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    LOC130067184 ATAC-STARR-seq lymphoblastoid silent region 13595 [ Homo sapiens (human) ]

    Gene ID: 130067184, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC130067184
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 13595
    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 LOC130067184 in Genome Data Viewer
    Location:
    chromosome: 22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (29603399..29603978)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30066761..30067340)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (29999388..29999967)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene THO complex subunit 5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:29947869-29948568 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13592 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:29949966-29950663 Neighboring gene nipsnap homolog 1 Neighboring gene Sharpr-MPRA regulatory region 2653 Neighboring gene Sharpr-MPRA regulatory region 10387 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:29976263-29976875 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13593 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18817 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr22:30002345-30002866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30009952-30010452 Neighboring gene ribulose-5-phosphate-3-epimerase pseudogene 4 Neighboring gene NF2, moesin-ezrin-radixin like (MERLIN) tumor suppressor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30026831-30027330 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30084213-30084714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30084715-30085214 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr22:30085434-30085934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30087218-30087838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30087839-30088460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30088461-30089081 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30101159-30101822 Neighboring gene MPRA-validated peak4478 silencer Neighboring gene CABP7 divergent transcript

    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 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_201599.1 

      Range
      101..680
      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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      29603399..29603978
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      30066761..30067340
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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