EQTL mapping identifies insertion- and deletion-specific eQTLs in multiple tissues

Jinyan Huang, Jun Chen, Jorge Esparza, Jun Ding, James T. Elder, Goncalo R. Abecasis, Young Ae Lee, G. Mark Lathrop, Miriam F. Moffatt, William O.C. Cookson, Liming Liang

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Genome-wide gene expression quantitative trait loci (eQTL) mapping have been focused on single-nucleotide polymorphisms and have helped interpret findings from diseases mapping studies. The functional effect of structure variants, especially short insertions and deletions (indel) has not been well investigated. Here we impute 1,380,133 indels based on the latest 1,000 Genomes Project panel into three eQTL data sets from multiple tissues. Imputation of indels increased 9.9% power and identifies indel-specific eQTLs for 325 genes. We find introns and vicinities of UTRs are more enriched of indel eQTLs and 3.6 (single-tissue)-9.2%(multi-tissue) of previous identified eSNPs were taggers of eindels. Functional analyses identifies epigenetics marks, gene ontology categories and disease GWAS loci affected by SNPs and indels eQTLs showing tissue-consistent or tissue-specific effects. This study provides new insights into the underlying genetic architecture of gene expression across tissues and new resource to interpret function of diseases and traits associated structure variants.

Original languageEnglish (US)
Article number6821
JournalNature communications
StatePublished - May 8 2015

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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