ArticleHuman genetics2018
Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS.
Article in Human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Genome-wide identification of associations between enhancer and alternative splicing in human and mouse.BMC genomics · 2022Article
- Enhancer-Gene Interaction Analyses Identified the Epidermal Growth Factor Receptor as a Susceptibility Gene for Type 2 Diabetes Mellitus.Diabetes & metabolism journal · 2021Article
- On fusion methods for knowledge discovery from multi-omics datasets.Computational and structural biotechnology journal · 2020Review
- A comparison of two workflows for regulome and transcriptome-based prioritization of genetic variants associated with myocardial mass.Genetic epidemiology · 2019Article
- Gene regulation and the architecture of complex human traits in the genomics era.Current opinion in psychology · 2019Review
- Integrative Approach to Reveal Cell Type Specificity and Gene Candidates for Psoriatic Arthritis Outside the MHC.Frontiers in genetics · 2019Article
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Authors and funding
7 authors.
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Abstract
Although Genome Wide Association Studies (GWAS) have led to many valuable insights into the genetic bases of common diseases over the past decade, the issue of missing heritability has surfaced, as the discovered main effect genetic variants found to date do not account for much of a trait's predicted genetic component. We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance. Each analyzed SNP pair consists of one SNP in a putative active enhancer and another SNP in a putative physically interacting gene promoter in a trait-relevant tissue. As a proof-of-principle case study, we used this approach to identify focused collections of SNP pairs that we analyzed in three independent Type 2 diabetes (T2D) GWAS. This approach led us to discover 35 significant SNP pairs, encompassing both novel signals and signals for which we have found orthogonal support from other sources. Nine of these pairs are consistent with eQTL results, two are consistent with our own capture C experiments, and seven involve signals supported by recent T2D literature.
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