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LOC130004578 ATAC-STARR-seq lymphoblastoid silent region 2738 [ Homo sapiens (human) ]

Gene ID: 130004578, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004578
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2738
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 LOC130004578 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (102065101..102065770)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (102950113..102950782)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (103824858..103825527)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927445 Neighboring gene armadillo like helical domain containing 3 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:103662223-103662886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3918 Neighboring gene uncharacterized LOC124902492 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2735 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103698366-103699565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3919 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3920 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103795088-103795895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3921 Neighboring gene HPS6 biogenesis of lysosomal organelles complex 2 subunit 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:103867277-103867778 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103870016-103871215 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2741 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2739 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2742 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103876901-103877603 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103877604-103878305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2745 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103880011-103880762 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:103880763-103881514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:103881515-103882264 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:103887116-103887946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2749 Neighboring gene LIM domain binding 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103897995-103899194 Neighboring gene PPARG related coactivator 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:103911632-103912831 Neighboring gene nucleolar and coiled-body phosphoprotein 1

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_184023.1 

    Range
    101..770
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    102065101..102065770
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    102950113..102950782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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