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LOC130064777 ATAC-STARR-seq lymphoblastoid silent region 10827 [ Homo sapiens (human) ]

Gene ID: 130064777, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064777
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10827
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 LOC130064777 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 (46746496..46746645)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (49572073..49572222)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (47249753..47249902)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene protein kinase D2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47213106-47213924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10822 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14846 Neighboring gene uncharacterized LOC107987269 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10824 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14847 Neighboring gene microRNA 320e Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47228602-47229146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47230777-47231320 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:47231865-47232408 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:47233845-47235044 Neighboring gene striatin 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10828 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10829 Neighboring gene fukutin related protein Neighboring gene Sharpr-MPRA regulatory region 2893 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:47287225-47288424 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47288509-47289110 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:47289111-47289712 Neighboring gene solute carrier family 1 member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10831 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:47291519-47292120 Neighboring gene heterogeneous nuclear ribonucleoprotein M pseudogene 2

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_199194.1 

    Range
    101..250
    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
    46746496..46746645
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    49572073..49572222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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