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LOC130062682 ATAC-STARR-seq lymphoblastoid silent region 9530 [ Homo sapiens (human) ]

Gene ID: 130062682, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130062682
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9530
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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Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (63444741..63444850)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (63649813..63649922)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904316 Neighboring gene vacuolar protein sorting 4 homolog B Neighboring gene proteasome 26S subunit, ATPase 5 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13468 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:61094350-61095549 Neighboring gene VPS4B-SERPINB5 intergenic CAGE-defined mid-level expression enhancer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:61134418-61135617 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:61142940-61144139 Neighboring gene serpin family B member 5 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:61178432-61178952 Neighboring gene serpin family B member 12

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_195574.1 

    Range
    101..210
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    63444741..63444850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    63649813..63649922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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