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    LOC130057813 ATAC-STARR-seq lymphoblastoid active region 9992 [ Homo sapiens (human) ]

    Gene ID: 130057813, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130057813
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 9992
    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 LOC130057813 in Genome Data Viewer
    Location:
    chromosome: 15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (84749484..84749563)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (82501872..82501951)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (85292715..85292794)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6771 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85229719-85230218 Neighboring gene neuromedin B Neighboring gene SEC11 homolog A, signal peptidase complex subunit Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85259023-85259588 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85259589-85260154 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85260155-85260718 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:85276857-85277760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9989 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9990 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85291347-85292186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9991 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41887 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85303845-85304346 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85309319-85309820 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85309821-85310320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9993 Neighboring gene zinc finger protein 592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85326319-85326906 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85325731-85326318 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_41909 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85346873-85347374 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85347375-85347874 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85359685-85360215 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85362343-85362874 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85362875-85363404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85370192-85370692 Neighboring gene skeletal muscle cis-regulatory module overlapping ALPK3 Neighboring gene alpha kinase 3 Neighboring gene uncharacterized LOC124900361 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:85405349-85405850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85406419-85406920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85406921-85407420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85426972-85427472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85427473-85427973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:85432908-85433476 Neighboring gene solute carrier family 28 member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:85467385-85467885 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9995 Neighboring gene RNA, U6 small nuclear 339, pseudogene

    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_192234.1 

      Range
      101..180
      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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      84749484..84749563
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      82501872..82501951
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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