Population-specific genome-wide mapping of expression quantitative trait loci in the colon of Chinese Han people

Abstract

Aim

To establish the colonic expression quantitative trait locus map in Chinese Han population and provide functional reference for interpreting genetic associations of diseases such as inflammatory bowel disease.

Methods

Colon mucosal biopsies and peripheral blood samples were obtained from forty-eight Chinese Han individuals. 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 Matrix eQTL R package to identify expression quantitative trait loci (eQTL). We used ChIPpeakAnno R package for annotation of the eQTL. Linkage disequilibrium between the eQTL to inflammatory bowel disease risk loci was also investigated.

Results

We identified 6377 SNP-transcript interactions (cis eQTL) in the colon of the Chinese. Majority of the eQTL located near by 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 colonic cis eQTL in Chinese, and 51 eQTL were identified in another 18 IBD risk loci.

Conclusions:

This study defined a population-specific catalog of colonic eQTL in 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 Chinese Han population.

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