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LOC130004035 ATAC-STARR-seq lymphoblastoid active region 3519 [ Homo sapiens (human) ]

Gene ID: 130004035, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004035
Gene description
ATAC-STARR-seq lymphoblastoid active region 3519
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 LOC130004035 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 (71748593..71748642)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (72619407..72619456)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (73508350..73508399)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene cadherin related 23 Neighboring gene uncharacterized LOC105378355 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73321825-73322348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73322349-73322872 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:73327348-73328169 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:73331571-73332072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73372049-73372563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73381965-73382568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73390204-73391034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73392929-73393464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73393465-73394000 Neighboring gene Sharpr-MPRA regulatory region 11817 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:73398641-73399578 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:73402475-73403119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3516 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:73417087-73417810 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73417811-73418534 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73447088-73447602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3517 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73460453-73461367 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73461368-73462281 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73476810-73477007 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73478924-73479672 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:73485282-73486481 Neighboring gene chromosome 10 open reading frame 105 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73489247-73489438 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3520 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73517352-73517887 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:73526094-73527293 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2466 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:73537763-73537918 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:73550045-73550944 Neighboring gene V-set immunoregulatory receptor Neighboring gene Sharpr-MPRA regulatory region 2121 Neighboring gene uncharacterized LOC124902446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:73570820-73571322 Neighboring gene microRNA 7152

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_183481.1 

    Range
    101..150
    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
    71748593..71748642
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    72619407..72619456
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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