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LOC130007218 ATAC-STARR-seq lymphoblastoid silent region 4155 [ Homo sapiens (human) ]

Gene ID: 130007218, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130007218
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4155
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 LOC130007218 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 (4911287..4911426)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (4918334..4918473)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (5020453..5020592)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902863 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 8 Neighboring gene Sharpr-MPRA regulatory region 13428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:4872941-4873441 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:4932879-4934078 Neighboring gene MPRA-validated peak1537 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5831 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:4939415-4939916 Neighboring gene potassium voltage-gated channel subfamily A member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:4962778-4963278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5833 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr12:4966717-4967360 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:5008995-5010194 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:5015702-5016901 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:5017696-5018452 Neighboring gene potassium voltage-gated channel subfamily A member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5835 Neighboring gene uncharacterized LOC100507560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5837 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:5136377-5137080 Neighboring gene eukaryotic translation initiation factor 3 subunit F 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_187887.1 

    Range
    101..240
    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
    4911287..4911426
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    4918334..4918473
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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