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LOC129936484 ATAC-STARR-seq lymphoblastoid active region 19681 [ Homo sapiens (human) ]

Gene ID: 129936484, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129936484
Gene description
ATAC-STARR-seq lymphoblastoid active region 19681
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 LOC129936484 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 (38143871..38143930)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38149540..38149599)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38185362..38185421)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene DLEC1 cilia and flagella associated protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38179733-38180676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19680 Neighboring gene acetyl-CoA acyltransferase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38196601-38197102 Neighboring gene uncharacterized LOC101928234 Neighboring gene MYD88 innate immune signal transduction adaptor Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38205703-38206902 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:38207186-38207801 Neighboring gene oxidative stress responsive kinase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14207 Neighboring gene Sharpr-MPRA regulatory region 12810 Neighboring gene solute carrier family 22 member 13 Neighboring gene CDC42 pseudogene 7

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_169495.1 

    Range
    101..160
    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
    38143871..38143930
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    38149540..38149599
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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