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    LOC130002214 ATAC-STARR-seq lymphoblastoid silent region 20118 [ Homo sapiens (human) ]

    Gene ID: 130002214, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130002214
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 20118
    Gene type
    biological region
    Feature type(s)
    regulatory: silencer
    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 a silencer based on its ability to repress 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 LOC130002214 in Genome Data Viewer
    Location:
    chromosome: 9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (98192417..98192966)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (110364358..110364915)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100954699..100955248)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902227 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28686 Neighboring gene tripartite motif containing 14 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20112 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100833954-100834454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100836915-100837721 Neighboring gene N-acetylneuraminate synthase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100849215-100849889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100849890-100850563 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:100852934-100853493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20115 Neighboring gene coronin 2A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:100921913-100922413 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100924760-100925260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28693 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100933363-100934198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100935871-100936704 Neighboring gene Sharpr-MPRA regulatory region 7304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100953772-100954426 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20117 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100957663-100958179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100960535-100961402 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:100961403-100962270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100963511-100964012 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100964013-100964512 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100965136-100965636 Neighboring gene TBC1 domain family member 2 Neighboring gene Sharpr-MPRA regulatory region 378 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr9:100984952-100986151 Neighboring gene ADP ribosylation factor like GTPase 8B pseudogene Neighboring gene microRNA 6854

    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 variants in ClinVar

    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_181660.1 

      Range
      101..650
      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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      98192417..98192966
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      110364358..110364915
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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