ArticleNature genetics2018
High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction.
Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 40 citations in OpenAlex.
- Cross-Phenotype Genome-Wide Association Study on the Shared Genetic Susceptibility to Systemic Sclerosis and Primary Biliary Cholangitis.Arthritis & rheumatology (Hoboken, N.J.) · 2025Pooled it
- Combined SNPs sequencing and allele specific proteomics capture reveal functional causality underpinning the 2p25 prostate cancer susceptibility locus.Nature communications · 2025Article
- Deciphering Immunometabolic Landscape in Rheumatoid Arthritis: Integrative Multiomics, Explainable Machine Learning and Experimental Validation.Journal of inflammation research · 2025Article
- Functional Validation of Noncoding Variants Associated With Nonsyndromic Orofacial Cleft.Human mutation · 2025Review
- High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus.Nature communications · 2024Article
- Functional dissection of complex and molecular trait variants at single nucleotide resolution.bioRxiv : the preprint server for biology · 2024Article
- Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development.Nature communications · 2024Article
- Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant.Cell genomics · 2023Article
- Allele-specific protein binding within theRMD open · 2023Article
- Functional characterization of human genomic variation linked to polygenic diseases.Trends in genetics : TIG · 2023Review
- A functional variant of CD40 modulates clearance of hepatitis B virus in hepatocytes via regulation of the ANXA2/CD40/BST2 axis.Human molecular genetics · 2023Article
- Identification of essential genes and immune cell infiltration in rheumatoid arthritis by bioinformatics analysis.Scientific reports · 2023Article
- SATB2, coordinated with CUX1, regulates IL-1β-induced senescence-like phenotype in endothelial cells by fine-tuning the atherosclerosis-associated p16Aging cell · 2023Article
- An Improved EMSA-based Method to Prioritize CandidateBio-protocol · 2022Article
- CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants.Cell genomics · 2022Article
- Post-GWAS functional analysis identifies CUX1 as a regulator of p16Nature aging · 2022Article
- Coupling high-throughput mapping with proteomics analysis delineates cis-regulatory elements at high resolution.Nucleic acids research · 2022Article
- Genome editing to define the function of risk loci and variants in rheumatic disease.Nature reviews. Rheumatology · 2021Review
- Post-GWAS functional studies reveal an RA-associated CD40-induced NF-kB signal transduction and transcriptional regulation network targeted by class II HDAC inhibitors.Human molecular genetics · 2021Article
- Biological classification of childhood arthritis: roadmap to a molecular nomenclature.Nature reviews. Rheumatology · 2021Review
Corrections and comments
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Authors and funding
16 authors at 5 institutions in 3 countries.
Funding
Abstract
Genome-wide association studies (GWAS) have identified many disease-associated noncoding variants, but cannot distinguish functional single-nucleotide polymorphisms (fSNPs) from others that reside incidentally within risk loci. To address this challenge, we developed an unbiased high-throughput screen that employs type IIS enzymatic restriction to identify fSNPs that allelically modulate the binding of regulatory proteins. We coupled this approach, termed SNP-seq, with flanking restriction enhanced pulldown (FREP) to identify regulation of CD40 by three disease-associated fSNPs via four regulatory proteins, RBPJ, RSRC2 and FUBP-1/TRAP150. Applying this approach across 27 loci associated with juvenile idiopathic arthritis, we identified 148 candidate fSNPs, including two that regulate STAT4 via the regulatory proteins SATB2 and H1.2. Together, these findings establish the utility of tandem SNP-seq/FREP to bridge the gap between GWAS and disease mechanism.
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What Socratic 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 Socratic graph.