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    LOC129932328 ATAC-STARR-seq lymphoblastoid active region 2390 [ Homo sapiens (human) ]

    Gene ID: 129932328, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129932328
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 2390
    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 LOC129932328 in Genome Data Viewer
    Location:
    chromosome: 1
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (205791632..205791691)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (205056304..205056363)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (205760760..205760819)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nuclear casein kinase and cyclin dependent kinase substrate 1 Neighboring gene small nucleolar RNA SNORA72 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:205708952-205709557 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205709558-205710164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205711268-205711871 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:205711872-205712474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2389 Neighboring gene RAB29, member RAS oncogene family Neighboring gene solute carrier family 41 member 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:205769142-205770092 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:205779391-205779622 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:205782120-205782620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:205803433-205803932 Neighboring gene peptidase M20 domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 4160 Neighboring gene uncharacterized LOC107985250

    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_165361.1 

      Range
      101..160
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      205791632..205791691
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      205056304..205056363
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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