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LOC129935902 ATAC-STARR-seq lymphoblastoid active region 17352 [ Homo sapiens (human) ]

Gene ID: 129935902, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129935902
Gene description
ATAC-STARR-seq lymphoblastoid active region 17352
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: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (234290963..234291012)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (234779968..234780017)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene secreted phosphoprotein 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:235066116-235066288 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:235072133-235073332 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:235077257-235077756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235079950-235080452 Neighboring gene uncharacterized LOC105373932 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235121411-235121911 Neighboring gene uncharacterized LOC105373933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17353 Neighboring gene ribosomal protein S20 pseudogene 12 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:235271392-235272591 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:235276379-235276880 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:235276881-235277380 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:235311534-235312034 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr2:235336101-235337300 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:235339493-235340044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17354 Neighboring gene long intergenic non-protein coding RNA 1891

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_168913.1 

    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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    234290963..234291012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    234779968..234780017
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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