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    LOC130062577 ATAC-STARR-seq lymphoblastoid active region 13389 [ Homo sapiens (human) ]

    Gene ID: 130062577, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130062577
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 13389
    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 LOC130062577 in Genome Data Viewer
    Location:
    chromosome: 18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (58534800..58535199)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (58735442..58735841)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (56202032..56202431)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene NEDD4 like E3 ubiquitin protein ligase Neighboring gene uncharacterized LOC105372143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:55862243-55862765 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:55862766-55863287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13384 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:55890569-55891162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13386 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:55914788-55915293 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:55977766-55977988 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:55982687-55983886 Neighboring gene Sharpr-MPRA regulatory region 8690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56045730-56046265 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:56045193-56045729 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:56059391-56059890 Neighboring gene MIR122 host gene Neighboring gene microRNA 3591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56160423-56160924 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56160925-56161424 Neighboring gene microRNA 122 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:56178733-56179504 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:56179505-56180274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9486 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13390 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:56202574-56203773 Neighboring gene alpha kinase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13395 Neighboring gene uncharacterized LOC105372145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13396 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13397 Neighboring gene ALPK2 eExon liver enhancer Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:56248863-56249363 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:56251884-56252518 Neighboring gene small nucleolar RNA, H/ACA box 108

    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_195469.1 

      Range
      101..500
      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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      58534800..58535199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      58735442..58735841
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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