ArticleNucleic acids research2015
Identifying causal regulatory SNPs in ChIP-seq enhancers.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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
26 citing papers in PubMed, 45 citations in OpenAlex.
- Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles.NPJ systems biology and applications · 2024Article
- Identification of ancestral gnathostome Gli3 enhancers with activity in mammals.Development, growth & differentiation · 2024Article
- SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes.bioRxiv : the preprint server for biology · 2023Article
- Genetic Effects of ITPK1 Polymorphisms on the Risk of Neural Tube Defects: a Population-Based Study.Reproductive sciences (Thousand Oaks, Calif.) · 2023Article
- A map of cis-regulatory modules and constituent transcription factor binding sites in 80% of the mouse genome.BMC genomics · 2022Article
- PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes.Database : the journal of biological databases and curation · 2022Article
- Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations.Genome research · 2022Article
- Mer Tyrosine Kinase (MERTK) modulates liver fibrosis progression and hepatocellular carcinoma development.Frontiers in immunology · 2022Article
- Genetic variants associated with alcohol dependence co-ordinate regulation of ADH genes in gastrointestinal and adipose tissues.Scientific reports · 2020Article
- Prospects for sociogenomics in avian cooperative breeding and parental care.Current zoology · 2020Article
- Mechanistic interpretation of non-coding variants for discovering transcriptional regulators of drug response.BMC biology · 2019Article
- Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2.Nucleic acids research · 2019Article
- Allele-specific enhancers mediate associations between LCAT and ABCA1 polymorphisms and HDL metabolism.PloS one · 2019Article
- Dichotomy in redundant enhancers points to presence of initiators of gene regulation.BMC genomics · 2018Article
- Integrative Genomic Analysis Predicts CausativeCancer research · 2018Article
- SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome.Bioinformatics (Oxford, England) · 2018Article
- Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells.Genome medicine · 2017Article
- Quantifying deleterious effects of regulatory variants.Nucleic acids research · 2017Article
- Finding the Sources of Missing Heritability within Rare Variants Through Simulation.Bioinformatics and biology insights · 2017Article
- Evaluating the impact of single nucleotide variants on transcription factor binding.Nucleic acids research · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
Thousands of non-coding SNPs have been linked to human diseases in the past. The identification of causal alleles within this pool of disease-associated non-coding SNPs is largely impossible due to the inability to accurately quantify the impact of non-coding variation. To overcome this challenge, we developed a computational model that uses ChIP-seq intensity variation in response to non-coding allelic change as a proxy to the quantification of the biological role of non-coding SNPs. We applied this model to HepG2 enhancers and detected 4796 enhancer SNPs capable of disrupting enhancer activity upon allelic change. These SNPs are significantly over-represented in the binding sites of HNF4 and FOXA families of liver transcription factors and liver eQTLs. In addition, these SNPs are strongly associated with liver GWAS traits, including type I diabetes, and are linked to the abnormal levels of HDL and LDL cholesterol. Our model is directly applicable to any enhancer set for mapping causal regulatory SNPs.
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.