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LOC129993240 ATAC-STARR-seq lymphoblastoid active region 22036 [ Homo sapiens (human) ]

Gene ID: 129993240, updated on 14-Oct-2023

Summary

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Gene symbol
LOC129993240
Gene description
ATAC-STARR-seq lymphoblastoid active region 22036
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 LOC129993240 in Genome Data Viewer
Location:
chromosome: 4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (152643214..152643283)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (155966370..155966439)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22035 Neighboring gene RPS3A pseudogene 18 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:153528082-153528582 Neighboring gene ribosomal protein S14 pseudogene 6 Neighboring gene transmembrane protein 154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22040 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:153600783-153601612 Neighboring gene uncharacterized LOC105377495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22044 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:153621867-153622378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153628279-153628780 Neighboring gene NANOG hESC enhancer GRCh37_chr4:153649784-153650339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:153661870-153662370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:153669773-153670273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22045 Neighboring gene tigger transposable element derived 4

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_172686.1 

    Range
    101..170
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    152643214..152643283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    155966370..155966439
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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