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LOC130058195 ATAC-STARR-seq lymphoblastoid silent region 7010 [ Homo sapiens (human) ]

Gene ID: 130058195, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058195
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7010
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 LOC130058195 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (1943173..1943672)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (1963145..1963644)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (1993174..1993673)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1945999-1946500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:1961835-1962392 Neighboring gene heparan sulfate-glucosamine 3-sulfotransferase 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1968509-1969070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1969071-1969634 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:1969635-1970196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:1970197-1970760 Neighboring gene Sharpr-MPRA regulatory region 1858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:1991100-1991989 Neighboring gene uncharacterized LOC124903625 Neighboring gene methionine sulfoxide reductase B1 Neighboring gene ribosomal protein L3 like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2003405-2004394 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:2007755-2008596 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10242 Neighboring gene NADH:ubiquinone oxidoreductase subunit B10

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_192616.1 

    Range
    101..600
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    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    1943173..1943672
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791799.1 Reference GRCh38.p14 PATCHES

    Range
    9321..9820
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    1963145..1963644
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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