ArticleAmerican journal of human genetics2013
Integrating GWAS and expression data for functional characterization of disease-associated SNPs: an application to follicular lymphoma.
Article in American journal of human genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it, 54 citations in OpenAlex.
- Pooled it
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- Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data.BioData mining · 2022Article
- Integrating Multimorbidity into a Whole-Body Understanding of Disease Using Spatial Genomics.Results and problems in cell differentiation · 2022Article
- Allele-specific expression: applications in cancer and technical considerations.Current opinion in genetics & development · 2021Review
- Integrating RNA-Seq With GWAS Reveals a Novel SNP in Immune-RelatedFrontiers in immunology · 2021Article
- Molecular mechanisms of coronary disease revealed using quantitative trait loci for TCF21 binding, chromatin accessibility, and chromosomal looping.Genome biology · 2020Article
- Functional Genomics of Healthy and Pathological Fetal Membranes.Frontiers in physiology · 2020Review
- Genomics of asthma, allergy and chronic rhinosinusitis: novel concepts and relevance in airway mucosa.Clinical and translational allergy · 2020Review
- Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology.American journal of human genetics · 2019Article
- Integrative Genomic Analysis Predicts CausativeCancer research · 2018Article
- Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS.Genome biology · 2017Article
- Genetic Regulation of Adipose Gene Expression and Cardio-Metabolic Traits.American journal of human genetics · 2017Article
- Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus.Human molecular genetics · 2017Article
- NCOA1 is a novel susceptibility gene for multiple myeloma in the Chinese population: A case-control study.PloS one · 2017Article
- Genetic factors underlying boron toxicity tolerance in rice: genome-wide association study and transcriptomic analysis.Journal of experimental botany · 2017Article
- Predictive long-range allele-specific mapping of regulatory variants and target transcripts.PloS one · 2017Article
- PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases.PLoS computational biology · 2016Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Development of post-GWAS (genome-wide association study) methods are greatly needed for characterizing the function of trait-associated SNPs. Strategies integrating various biological data sets with GWAS results will provide insights into the mechanistic role of associated SNPs. Here, we present a method that integrates RNA sequencing (RNA-seq) and allele-specific expression data with GWAS data to further characterize SNPs associated with follicular lymphoma (FL). We investigated the influence on gene expression of three established FL-associated loci-rs10484561, rs2647012, and rs6457327-by measuring their correlation with human-leukocyte-antigen (HLA) expression levels obtained from publicly available RNA-seq expression data sets from lymphoblastoid cell lines. Our results suggest that SNPs linked to the protective variant rs2647012 exert their effect by a cis-regulatory mechanism involving modulation of HLA-DQB1 expression. In contrast, no effect on HLA expression was observed for the colocalized risk variant rs10484561. The application of integrative methods, such as those presented here, to other post-GWAS investigations will help identify causal disease variants and enhance our understanding of biological disease mechanisms.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.