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    LOC129936957 ATAC-STARR-seq lymphoblastoid active region 20016 [ Homo sapiens (human) ]

    Gene ID: 129936957, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129936957
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 20016
    Gene type
    biological region
    Feature type(s)
    regulatory: enhancer
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    This genomic sequence represents an accessible chromatin region that was validated as an enhancer based on its ability to activate an origin of replication minimal core promoter by the ATAC-STARR-seq (assay for transposase-accessible chromatin with self-transcribing active regulatory region sequencing) massively parallel reporter assay (MPRA) in GM12878 lymphoblastoid cells. [provided by RefSeq, May 2023]
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    Genomic context

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    See LOC129936957 in Genome Data Viewer
    Location:
    chromosome: 3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (59444320..59444369)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (59484622..59484671)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (59430046..59430095)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377109 Neighboring gene FAM3 metabolism regulating signaling molecule D Neighboring gene CFAP20 domain containing Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:58792456-58792956 Neighboring gene CFAP20DC antisense RNA 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58828169-58828785 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:58859831-58861030 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:58876285-58876824 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:58884619-58885120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20014 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:58940883-58941482 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:58983704-58984903 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:59017398-59018230 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:59044085-59044335 Neighboring gene CFAP20DC divergent transcript Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:59113978-59114502 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:59114503-59115026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14493 Neighboring gene Sharpr-MPRA regulatory region 3507 Neighboring gene SNRPB2 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:59599597-59599768 Neighboring gene hCG1813818

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. ATAC-STARR-seq reveals transcription factor-bound activators and silencers within chromatin-accessible regions of the human genome. Hansen TJ, et al. Genome Res, 2022 Aug 25. PMID 35858748, Free PMC Article

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See Variation Viewer (GRCh37.p13)

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_169968.1 

      Range
      101..150
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      59444320..59444369
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      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      59484622..59484671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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