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LOC129993630 ATAC-STARR-seq lymphoblastoid active region 22346 [ Homo sapiens (human) ]

Gene ID: 129993630, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129993630
Gene description
ATAC-STARR-seq lymphoblastoid active region 22346
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 LOC129993630 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 (7794689..7794788)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (7733807..7733906)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (7794802..7794901)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986403 Neighboring gene long intergenic non-protein coding RNA 2142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7395567-7396332 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7394801-7395566 Neighboring gene uncharacterized LOC105374646 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7420020-7420743 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7420744-7421468 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:7422307-7423176 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7424665-7425194 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7425195-7425722 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:7427184-7427875 Neighboring gene adenylate cyclase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7480982-7481482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7481483-7481983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7515349-7515849 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7526205-7526704 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7596934-7597448 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7597449-7597963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:7663263-7663836 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr5:7663837-7664409 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:7667125-7668324 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:7683613-7683799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22345 Neighboring gene Sharpr-MPRA regulatory region 1766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7815313-7815850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7816087-7816815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:7816816-7817543 Neighboring gene cilia and flagella associated protein 90 Neighboring gene FAST kinase domains 3 Neighboring gene 5-methyltetrahydrofolate-homocysteine methyltransferase reductase

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_173076.1 

    Range
    101..200
    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
    7794689..7794788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    7733807..7733906
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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