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LOC129994781 ATAC-STARR-seq lymphoblastoid active region 23239 [ Homo sapiens (human) ]

Gene ID: 129994781, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129994781
Gene description
ATAC-STARR-seq lymphoblastoid active region 23239
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 LOC129994781 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 (139560915..139561084)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (140085996..140086165)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (138940500..138940669)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901083 Neighboring gene nuclear receptor coactivator 4 pseudogene 4 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:138903317-138903864 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:138903865-138904410 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23238 Neighboring gene ubiquitin conjugating enzyme E2 D2 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:138920017-138920213 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:138922617-138923178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138928627-138929128 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16415 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23240 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23242 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138947583-138948084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138982696-138983196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:138983197-138983697 Neighboring gene heat shock protein family E (Hsp10) member 1 pseudogene 15 Neighboring gene H3 histone pseudogene 25

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_174227.1 

    Range
    101..270
    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
    139560915..139561084
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    140085996..140086165
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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