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LOC130064468 ATAC-STARR-seq lymphoblastoid silent region 10633 [ Homo sapiens (human) ]

Gene ID: 130064468, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064468
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10633
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 LOC130064468 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 (40576262..40576351)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (43396878..43396967)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (41082168..41082257)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10628 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10629 Neighboring gene SERTAD3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14655 Neighboring gene biliverdin reductase B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10630 Neighboring gene spectrin beta, non-erythrocytic 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:41029231-41029526 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10631 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14656 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10632 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10635 Neighboring gene SH3KBP1 binding protein 1 Neighboring gene Sharpr-MPRA regulatory region 6117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14657 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41108540-41109063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10637 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10639 Neighboring gene Sharpr-MPRA regulatory region 12022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14658 Neighboring gene latent transforming growth factor beta binding protein 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41119811-41120358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14659 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:41128498-41129138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14660

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_198885.1 

    Range
    101..190
    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
    40576262..40576351
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    43396878..43396967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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