan Project and, in part, by a Grant-in-Aid for Scientific Research (B) (26293180) funded by the Ministry of Education, Culture, Sports, Science, and Technology, Japan.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

535_2015_1135_MOESM1_ESM.pdf (952 kb)
Supplementary material (PDF 952 kb)


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Copyright information

© Japanese Society of Gastroenterology 2015

Authors and Affiliations

  • Yuta Fuyuno
    • 1
    • 2
  • Keiko Yamazaki
    • 1
  • Atsushi Takahashi
    • 3
  • Motohiro Esaki
    • 2
  • Takaaki Kawaguchi
    • 4
  • Masakazu Takazoe
    • 4
  • Takayuki Matsumoto
    • 2
  • Toshiyuki Matsui
    • 5
  • Hiroki Tanaka
    • 6
  • Satoshi Motoya
    • 6
  • Yasuo Suzuki
    • 7
  • Yutaka Kiyohara
    • 8
  • Takanari Kitazono
    • 4
  • Michiaki Kubo
    • 9
    Email author
  1. 1.Laboratory for Genotyping Development, Center for Integrative Medical SciencesRIKEN Yokohama InstituteYokohamaJapan
  2. 2.Department of Medicine and Clinical Science, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
  3. 3.Laboratory for Statistical Analysis, Center for Integrative Medical SciencesRIKENYokohamaJapan
  4. 4.Division of Gastroenterology, Department of MedicineTokyo Yamate Medical CenterTokyoJapan
  5. 5.Department of GastroenterologyFukuoka University Chikushi HospitalFukuokaJapan
  6. 6.Department of GastroenterologySapporo-Kosei General HospitalSapporoJapan
  7. 7.Department of Internal Medicine, Faculty of MedicineToho UniversityChibaJapan
  8. 8.Department of Environmental Medicine, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
  9. 9.Center for Integrative Medical SciencesRIKEN Yokohama InstituteYokohamaJapan

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