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LOC129932627 ATAC-STARR-seq lymphoblastoid active region 2640 [ Homo sapiens (human) ]

Gene ID: 129932627, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932627
Gene description
ATAC-STARR-seq lymphoblastoid active region 2640
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 LOC129932627 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (225999198..225999307)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (225187112..225187221)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (226186899..226187008)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226126985-226127562 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1867 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226131035-226131614 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226133351-226133930 Neighboring gene left-right determination factor 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226138649-226139186 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:226146947-226147117 Neighboring gene NADH:ubiquinone oxidoreductase subunit A3 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2638 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2639 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1868 Neighboring gene SDE2 telomere maintenance homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2642 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2643 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2644 Neighboring gene H3-3A divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr1:226249972-226250137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2645 Neighboring gene H3.3 histone A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:226270255-226271122 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1872 Neighboring gene long intergenic non-protein coding RNA 1703

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_165652.1 

    Range
    101..210
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    225999198..225999307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    225187112..225187221
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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