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    LOC130058444 ATAC-STARR-seq lymphoblastoid active region 10395 [ Homo sapiens (human) ]

    Gene ID: 130058444, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130058444
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 10395
    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 LOC130058444 in Genome Data Viewer
    Location:
    chromosome: 16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (10877456..10877505)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (10913426..10913475)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (10971313..10971362)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NUBP iron-sulfur cluster assembly factor 1, cytosolic Neighboring gene NANOG hESC enhancer GRCh37_chr16:10883659-10884197 Neighboring gene trans-golgi network vesicle protein 23 homolog A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7194 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10390 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:10932437-10932956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10391 Neighboring gene Rho GTPase activating protein 21 pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:10964767-10965966 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10393 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10397 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10398 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10399 Neighboring gene class II major histocompatibility complex transactivator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10400 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10401 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7195 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10404 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10405 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10406 Neighboring gene Sharpr-MPRA regulatory region 12638 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11066007-11066184 Neighboring gene C-type lectin domain containing 16A Neighboring gene Dexi homolog Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11073759-11074260 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:11074261-11074760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7196 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:11099817-11100053 Neighboring gene NANOG hESC enhancer GRCh37_chr16:11101530-11102234 Neighboring gene Sharpr-MPRA regulatory region 10204 Neighboring gene ribosomal protein L7 pseudogene 46

    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_192865.1 

      Range
      101..150
      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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      10877456..10877505
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      10913426..10913475
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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