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LOC130004131 ATAC-STARR-seq lymphoblastoid active region 3608 [ Homo sapiens (human) ]

Gene ID: 130004131, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004131
Gene description
ATAC-STARR-seq lymphoblastoid active region 3608
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 LOC130004131 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 (75233906..75234055)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (76107414..76107563)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (76993664..76993813)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 8 Neighboring gene ribosomal protein S26 pseudogene 42 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:76898750-76898917 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:76901445-76901944 Neighboring gene MPRA-validated peak1024 silencer Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr10:76966815-76967564 Neighboring gene Sharpr-MPRA regulatory region 10124 Neighboring gene Sharpr-MPRA regulatory region 7934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:76982209-76982964 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:76983719-76984474 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr10:76985985-76986738 Neighboring gene voltage dependent anion channel 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2513 Neighboring gene Sharpr-MPRA regulatory region 13796 Neighboring gene catechol-O-methyltransferase domain containing 1 Neighboring gene VISTA enhancer hs1437 Neighboring gene ribosomal protein L39 pseudogene 25 Neighboring gene high mobility group AT-hook 1 pseudogene 5

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_183577.1 

    Range
    101..250
    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
    75233906..75234055
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    76107414..76107563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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