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LOC130063982 ATAC-STARR-seq lymphoblastoid silent region 10376 [ Homo sapiens (human) ]

Gene ID: 130063982, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063982
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10376
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 LOC130063982 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 (18173558..18173867)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18307691..18308000)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18284368..18284677)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microtubule associated serine/threonine kinase 3 Neighboring gene uncharacterized LOC124904650 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18256091-18256592 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18256593-18257093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14300 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18263346-18264238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10374 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18267436-18268294 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18270202-18270406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18271190-18271739 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10375 Neighboring gene phosphoinositide-3-kinase regulatory subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18285185-18285850 Neighboring gene IFI30 lysosomal thiol reductase Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10377 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14305 Neighboring gene MPV17 mitochondrial inner membrane protein like 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18314094-18314876 Neighboring gene Sharpr-MPRA regulatory region 13953 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14306 Neighboring gene uncharacterized LOC102725254 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10379 Neighboring gene RAB3A, member RAS oncogene family

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_198399.1 

    Range
    101..410
    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
    18173558..18173867
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    18307691..18308000
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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