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    LOC129997724 ATAC-STARR-seq lymphoblastoid silent region 17812 [ Homo sapiens (human) ]

    Gene ID: 129997724, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129997724
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 17812
    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 LOC129997724 in Genome Data Viewer
    Location:
    chromosome: 7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (522641..522950)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (623619..623928)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (562278..562587)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:499317-500044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:500045-500772 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:510601-511557 Neighboring gene Sharpr-MPRA regulatory region 3057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:515046-515940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:519557-520077 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:530277-531056 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:531057-531836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:535084-536005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:536006-536926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:543335-544112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:549933-550440 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:550441-550948 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:551965-552472 Neighboring gene Sharpr-MPRA regulatory region 8552 Neighboring gene NANOG hESC enhancer GRCh37_chr7:555259-555760 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:556430-557352 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:558275-559196 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17808 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17809 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:561041-561962 Neighboring gene platelet derived growth factor subunit A Neighboring gene ReSE screen-validated silencer GRCh37_chr7:570324-570520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:572659-573216 Neighboring gene PDGFA divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:578299-579242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:579243-580184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:592082-592582 Neighboring gene PRKAR1B antisense RNA 2 Neighboring gene protein kinase cAMP-dependent type I regulatory subunit beta Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:611753-612521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:612522-613291 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:630646-630792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17813 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:643285-643970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25473 Neighboring gene PRKAR1B antisense RNA 1

    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_177165.1 

      Range
      101..410
      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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      522641..522950
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      623619..623928
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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