Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
Open accessAbstract
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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The majority of schizophrenia-associated variants do not directly index coding changes affecting protein structure.
“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
The Abstract reports that about 93% of disease- and trait-associated GWAS variants lie in noncoding sequence. The section on regulatory DNA also finds that most intronic GWAS SNPs within DHSs do not strongly tag coding SNPs. These findings support the general point, but the paper does not establish that a majority of schizophrenia-associated variants specifically lack links to protein-structure changes. (LLM, conf=0.84)
Experimental — accuracy not yet measuredThe majority of multiple sclerosis risk variants appear to localise to gene regulatory regions, rather than coding sequence, and specifically to enhancer elements active in stimulated immune cell subsets.
“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]
The Abstract states that about 93% of disease- and trait-associated variants overall lie in noncoding sequence. The ‘De novo identification of pathogenic cell types’ section reports enrichment of MS-associated variants in regulatory DNA of particular immune cell types, but does not establish that a majority of MS risk variants lie in regulatory regions rather than coding sequence. The separate claim about enhancers in stimulated immune cells carries citation 56, not this citation. (LLM, conf=0.84)
Experimental — accuracy not yet measuredA major component of the heritability of nearly all common diseases partitions to regions with enhancer-like signatures, particularly in disease-relevant cell types.
“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]
The section “Disease- and trait-associated variants are concentrated in regulatory DNA” (page unavailable) reports enrichment of GWAS-associated variants in DNase I hypersensitive sites across many diseases and traits. “De novo identification of pathogenic cell types” reports enrichment in particular cell types for Crohn’s disease, multiple sclerosis, and a cardiac trait. The paper does not quantify the share of heritability partitioning to these regions, establish this for nearly all common diseases, or show that the enriched regions specifically have enhancer-like signatures. (LLM, conf=0.87)
Experimental — accuracy not yet measuredThe heritable component of common disease risk distributes largely to non-coding regions and appears particularly enriched in enhancers specific to disease-relevant cell types.
“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]
The Abstract reports that about 93% of disease- and trait-associated GWAS variants lie in noncoding sequence. The Discussion and ‘De novo identification of pathogenic cell types’ section report enrichment in regulatory DNA active in disease-relevant cell types. The paper measures enrichment in DNase I hypersensitive sites, however, not specifically in enhancers, and does not quantify the heritable component of risk. (LLM, conf=0.85)
Experimental — accuracy not yet measuredGWAS-detected genetic variants associated with complex traits and diseases are typically non-coding, non-promoter associated and highly enriched in enhancers.
“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]
The introductory passage reports that about 93% of disease- and trait-associated variants are noncoding. The section ‘Disease- and trait-associated variants are concentrated in regulatory DNA’ reports enrichment in DNase I hypersensitive sites (DHSs), and ‘DHSs harboring GWAS variants control distant phenotype-relevant genes’ identifies some of those sites as enhancers. The paper does not establish that GWAS variants are typically non-promoter-associated or specifically highly enriched in enhancers, rather than in regulatory DNA more broadly; page numbers were not supplied in our copy. (LLM, conf=0.87)
Experimental — accuracy not yet measured
The vast majority of disease-risk genetic variants are located in non-coding regions of the genome.
“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 <b>-</b> risk association (2019) · cites this paper as [5]
Functional and epigenomic annotation studies suggest that other elements of the immune system may be involved in MS.
“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]
Non-coding variants can influence traits and cause diseases by altering gene expression.
“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]
Most disease-associated genetic variation lies in non-coding regions enriched for regulatory elements that control expression and splicing of target genes.
“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]
Histone modifications can reliably be measured across the genome using ChIP-seq, while chromatin accessibility is typically measured by either DNase-seq or ATAC-seq.
“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]
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.
“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]
More than 90% of disease-associated single-nucleotide variants are localized in noncoding regions with unknown target genes.
“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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- 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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Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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