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LOC130058667 ATAC-STARR-seq lymphoblastoid active region 10586 [ Homo sapiens (human) ]

Gene ID: 130058667, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130058667
Gene description
ATAC-STARR-seq lymphoblastoid active region 10586
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 LOC130058667 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (23670414..23670643)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (23946217..23946446)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (23681735..23681964)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase subunit AB1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:23605373-23605549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7281 Neighboring gene partner and localizer of BRCA2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:23651698-23651932 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23653060-23653849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10585 Neighboring gene dynactin subunit 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23698309-23698810 Neighboring gene polo like kinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:23716303-23716803 Neighboring gene endoplasmic reticulum to nucleus signaling 2 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:23740522-23741453 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:23766235-23766880 Neighboring gene calcineurin like EF-hand protein 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_193088.1 

    Range
    101..330
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    23670414..23670643
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    23946217..23946446
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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