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LOC129937685 ATAC-STARR-seq lymphoblastoid active region 20632 [ Homo sapiens (human) ]

Gene ID: 129937685, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129937685
Gene description
ATAC-STARR-seq lymphoblastoid active region 20632
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 LOC129937685 in Genome Data Viewer
Location:
chromosome: 3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (141452132..141452271)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (144199775..144199914)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (141170974..141171113)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909441 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20622 Neighboring gene PHF5A pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20623 Neighboring gene zinc finger and BTB domain containing 38 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:141086748-141087947 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20625 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:141092856-141093449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20630 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:141111788-141112397 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:141112398-141113008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20631 Neighboring gene uncharacterized LOC124906291 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:141170008-141170180 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:141174421-141175063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14777 Neighboring gene keratin 18 pseudogene 35 Neighboring gene RAS p21 protein activator 2 Neighboring gene putative uncharacterized protein MSANTD5

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_170695.1 

    Range
    101..240
    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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    141452132..141452271
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    144199775..144199914
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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