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    LOC130000356 ATAC-STARR-seq lymphoblastoid silent region 19187 [ Homo sapiens (human) ]

    Gene ID: 130000356, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130000356
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 19187
    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 LOC130000356 in Genome Data Viewer
    Location:
    chromosome: 8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (51933152..51933281)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (52308787..52308916)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (52845712..52845841)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene peroxidasin like Neighboring gene uncharacterized LOC105375833 Neighboring gene MPRA-validated peak7013 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52721378-52721900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52721901-52722422 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19186 Neighboring gene protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:52837590-52838789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27342 Neighboring gene PCMTD1 divergent transcript Neighboring gene uncharacterized LOC124901944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27343 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:52959497-52959996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:53013330-53014276 Neighboring gene uncharacterized LOC124901945 Neighboring gene ST18 C2H2C-type zinc finger transcription factor

    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_179802.1 

      Range
      101..230
      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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      51933152..51933281
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      52308787..52308916
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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