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LOC130057892 ATAC-STARR-seq lymphoblastoid active region 10055 [ Homo sapiens (human) ]

Gene ID: 130057892, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057892
Gene description
ATAC-STARR-seq lymphoblastoid active region 10055
Gene type
biological region
Feature type(s)
regulatory: enhancer
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 an enhancer based on its ability to activate 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 LOC130057892 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (89781938..89781997)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (87537826..87537885)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (90325169..90325228)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene mitochondrial ribosomal protein L15 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90310867-90311584 Neighboring gene uncharacterized LOC124903550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6806 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:90326293-90326955 Neighboring gene mesoderm posterior bHLH transcription factor 2 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:90326956-90327617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90327618-90328280 Neighboring gene alanyl aminopeptidase, membrane Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90335518-90336018 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:90347169-90348368 Neighboring gene ANPEP proximal promoter Neighboring gene FOXA motif-containing MPRA enhancer 170 Neighboring gene ANPEP distal promoter Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90365008-90365508 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90365509-90366009 Neighboring gene uncharacterized LOC124903551 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:90367927-90368600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10056

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_192313.1 

    Range
    101..160
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    89781938..89781997
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    87537826..87537885
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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