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    LOC130060401 ATAC-STARR-seq lymphoblastoid active region 11813 [ Homo sapiens (human) ]

    Gene ID: 130060401, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130060401
    Gene description
    ATAC-STARR-seq lymphoblastoid active region 11813
    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 LOC130060401 in Genome Data Viewer
    Location:
    chromosome: 17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (17824331..17824510)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (17771017..17771196)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (17727645..17727824)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17722069-17722789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11811 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:17726733-17726883 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8257 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17730461-17731182 Neighboring gene microRNA 6777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17731183-17731904 Neighboring gene sterol regulatory element binding transcription factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17733682-17734430 Neighboring gene microRNA 33b Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17734431-17735178 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17739175-17740076 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17740077-17740979 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17740980-17741881 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17743523-17744042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8261 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17745179-17745680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17747581-17748101 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17751860-17752706 Neighboring gene Sharpr-MPRA regulatory region 7387 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:17762139-17762639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11815 Neighboring gene target of myb1 like 2 membrane trafficking protein Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:17779053-17780252 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17780613-17781334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17787373-17788134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17788135-17788894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17792123-17792624 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11817 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17817644-17818266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17823655-17824188 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17824189-17824722 Neighboring gene Sharpr-MPRA regulatory region 12990 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17825257-17825790 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17825791-17826324 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17826325-17826857 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11818 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8262 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:17875207-17875776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11819 Neighboring gene uncharacterized LOC107984989 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:17884370-17884870 Neighboring gene dynein regulatory complex subunit 3 Neighboring gene brain protein I3 pseudogene 3

    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_195730.1 

      Range
      101..280
      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_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      17824331..17824510
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      17771017..17771196
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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