ArticleAmerican journal of human genetics2015
Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci.
Article in American journal of human genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 3 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
83 citing papers in PubMed, 3 syntheses or guidelines pooled it, 130 citations in OpenAlex.
- Cross-Trait Meta-Analysis Reveals a Genetic Link between Inflammation and Aging in Giant Cell Arteritis.Aging and disease · 2025Pooled it
- A Review of Statistical Methods for Identifying Trait-Relevant Tissues and Cell Types.Frontiers in genetics · 2020Pooled it
- Functional implications of disease-specific variants in loci jointly associated with coeliac disease and rheumatoid arthritis.Human molecular genetics · 2016Pooled it
- Identifying independent causal cell types for human diseases and risk variants.Cell genomics · 2026Article
- X-linked spondyloepiphyseal dysplasia tarda misdiagnosed as growth hormone deficiency: identification of a novel intronic TRAPPC2 variant by whole-genome sequencing.BMC pediatrics · 2026Article
- Genome-Wide Discovery Reveals Adipose-Specific and Systemic Regulators of Insulin Resistance.medRxiv : the preprint server for health sciences · 2026Article
- Multi-omics approaches for understanding gene-environment interactions in noncommunicable diseases: techniques, translation, and equity issues.Human genomics · 2025Review
- Untangling the genetics of beta cell dysfunction and death in type 1 diabetes.Molecular metabolism · 2024Review
- Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects.American journal of human genetics · 2024Article
- An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants.Genome research · 2023Article
- Functional Enrichment Analysis Identifying Regulatory Information Associated with Human Fracture.Calcified tissue international · 2023Article
- Evaluating the Contribution of Cell Type-Specific Alternative Splicing to Variation in Lipid Levels.Circulation. Genomic and precision medicine · 2023Article
- A scalable Bayesian functional GWAS method accounting for multivariate quantitative functional annotations with applications for studying Alzheimer disease.HGG advances · 2022Article
- Single-Cell Chromatin Accessibility Data Combined with GWAS Improves Detection of Relevant Cell Types in 59 Complex Phenotypes.International journal of molecular sciences · 2022Article
- Human Genomics and Drug Development.Cold Spring Harbor perspectives in medicine · 2022Review
- Integrative analysis of 3604 GWAS reveals multiple novel cell type-specific regulatory associations.Genome biology · 2022Article
- echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline.Bioinformatics (Oxford, England) · 2022Article
- Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data.Briefings in bioinformatics · 2021Article
- Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility.Nature communications · 2021Article
- Fine-mapping, trans-ancestral and genomic analyses identify causal variants, cells, genes and drug targets for type 1 diabetes.Nature genetics · 2021Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 7 institutions in 3 countries.
Funding
Abstract
Identifying genomic annotations that differentiate causal from trait-associated variants is essential to fine mapping disease loci. Although many studies have identified non-coding functional annotations that overlap disease-associated variants, these annotations often colocalize, complicating the ability to use these annotations for fine mapping causal variation. We developed a statistical approach (Genomic Annotation Shifter [GoShifter]) to assess whether enriched annotations are able to prioritize causal variation. GoShifter defines the null distribution of an annotation overlapping an allele by locally shifting annotations; this approach is less sensitive to biases arising from local genomic structure than commonly used enrichment methods that depend on SNP matching. Local shifting also allows GoShifter to identify independent causal effects from colocalizing annotations. Using GoShifter, we confirmed that variants in expression quantitative trail loci drive gene-expression changes though DNase-I hypersensitive sites (DHSs) near transcription start sites and independently through 3' UTR regulation. We also showed that (1) 15%-36% of trait-associated loci map to DHSs independently of other annotations; (2) loci associated with breast cancer and rheumatoid arthritis harbor potentially causal variants near the summits of histone marks rather than full peak bodies; (3) variants associated with height are highly enriched in embryonic stem cell DHSs; and (4) we can effectively prioritize causal variation at specific loci.
Indexed as
Identifiers
What OpenQuestion holds
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.