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    LOC129992041 ATAC-STARR-seq lymphoblastoid silent region 15170 [ Homo sapiens (human) ]

    Gene ID: 129992041, updated on 12-Sep-2024

    Summary

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    Gene symbol
    LOC129992041
    Gene description
    ATAC-STARR-seq lymphoblastoid silent region 15170
    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 LOC129992041 in Genome Data Viewer
    Location:
    chromosome: 4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (2468649..2468818)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (2467407..2467576)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (2470376..2470545)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2424482-2425072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2425073-2425662 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2425663-2426252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2426253-2426841 Neighboring gene cilia and flagella associated protein 99 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15169 Neighboring gene uncharacterized LOC105374353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2465175-2465674 Neighboring gene uncharacterized LOC107986250 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2470739-2471311 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21175 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2478879-2479379 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2480295-2480819 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21176 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:2487795-2488296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21177 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2491261-2492041 Neighboring gene ring finger protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15171 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15172 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15173 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15176 Neighboring gene Sharpr-MPRA regulatory region 6001 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2556971-2557807 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2557808-2558643 Neighboring gene family with sequence similarity 193 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2561739-2562277 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2597477-2598429 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2598430-2599381 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2599382-2600334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2620021-2620522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2625441-2626235 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2632219-2632720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2632721-2633220 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2648543-2649043 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2660247-2660748 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:2660749-2661248 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:2672935-2673479 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21179 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21180

    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_171487.1 

      Range
      101..270
      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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      2468649..2468818
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      2467407..2467576
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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