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Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
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Predictions of Genetic Disease: Many genome-wide association studies (GWAS) have identified loci and variants associated with disease, but the ability to predict disease on the basis of these genetic variants remains small. Maurano et al. (p. 1190 ; see the Perspective by Schadt and Chang ; see the cover) characterize the location of GWAS variants in the genome with respect to their proximity to regulatory DNA [marked by deoxyribonuclease I (DNase I) hypersensitive sites] by tissue type, disease, and enrichments in physiologically relevant transcription factor binding sites and networks. They found many noncoding disease associations in regulatory DNA, indicating tissue and developmental-specific regulatory roles for many common genetic variants and thus enabling links to be made between gene regulation and adult-onset disease.
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“As the majority of schizophrenia-associated variants do not directly index coding changes affecting protein structure”
From DNA methylation meta-analysis reveals cellular alterations in psychosis and markers of treatment-resistant schizophrenia (2021) · cites this paper as Maurano et al., 2012
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“The second challenge is that the majority of MS risk variants appear to localise to gene regulatory regions, rather than coding sequence,55 and specifically to enhancer elements active in stimulated immune cell subsets.56”
From Genome‐wide association studies of multiple sclerosis (2018) · cites this paper as [55]
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“It is now widely recognized that a major component of the heritability of nearly all common diseases partitions to these regions, and in particular to regions that have enhancer-like signatures in disease-relevant cell types65.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [65]
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“Although most causal genetic variants for Mendelian disorders fall in protein-coding regions, the heritable component of common disease risk distributes largely to non-coding regions, and appears to be particularly enriched in enhancers that are specific to disease-relevant cell types.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [65]
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“The importance of enhancer variation in human pathology has been further highlighted by genome-wide association studies (GWAS), since GWAS-detected genetic variants associated with complex traits and diseases are typically non-coding, non-promoter associated and highly enriched in enhancers [184, 208, 209].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [209]
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“The vast majority of these disease-risk genetic variants are located in non-coding regions of the genome (5).”
From Brain cell type–specific enhancer–promoter interactome maps and disease - risk association (2019) · cites this paper as [5]
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“While the T cell component plays an important role, functional and epigenomic annotation studies have begun to suggest that other elements of the immune system may be involved as well.(7, 8)”
From Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility (2019) · cites this paper as [8]
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“Beyond impacting isoform composition through splicing modulation, non-coding variants can influence traits and cause diseases by altering gene expression23,24.”
From Advancing regulatory variant effect prediction with AlphaGenome (2026) · cites this paper as [24]
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“The majority of disease-associated genetic variation lies in non-coding regions (7) enriched for non-coding RNAs and cis regulatory elements that regulate gene expression and splicing of their cognate coding gene targets (8, 9).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [7]
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“Histone modifications can reliably be measured across the genome using chromatin immunoprecipitation followed by sequencing (ChIP-seq), while chromatin accessibility is typically measured by either DNase hypersensitivity analysis (DNase-seq) [168] or assay for transposase-accessible chromatin using sequencing”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [168]
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“A large portion of GWAS variants and even variants in high LD with the lead variant fall within non-coding regions of the genome, making their functional importance difficult to infer [168].”
From Genetic architecture of Alzheimer's disease (2020) · cites this paper as [168]
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“More than 90% of disease-associated SNVs (daSNVs) are localized in noncoding regions with unknown target genes40”
From Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression (2020) · cites this paper as [40]
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Metadata
- Authors
- Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., Shafer, A., Neri, F., Lee, K., Kutyavin, T., Stehling-Sun, S., Johnson, A. K., Canfield, T. K., Giste, E., Diegel, M., Bates, D., Hansen, R. S., Neph, S., Sabo, P. J., Heimfeld, S., Raubitschek, A., Ziegler, S., Cotsapas, C., Sotoodehnia, N., Glass, I., Sunyaev, S. R., Kaul, R., & Stamatoyannopoulos, J. A.
- Affiliations
- University of Washington (US)
- Chinese Academy of Sciences (CN)
- Fred Hutch Cancer Center (US)
- Benaroya Research Institute (US)
- Yale University (US)
- Brigham and Women's Hospital (US)
- Corresponding author
- Maurano, Matthew T.
- Humbert, Richard
- Rynes, Eric
- Stamatoyannopoulos, John A.
- ORCID
- Venue
- Science
- Published
- 2012-09-07
- Volume
- 337
- Issue
- 6099
- Pages
- 1190-1195
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3771521
- OpenAlex
- W2078059415
- Cited by
- 3,716
- References
- 47
- Citations by year
- 2026: 215 · 2025: 261 · 2024: 296 · 2023: 260 · 2022: 288 · 2021: 352 · 2020: 306 · 2019: 273 · 2018: 270 · 2017: 252 · 2016: 269 · 2015: 249 · 2014: 239 · 2013: 163 · 2012: 17
- FWCI
- 126.66
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (R01HL088456)
- National Institute of Mental Health (F31MH094073)
- National Human Genome Research Institute (U54HG004592)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK056465)
- National Institute of Environmental Health Sciences (U01ES01156, U01ES017156)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (R24HD000836)
- 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 › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- non-coding variants, regulatory DNA, DNase I hypersensitive sites, common diseases, fetal development, prenatal exposure, transcription factor binding sites, regulatory networks, Crohn's disease, multiple sclerosis, electrocardiogram, disease-associated variants
- MeSH terms
- Alleles, Chromatin, Crohn Disease, Deoxyribonuclease I, Disease, DNA, Electrocardiography, Fetus, Humans, Multiple Sclerosis, Phenotype, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Transcription Factors, Genetic Variation, Genome, Human, Polymorphism, Single Nucleotide, Fetal Development, Regulatory Elements, Transcriptional, Gene Regulatory Networks, Genome-Wide Association Study
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