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LOC130003930 ATAC-STARR-seq lymphoblastoid active region 3447 [ Homo sapiens (human) ]

Gene ID: 130003930, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003930
Gene description
ATAC-STARR-seq lymphoblastoid active region 3447
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 LOC130003930 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (64041352..64041431)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (64899089..64899168)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (65801112..65801191)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902439 Neighboring gene nuclear pore associated protein 1 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2412 Neighboring gene uncharacterized LOC105378333 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:65801475-65801975 Neighboring gene Sharpr-MPRA regulatory region 2403 Neighboring gene Sharpr-MPRA regulatory region 9742 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:65880319-65880911 Neighboring gene DBF4 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 9231 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:66144462-66145292 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:66145293-66146122 Neighboring gene MPRA-validated peak969 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr10:66266441-66266965 Neighboring gene uncharacterized LOC105378335 Neighboring gene ribosomal protein L17 pseudogene 35

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_183376.1 

    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    64041352..64041431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    64899089..64899168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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