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    LOC129998984 ATAC-STARR-seq lymphoblastoid silent region 18464 [ Homo sapiens (human) ]

    Gene ID: 129998984, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129998984
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 18464
    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 LOC129998984 in Genome Data Viewer
    Location:
    chromosome: 7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (100867035..100867124)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (102107135..102107224)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (100464657..100464746)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene EPH receptor B4 Neighboring gene RNA, 7SL, cytoplasmic 750, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100425149-100425944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100426741-100427536 Neighboring gene solute carrier family 12 member 9 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100432899-100433818 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100433819-100434738 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100434739-100435658 Neighboring gene SLC12A9 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26389 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100456152-100456652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100456653-100457153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100457811-100458310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100458529-100459030 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26390 Neighboring gene microRNA 6875 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100471610-100472274 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:100472275-100472939 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18466 Neighboring gene thyroid hormone receptor interactor 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100478564-100479401 Neighboring gene serrate, RNA effector molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:100483425-100484158

    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_178429.1 

      Range
      101..190
      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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      100867035..100867124
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      102107135..102107224
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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