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LOC130057034 ATAC-STARR-seq lymphoblastoid active region 9389 [ Homo sapiens (human) ]

Gene ID: 130057034, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057034
Gene description
ATAC-STARR-seq lymphoblastoid active region 9389
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 LOC130057034 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 (50003606..50003795)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (47811952..47812141)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (50295803..50295992)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724587 Neighboring gene ATPase phospholipid transporting 8B4 (putative) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:50201373-50201873 Neighboring gene RNA, 5S ribosomal pseudogene 394 Neighboring gene Sharpr-MPRA regulatory region 771 Neighboring gene Sharpr-MPRA regulatory region 7155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9390 Neighboring gene NANOG hESC enhancer GRCh37_chr15:50408634-50409147 Neighboring gene ATP8B4 intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6424 Neighboring gene solute carrier family 27 member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:50502954-50503533 Neighboring gene RNA, 7SL, cytoplasmic 494, pseudogene Neighboring gene histidine decarboxylase

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_191455.1 

    Range
    101..290
    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
    50003606..50003795
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    47811952..47812141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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