ArticleGenome biology2022
Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 4 of them syntheses that pooled it.
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Who cites it
26 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Multi-population GWAS meta-analysis identifies bladder cancer susceptibility loci and highlights genetic regulation of smoking-related risk.Nature communications · 2026Pooled it
- Large-scale multi-trait genome-wide analysis for inflammatory bowel disease reveals new insights into its molecular mechanisms and emphasizes the roles of systemic immune regulation.Briefings in bioinformatics · 2025Pooled it
- Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population.Nature communications · 2023Pooled it
- Pulmonary Function and Blood DNA Methylation: A Multiancestry Epigenome-Wide Association Meta-analysis.American journal of respiratory and critical care medicine · 2022Pooled it
- EpiATLAS - a reference for human epigenomic research.bioRxiv : the preprint server for biology · 2026Article
- Smoking drives an epigenetic memory of aberrant hematopoiesis.medRxiv : the preprint server for health sciences · 2026Article
- Bidirectional Mendelian Randomization Suggests Causal Effects of 731 Immunophenotypes on Vitiligo Pathogenesis.Clinical, cosmetic and investigational dermatology · 2026Article
- Article
- Causal relationship between immune cells and venous thromboembolism: a bidirectional two-sample Mendelian randomization study.Thrombosis journal · 2025Article
- Genetic-by-age interaction analyses on complex traits in UK Biobank and their potential to identify effects on longitudinal trait change.Genome biology · 2024Article
- DNA-binding factor footprints and enhancer RNAs identify functional non-coding genetic variants.Genome biology · 2024Article
- Admixture Mapping of Chronic Kidney Disease and Risk Factors in Hispanic/Latino Individuals From Central America Country of Origin.Circulation. Genomic and precision medicine · 2024Article
- Non-coding variants impact cis-regulatory coordination in a cell type-specific manner.Genome biology · 2024Article
- Leveraging functional genomic annotations and genome coverage to improve polygenic prediction of complex traits within and between ancestries.Nature genetics · 2024Article
- Epigenomic insights into common human disease pathology.Cellular and molecular life sciences : CMLS · 2024Review
- FORGEdb: a tool for identifying candidate functional variants and uncovering target genes and mechanisms for complex diseases.Genome biology · 2024Article
- Causal relationship between plasma lipidome and four types of pancreatitis: a bidirectional Mendelian randomization study.Frontiers in endocrinology · 2024Article
- Associations between the New DNA-Methylation-Based Telomere Length Estimator, the Mediterranean Diet and Genetics in a Spanish Population at High Cardiovascular Risk.Antioxidants (Basel, Switzerland) · 2023Article
- Ancestry-driven metabolite variation provides insights into disease states in admixed populations.Genome medicine · 2023Article
- Identification of Candidate Genes Associated with Yak Body Size Using a Genome-Wide Association Study and Multiple Populations of Information.Animals : an open access journal from MDPI · 2023Article
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Authors and funding
13 authors.
Funding
Abstract
backgroundGenome-wide association study (GWAS) single nucleotide polymorphisms (SNPs) are known to preferentially co-locate to active regulatory elements in tissues and cell types relevant to disease aetiology. Further characterisation of associated cell type-specific regulation can broaden our understanding of how GWAS signals may contribute to disease risk.
resultsTo gain insight into potential functional mechanisms underlying GWAS associations, we developed FORGE2 ( https://forge2.altiusinstitute.org/ ), which is an updated version of the FORGE web tool. FORGE2 uses an expanded atlas of cell type-specific regulatory element annotations, including DNase I hotspots, five histone mark categories and 15 hidden Markov model (HMM) chromatin states, to identify tissue- and cell type-specific signals. An analysis of 3,604 GWAS from the NHGRI-EBI GWAS catalogue yielded at least one significant disease/trait-tissue association for 2,057 GWAS, including > 400 associations specific to epigenomic marks in immune tissues and cell types, > 30 associations specific to heart tissue, and > 60 associations specific to brain tissue, highlighting the key potential of tissue- and cell type-specific regulatory elements. Importantly, we demonstrate that FORGE2 analysis can separate previously observed accessible chromatin enrichments into different chromatin states, such as enhancers or active transcription start sites, providing a greater understanding of underlying regulatory mechanisms. Interestingly, tissue-specific enrichments for repressive chromatin states and histone marks were also detected, suggesting a role for tissue-specific repressed regions in GWAS-mediated disease aetiology.
conclusionIn summary, we demonstrate that FORGE2 has the potential to uncover previously unreported disease-tissue associations and identify new candidate mechanisms. FORGE2 is a transparent, user-friendly web tool for the integrative analysis of loci discovered from GWAS.
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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.