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LOC130004948 ATAC-STARR-seq lymphoblastoid silent region 2931 [ Homo sapiens (human) ]

Gene ID: 130004948, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004948
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2931
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 LOC130004948 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 (127906947..127907066)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (128805476..128805595)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (129705211..129705330)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene BUB1 mitotic checkpoint serine/threonine kinase pseudogene 1 Neighboring gene clarin 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:129702059-129702280 Neighboring gene protein tyrosine phosphatase receptor type E Neighboring gene uncharacterized LOC124902557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129733337-129734076 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129775634-129776134 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129820967-129821467 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129843223-129843724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:129843725-129844224 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4198 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:129860232-129861431 Neighboring gene lncRNA antisense to PTPRE protein-coding gene

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_184393.1 

    Range
    101..220
    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
    127906947..127907066
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    128805476..128805595
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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