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    LOC130006111 ATAC-STARR-seq lymphoblastoid active region 5040 [ Homo sapiens (human) ]

    Gene ID: 130006111, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130006111
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 5040
    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 LOC130006111 in Genome Data Viewer
    Location:
    chromosome: 11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66268198..66268247)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66261870..66261920)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66035669..66035718)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene phosphofurin acidic cluster sorting protein 1 Neighboring gene uncharacterized LOC124902694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66021063-66021564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3581 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66025772-66026740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66033680-66034562 Neighboring gene kinesin light chain 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3583 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66036329-66037210 Neighboring gene KLC2 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:66039357-66040556 Neighboring gene uncharacterized LOC107984340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66049917-66050420 Neighboring gene KLC2 antisense RNA 2 Neighboring gene RAB1B, member RAS oncogene family Neighboring gene cornichon family AMPA receptor auxiliary protein 2

    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_185556.1 

      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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      66268198..66268247
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      66261870..66261920
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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