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LOC130003640 ATAC-STARR-seq lymphoblastoid active region 3242 [ Homo sapiens (human) ]

Gene ID: 130003640, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130003640
Gene description
ATAC-STARR-seq lymphoblastoid active region 3242
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 LOC130003640 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 (31707696..31707885)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (31739106..31739295)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (31996624..31996813)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376484 Neighboring gene glutamate dehydrogenase 1 pseudogene 5 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31954277-31955148 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31955149-31956018 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:31966287-31966838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:31983575-31984136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:31984137-31984698 Neighboring gene macrophage enriched lincRNA repressor of IFN-gamma signaling Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:32048354-32049250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3243 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:32054478-32055115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:32062977-32063974 Neighboring gene Rho GTPase activating protein 12 Neighboring gene MPRA-validated peak921 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:32189989-32190489 Neighboring gene uncharacterized LOC107984219 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2280 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:32229391-32230590 Neighboring gene high mobility group box 1 pseudogene 7 Neighboring gene uncharacterized LOC105376485 Neighboring gene ribosomal protein L34 pseudogene 19

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_183086.1 

    Range
    101..290
    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
    31707696..31707885
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    31739106..31739295
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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