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LOC130056921 ATAC-STARR-seq lymphoblastoid active region 9300 [ Homo sapiens (human) ]

Gene ID: 130056921, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056921
Gene description
ATAC-STARR-seq lymphoblastoid active region 9300
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 LOC130056921 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 (42401634..42401683)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (40207677..40207726)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (42693832..42693881)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene glucosidase alpha, neutral C Neighboring gene BCL2 interacting protein 3 pseudogene 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:42652107-42652607 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:42655654-42656620 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42676684-42677239 Neighboring gene uncharacterized LOC105370794 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:42677734-42678933 Neighboring gene calpain 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9299 Neighboring gene zinc finger protein 106 Neighboring gene RNA, U6 small nuclear 188, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42749529-42750361 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:42750362-42751193 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9301 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9303 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:42787505-42788048 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:42788049-42788592 Neighboring gene synaptosome associated protein 23 Neighboring gene MPRA-validated peak2311 silencer Neighboring gene leucine rich repeat containing 57

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_191342.1 

    Range
    101..150
    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
    42401634..42401683
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    40207677..40207726
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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