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LOC130064581 ATAC-STARR-seq lymphoblastoid silent region 10713 [ Homo sapiens (human) ]

Gene ID: 130064581, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064581
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10713
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 LOC130064581 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 (42387405..42387584)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (45206790..45206969)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (42891557..42891736)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10707 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:42818801-42819301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10708 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10710 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10711 Neighboring gene transmembrane protein 145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:42853955-42854456 Neighboring gene multiple EGF like domains 8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:42866515-42867014 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:42873179-42874132 Neighboring gene microRNA 8077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10712 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14715 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:42901001-42901684 Neighboring gene uncharacterized LOC101930071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:42901685-42902368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:42910752-42911558 Neighboring gene LIPE antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14718 Neighboring gene cornifelin Neighboring gene lipase E, hormone sensitive type Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10715 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10716 Neighboring gene C-X-C motif chemokine ligand 17

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_198998.1 

    Range
    101..280
    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
    42387405..42387584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    45206790..45206969
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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