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    LOC129934355 ATAC-STARR-seq lymphoblastoid silent region 11773 [ Homo sapiens (human) ]

    Gene ID: 129934355, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129934355
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 11773
    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 LOC129934355 in Genome Data Viewer
    Location:
    chromosome: 2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (96638032..96638241)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (97144666..97144875)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (97303769..97303978)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97196747-97197538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97197539-97198328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11771 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16221 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:97204265-97204810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16222 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97219546-97220071 Neighboring gene AT-rich interaction domain 5A Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97230045-97230545 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:97230616-97231116 Neighboring gene KAT8 regulatory NSL complex subunit 3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:97273727-97274926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16223 Neighboring gene fer-1 like family member 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97326800-97327300 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:97327301-97327801 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:97351655-97352380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97359457-97359958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97360677-97361221 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:97361222-97361765 Neighboring gene lectin, mannose binding 2 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:97404177-97405116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:97405117-97406054

    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_167373.1 

      Range
      101..310
      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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      96638032..96638241
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      97144666..97144875
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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