ArticleAmerican journal of human genetics2018
An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation.
Article in American journal of human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
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Who cites it
54 citing papers in PubMed, 1 synthesis or guideline pooled it, 98 citations in OpenAlex.
- The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases.BMC medical genomics · 2022Pooled it
- Long noncoding RNA LINC00339 promotes osteoporosis development via modulating of regulator CDC42 by binding PARP1.Non-coding RNA research · 2025Article
- Allele-Specific Regulation of PAXIP1-AS1 by SMC3/CEBPB at rs112651172 in Psychiatric Disorders Drives Synaptic and Behavioral Dysfunctions in Mice.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Integrated Omics and Multicohort Analyses Identify an Enhancer Variant Linking Ferroptosis to Precision Therapy in Prostate Cancer.Cancer research · 2025Article
- Genetic modulation of lncPSMB1 confers non-syndromic cleft lip with or without cleft palate susceptibility by promoting cell apoptosis.Communications biology · 2025Article
- Analysis of biased allelic enhancer activity of schizophrenia-linked common variants.Communications biology · 2025Article
- Genetic transcriptional regulation profiling of cartilage reveals pathogenesis of osteoarthritis.EBioMedicine · 2025Article
- RUNX2 Phase Separation Mediates Long-Range Regulation Between Osteoporosis-Susceptibility Variant and XCR1 to Promote Osteoblast Differentiation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Non-coding RNAs in osteoarthritis and osteoporosis-related hip fractures: molecular biomarkers for precision diagnosis and prognosis.Frontiers in endocrinology · 2025Review
- Analysis of Transcriptional Regulation in Bone Cells.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Functional mechanism and clinical implications of LINC00339 in delayed fracture healing.Journal of orthopaedic surgery and research · 2024Article
- Identification of key genes and long non‑coding RNA expression profiles in osteoporosis with rheumatoid arthritis based on bioinformatics analysis.BMC musculoskeletal disorders · 2024Article
- Review
- A regulatory variant impacting TBX1 expression contributes to basicranial morphology in Homo sapiens.American journal of human genetics · 2024Article
- Integrative high-throughput enhancer surveying and functional verification divulges a YY2-condensed regulatory axis conferring risk for osteoporosis.Cell genomics · 2024Article
- An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long-range loop formation.Cell proliferation · 2024Article
- The osteoporosis susceptibility SNP rs188303909 at 2q14.2 regulates EN1 expression by modulating DNA methylation and E2F6 binding.Journal of molecular medicine (Berlin, Germany) · 2024Article
- Dual disease co-expression analysis reveals potential roles of estrogen-related genes in postmenopausal osteoporosis and Parkinson's disease.Frontiers in genetics · 2024Article
- High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes.American journal of human genetics · 2023Article
- GWAS meta-analyses clarify the genetics of cervical phenotypes and inform risk stratification for cervical cancer.Human molecular genetics · 2023Article
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Authors and funding
15 authors at 1 institution in 1 country.
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Abstract
Genome-wide association studies (GWASs) have reproducibly associated variants within intergenic regions of 1p36.12 locus with osteoporosis, but the functional roles underlying these noncoding variants are unknown. Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339) (∼360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.
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