title: Population-specific genome-wide mapping of expression quantitative trait loci in the colon of Han Chinese.
abstract: OBJECTIVE
  To establish the colonic expression quantitative trait locus map in Han Chinese population and provide a functional reference for interpreting genetic associations of diseases such as inflammatory bowel disease (IBD).
  
  
  METHODS
  Colonic mucosal biopsies and peripheral blood samples were obtained from 48 Chinese Han individuals (24 ulcerative colitis patients and 24 healthy controls). Transcription profiling was performed using human whole genome expression array. Genotyping was done using a population-specific genotype array. Imputation was performed using IMPUTE2. Association between genotypes and gene expression was analyzed using a Matrix Expression Quantitative Trait Loci (eQTL) R package to identify eQTL. We used ChIPpeakAnno R package for annotation of the eQTL. Linkage disequilibrium between the eQTL and IBD risk loci was also investigated.
  
  
  RESULTS
  We identified 6 377 single nucleotide polymorphism-transcript interactions (cis-eQTL) in the colon of the Chinese participants. Most of the eQTL located near the transcription starting sites and overlapped with histone modification marks on the genome. A significant proportion of the eQTL were found to be within transcription factor-binding sites. Two IBD risk loci were found to be colon cis-eQTL in Chinese individuals, and 51 cis-eQTL were identified in another 18 IBD risk loci.
  
  
  CONCLUSIONS
  This study defined a population-specific catalogue of colon eQTL in the Chinese population. Potential functional variants of IBD association signals were identified. We provided a useful reference dataset for fine mapping IBD risk loci and identifying causal variants in the Chinese Han population.
authors.affiliation: State Key Lab of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi Province, China.
authors.forename: Chang Cun
authors.initials: CC
authors.lastname: Guo
authors.affiliation: Department of Gastroenterology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China.
authors.forename: Ni
authors.initials: N
authors.lastname: Wei
authors.affiliation: State Key Lab of Cancer Biology, Fourth Military Medical University, Xi'an, Shaanxi Province, China.
authors.forename: Shu Hui
authors.initials: SH
authors.lastname: Liang
authors.affiliation: Department of Gastroenterology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China.
authors.forename: Biao Luo
authors.initials: BL
authors.lastname: Wang
authors.affiliation: Department of Gastroenterology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China.
authors.forename: Su Mei
authors.initials: SM
authors.lastname: Sha
authors.affiliation: Department of Gastroenterology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China.
authors.forename: Kai Chun
authors.initials: KC
authors.lastname: Wu
mesh_terms: D016022:Case-Control Studies; D003093:Colitis, Ulcerative / Q000235:genetics* / Q000378:metabolism; D003106:Colon / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D005787:Gene Frequency; D063990:Gene Ontology; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D042421:Histone Code / Q000235:genetics; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D014158:Transcription, Genetic
keywords: Chinese Han population; expression quantitative trait locus; inflammatory bowel diseases; single nucleotide polymorphisms; ulcerative colitis