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LOC130064862 ATAC-STARR-seq lymphoblastoid silent region 10884 [ Homo sapiens (human) ]

Gene ID: 130064862, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064862
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10884
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 LOC130064862 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (48492954..48493163)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (51487111..51487320)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (48996211..48996420)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48964846-48965804 Neighboring gene glutamate rich WD repeat containing 1 Neighboring gene uncharacterized LOC105372430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48971727-48972227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:48972285-48973278 Neighboring gene potassium inwardly rectifying channel subfamily J member 14 Neighboring gene MPRA-validated peak3539 silencer Neighboring gene cytohesin 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:48993225-48993796 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10882 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10883 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:48996420-48996611 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10886 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:48997173-48997673 Neighboring gene lemur tyrosine kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10887 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10888 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:49017633-49017779 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49046825-49047364 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49048751-49049694 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49054849-49055373 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49057162-49058100 Neighboring gene Sharpr-MPRA regulatory regions 10218 and 12364 Neighboring gene sulfotransferase family 2B member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14898 Neighboring gene family with sequence similarity 83 member E Neighboring gene sperm acrosome associated 4

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_199279.1 

    Range
    101..310
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    48492954..48493163
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    51487111..51487320
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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