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LOC129994182 ATAC-STARR-seq lymphoblastoid active region 22762 [ Homo sapiens (human) ]

Gene ID: 129994182, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994182
Gene description
ATAC-STARR-seq lymphoblastoid active region 22762
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 LOC129994182 in Genome Data Viewer
Location:
chromosome: 5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (88736526..88736575)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (89217658..89217707)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (88032343..88032392)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MIR9-2 host gene Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87967483-87968095 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87968096-87968709 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22758 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:87971545-87972110 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87975792-87976292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87981074-87981697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:87980449-87981073 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87985094-87985772 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:87985773-87986452 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:87987008-87987234 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:87991751-87992730 Neighboring gene MEF2C antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22761 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:88039231-88040430 Neighboring gene microRNA 9-2 Neighboring gene glioma stem cell association long noncoding RNA Neighboring gene myocyte enhancer factor 2C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22764 Neighboring gene Sharpr-MPRA regulatory region 14259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22765 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:88185154-88185690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:88185691-88186225 Neighboring gene MEF2C antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 5119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16165 Neighboring gene VISTA enhancer hs503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22768 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22770 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22773 Neighboring gene VISTA enhancer hs789 Neighboring gene uncharacterized LOC105379074 Neighboring gene uncharacterized LOC105379073

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_173628.1 

    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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    88736526..88736575
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    89217658..89217707
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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