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    LOC130061584 ATAC-STARR-seq lymphoblastoid silent region 8923 [ Homo sapiens (human) ]

    Gene ID: 130061584, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130061584
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 8923
    Gene type
    biological region
    Feature type(s)
    regulatory: silencer
    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 a silencer based on its ability to repress 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 LOC130061584 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 (73310890..73311439)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (74200696..74201245)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (71307029..71307578)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12691 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:71227250-71228026 Neighboring gene component of oligomeric golgi complex 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12692 Neighboring gene VCP nuclear cofactor family member 1 Neighboring gene mitochondrial nucleoid associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12693 Neighboring gene cleavage and polyadenylation specific factor 4 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12694 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71280886-71281442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71281998-71282553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71282554-71283108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12695 Neighboring gene Sharpr-MPRA regulatory region 4436 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71287907-71288788 Neighboring gene CDC42 effector protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71314086-71314838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71332871-71333770 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71343461-71344310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71348097-71348598 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71348599-71349098 Neighboring gene Sharpr-MPRA regulatory region 1327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71357197-71357868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71359686-71360661 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71361126-71361628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71375179-71375680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71376229-71376730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71376731-71377230 Neighboring gene sidekick cell adhesion molecule 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71396825-71397329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71397330-71397833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12698 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71434193-71434693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12699 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47326 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71487500-71488358 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71488359-71489217 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71501870-71502807 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71503745-71504682 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71507033-71507902 Neighboring gene uncharacterized LOC101928251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71530725-71531437 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71533005-71533777 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71536899-71537463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71542356-71542892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71544460-71544960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71544961-71545461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71556405-71557010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71557011-71557617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71560304-71560804 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:71561780-71562370 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr17:71562371-71562960 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71563551-71564139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71584531-71585034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71585035-71585539 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:71585540-71586043 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:71586044-71586548 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71591289-71591834 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:71608178-71608714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:71621555-71622080 Neighboring gene uncharacterized LOC124904054

    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_196732.1 

      Range
      101..650
      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
      73310890..73311439
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      74200696..74201245
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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