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LOC130008796 ATAC-STARR-seq lymphoblastoid silent region 4876 [ Homo sapiens (human) ]

Gene ID: 130008796, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008796
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4876
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 LOC130008796 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (111842114..111842293)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (111819025..111819204)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (112279918..112280097)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:112123487-112124188 Neighboring gene acyl-CoA dehydrogenase family member 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112194124-112194765 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:112195407-112196048 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:112196049-112196688 Neighboring gene NANOG hESC enhancer GRCh37_chr12:112199468-112200003 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:112204196-112204965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112210937-112211508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7039 Neighboring gene aldehyde dehydrogenase 2 family member Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112228790-112229715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:112229716-112230640 Neighboring gene microRNA 6761 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:112272338-112273217 Neighboring gene MAPKAPK5 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4877 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7041 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:112282209-112282377 Neighboring gene MAPK activated protein kinase 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:112292092-112292249 Neighboring gene ribosomal protein S2 pseudogene 41 Neighboring gene ADAM metallopeptidase domain 1A (pseudogene)

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_187365.1 

    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    111842114..111842293
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    111819025..111819204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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