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    LOC129937863 ATAC-STARR-seq lymphoblastoid active region 20776 [ Homo sapiens (human) ]

    Gene ID: 129937863, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129937863
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 20776
    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 LOC129937863 in Genome Data Viewer
    Location:
    chromosome: 3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (168214033..168214152)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (170997920..170998039)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (167931821..167931940)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene high mobility group nucleosomal binding domain 2 pseudogene 26 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:167729036-167729547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20773 Neighboring gene golgi integral membrane protein 4 Neighboring gene NANOG hESC enhancer GRCh37_chr3:167799674-167800287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14868 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:167813739-167814240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20774 Neighboring gene CRISPRi-validated cis-regulatory element chr3.4789 Neighboring gene Sharpr-MPRA regulatory region 6960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20777 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:167990063-167990598 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20778 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20779 Neighboring gene NANOG hESC enhancer GRCh37_chr3:167993395-167993896 Neighboring gene EGF like and EMI domain containing 1, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:168102881-168103380 Neighboring gene MPRA-validated peak4911 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:168231986-168232502 Neighboring gene RNA, U2 small nuclear 20, pseudogene Neighboring gene microRNA 551b

    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_170873.1 

      Range
      101..220
      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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      168214033..168214152
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      170997920..170998039
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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