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    LOC129996543 ATAC-STARR-seq lymphoblastoid active region 24624 [ Homo sapiens (human) ]

    Gene ID: 129996543, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129996543
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 24624
    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 LOC129996543 in Genome Data Viewer
    Location:
    chromosome: 6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (44000692..44000841)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (43832396..43832545)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (43968429..43968578)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375070 Neighboring gene long intergenic non-protein coding RNA 1512 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43878694-43879258 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43879259-43879821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43880895-43881684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43893291-43894024 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43911713-43912238 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43918399-43919384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43932755-43933254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24623 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43952691-43953286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:43957693-43958202 Neighboring gene uncharacterized LOC124901321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43961654-43962154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:43972319-43972950 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:43977969-43979168 Neighboring gene long intergenic non-protein coding RNA 3040 Neighboring gene stem cell inhibitory RNA transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44007317-44008074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44009776-44010524 Neighboring gene Sharpr-MPRA regulatory region 2143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24625 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44019358-44019952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44022316-44022816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24626 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:44030458-44031420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17247 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24629 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24630 Neighboring gene Sharpr-MPRA regulatory region 9341 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91788 Neighboring gene Sharpr-MPRA regulatory region 15428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44069931-44070480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44070481-44071029 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91802 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91811 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:44075151-44075650 Neighboring gene ribosomal protein L29 pseudogene 16 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91827 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91835 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_91840 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17252 Neighboring gene mitochondrial ribosomal protein L14 Neighboring gene transmembrane protein 63B

    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_175989.1 

      Range
      101..250
      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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      44000692..44000841
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      43832396..43832545
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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