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    LOC130004747 ATAC-STARR-seq lymphoblastoid active region 4056 [ Homo sapiens (human) ]

    Gene ID: 130004747, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130004747
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 4056
    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 LOC130004747 in Genome Data Viewer
    Location:
    chromosome: 10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (110864768..110865147)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (111748552..111748931)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (112624526..112624905)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 20 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112523918-112524418 Neighboring gene RNA, 5S ribosomal pseudogene 327 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:112534241-112535440 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112571707-112572272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4043 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:112589780-112589960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4046 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4049 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4050 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:112605645-112606144 Neighboring gene uncharacterized LOC124902499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4051 Neighboring gene CRISPRi-validated cis-regulatory element chr10.4148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4053 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112619133-112619632 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4054 Neighboring gene uncharacterized LOC124902500 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4055 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4057 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2823 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:112630184-112630794 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2824 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2826 Neighboring gene PDCD4 antisense RNA 1 Neighboring gene programmed cell death 4 Neighboring gene microRNA 4680

    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_184192.1 

      Range
      101..480
      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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      110864768..110865147
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      111748552..111748931
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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