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LOC129997130 ATAC-STARR-seq lymphoblastoid active region 25045 [ Homo sapiens (human) ]

Gene ID: 129997130, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129997130
Gene description
ATAC-STARR-seq lymphoblastoid active region 25045
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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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (129662500..129662569)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (130857107..130857176)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene laminin subunit alpha 2 Neighboring gene uncharacterized LOC124901401 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:129811717-129812916 Neighboring gene uncharacterized LOC102723409 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:129822854-129824053 Neighboring gene Sharpr-MPRA regulatory region 13537 Neighboring gene MPRA-validated peak6120 silencer Neighboring gene Rho GTPase activating protein 18 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17532 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17533 Neighboring gene Sharpr-MPRA regulatory region 14599 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25047 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25049 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_89620 Neighboring gene beta-1,3-N-acetylgalactosaminyltransferase 2 pseudogene 1 Neighboring gene ribosomal protein L5 pseudogene 21

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

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_176576.1 

    Range
    101..170
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    129662500..129662569
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    130857107..130857176
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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