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LOC129995588 ATAC-STARR-seq lymphoblastoid active region 23857 [ Homo sapiens (human) ]

Gene ID: 129995588, updated on 27-Aug-2024

Summary

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Gene symbol
LOC129995588
Gene description
ATAC-STARR-seq lymphoblastoid active region 23857
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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Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (683951..684030)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (540839..540918)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene exocyst complex component 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:659114-660062 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:660063-661010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23858 Neighboring gene MARK2 pseudogene 18 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:692466-693352 Neighboring gene HUS1 checkpoint clamp component B Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:694782-695290 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:701331-701850 Neighboring gene MPRA-validated peak5620 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16818 Neighboring gene uncharacterized LOC105374873 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancers GRCh37_chr6:829333-829880 and GRCh37_chr6:829881-830426 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:839153-839702 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:862355-863554 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:867961-868143 Neighboring gene uncharacterized LOC101927691

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

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_175034.1 

    Range
    101..180
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    683951..684030
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    540839..540918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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