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    LOC130057903 ATAC-STARR-seq lymphoblastoid active region 10065 [ Homo sapiens (human) ]

    Gene ID: 130057903, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130057903
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 10065
    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 LOC130057903 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 (90191342..90191431)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (87947367..87947456)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (90734574..90734663)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90644982-90645836 Neighboring gene isocitrate dehydrogenase (NADP(+)) 2 Neighboring gene IDH2 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90664819-90665318 Neighboring gene Sharpr-MPRA regulatory region 4454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90686773-90687307 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10063 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701094-90701611 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90701612-90702128 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704142-90704734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90704735-90705327 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:90707039-90707194 Neighboring gene RNA, 7SL, cytoplasmic 346, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90717667-90718167 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90721295-90722200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:90727462-90728195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6815 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10067 Neighboring gene semaphorin 4B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:90744110-90745081 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10068 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:90754487-90755686 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:90755750-90755924 Neighboring gene Sharpr-MPRA regulatory region 13535 Neighboring gene ribosomal protein S12 pseudogene 26 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90764595-90765433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6818 Neighboring gene GDP-D-glucose phosphorylase 1 Neighboring gene calcium and integrin binding 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_192324.1 

      Range
      101..190
      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
      90191342..90191431
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      87947367..87947456
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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