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LOC130057510 ATAC-STARR-seq lymphoblastoid active region 9741 [ Homo sapiens (human) ]

Gene ID: 130057510, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057510
Gene description
ATAC-STARR-seq lymphoblastoid active region 9741
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 LOC130057510 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 (74100156..74100255)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (71966071..71966170)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74392497..74392596)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene golgin A6 family member A Neighboring gene RNA, 7SL, cytoplasmic 429, pseudogene Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:74378600-74379309 Neighboring gene uncharacterized LOC107987224 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:74383297-74384097 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74386258-74386774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74389067-74389658 Neighboring gene COMM domain containing 4 pseudogene 2 Neighboring gene immunoglobulin superfamily containing leucine rich repeat 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74403072-74403264 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74414944-74415550 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74422233-74423142 Neighboring gene uncharacterized LOC283731 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74423143-74424051 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74428171-74428862 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:74432814-74433345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9743 Neighboring gene uncharacterized LOC124903523

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_191931.1 

    Range
    101..200
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    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
    74100156..74100255
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    71966071..71966170
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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