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LOC130065979 ATAC-STARR-seq lymphoblastoid silent region 12970 [ Homo sapiens (human) ]

Gene ID: 130065979, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065979
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12970
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 LOC130065979 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (46021584..46021743)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (47757613..47757772)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (44650223..44650382)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44603922-44604458 Neighboring gene ferritin light chain pseudogene 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44624055-44624562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:44632651-44633302 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:44633303-44633954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:44640983-44641493 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12969 Neighboring gene SLC12A5 and MMP9 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12971 Neighboring gene matrix metallopeptidase 9 Neighboring gene solute carrier family 12 member 5 Neighboring gene Sharpr-MPRA regulatory region 13245 Neighboring gene Sharpr-MPRA regulatory region 3425 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17957 Neighboring gene nuclear receptor coactivator 5 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:44717073-44717887 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:44717888-44718701 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17960 Neighboring gene ribosomal protein L13 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_200396.1 

    Range
    101..260
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    46021584..46021743
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    47757613..47757772
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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