HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants
Open accessAbstract
The resolution of genome-wide association studies (GWAS) is limited by the linkage disequilibrium (LD) structure of the population being studied. Selecting the most likely causal variants within an LD block is relatively straightforward within coding sequence, but is more difficult when all variants are intergenic. Predicting functional non-coding sequence has been recently facilitated by the availability of conservation and epigenomic information. We present HaploReg, a tool for exploring annotations of the non-coding genome among the results of published GWAS or novel sets of variants. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals and their effect on regulatory motifs. Sets of SNPs, such as those resulting from GWAS, are analyzed for an enrichment of cell type-specific enhancers. HaploReg will be useful to researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. The HaploReg database is available at http://compbio.mit.edu/HaploReg.
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rs1057233 changes the target sequence and binding of miR-569.
“rs1057233 changes the target sequence and binding of miR-56933”
From A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease (2017) · cites this paper as [33]
The Methods section describes predictions of regulatory motif changes, and the Usage section discusses a different SNP, rs9271055, affecting an Ets-family binding site. Searches for rs1057233 and miR-569 found no passage in our copy addressing their target sequence or binding. (LLM, conf=0.76)
Experimental — accuracy not yet measuredrs1057233 was previously found to be associated with systemic lupus erythematosus, body mass index, and proinsulin levels.
“Interestingly, rs1057233 was previously found to be associated with systemic lupus erythematosus33, body mass index40 and proinsulin levels41”
From A common haplotype lowers PU.1 expression in myeloid cells and delays onset of Alzheimer's disease (2017) · cites this paper as [33]
Citation 33 is attached to the lupus association, not the body-mass-index or proinsulin claims. The USAGE section discusses a lupus GWAS but names rs9271100 and rs9271055, not rs1057233; a search for rs1057233 found no passage linking it to lupus in our copy. (LLM, conf=0.75)
Experimental — accuracy not yet measuredOf 1,873 prioritized variants, 71-99% have regulatory potential when considering all tissues according to RegulomeDB and HaploReg.
“Of these variants, 71–99% have regulatory potential when considering all tissues according to RegulomeDB56 and HaploReg57”
From Genetic meta-analysis of diagnosed Alzheimer’s disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing (2019) · cites this paper as [57]
Bioinformatic annotation suggested that the 19p13.3 risk locus contains regulatory elements and that the risk variant(s) might confer disease susceptibility by modulating expression of target genes.
“Notably, these data suggested the presence of regulatory elements at the identified loci, and therefore the risk variant(s) might confer disease susceptibility by modulating the expression of target genes.”
From A regulatory variant at 19p13.3 is associated with primary biliary cholangitis risk and ARID3A expression (2023) · cites this paper as [15]
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Self-citation
- Authors
- Ward, L. D., & Kellis, M.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Ward, L. D.
- Kellis, M.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2011-11-07
- Volume
- 40
- Issue
- D1
- Pages
- D930-D934
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3245002
- OpenAlex
- W2123411711
- Cited by
- 2,229
- References
- 35
- Citations by year
- 2026: 45 · 2025: 87 · 2024: 92 · 2023: 102 · 2022: 151 · 2021: 195 · 2020: 204 · 2019: 220 · 2018: 208 · 2017: 239 · 2016: 232 · 2015: 209 · 2014: 144 · 2013: 84 · 2012: 14
- FWCI
- 48.29
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Science Foundation (0644282)
- National Institutes of Health
- National Human Genome Research Institute (RC1HG005334, R01HG004037)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- non-coding variants, linkage disequilibrium, chromatin state, regulatory motifs, sequence conservation, cell type-specific enhancers, 1000 Genomes Project, small indels, variant annotation, epigenomics
- MeSH terms
- Animals, Base Sequence, Chromatin, Enhancer Elements, Genetic, Genetic Linkage, Regulatory Sequences, Nucleic Acid, Linkage Disequilibrium, Conserved Sequence, Polymorphism, Single Nucleotide, Genomics, Databases, Nucleic Acid, INDEL Mutation, Genome-Wide Association Study, Molecular Sequence Annotation, Nucleotide Motifs
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