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LOC130005527 ATAC-STARR-seq lymphoblastoid active region 4588 [ Homo sapiens (human) ]

Gene ID: 130005527, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130005527
Gene description
ATAC-STARR-seq lymphoblastoid active region 4588
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 LOC130005527 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (34052945..34053014)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (34189975..34190044)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (34074492..34074561)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4587 Neighboring gene uncharacterized LOC105376621 Neighboring gene uncharacterized LOC124902659 Neighboring gene Sharpr-MPRA regulatory region 4704 Neighboring gene CRISPRi-validated cis-regulatory element chr11.1732 Neighboring gene CRISPRi-validated cis-regulatory element chr11.1733 Neighboring gene CRISPRi-validated cis-regulatory element chr11.1734 Neighboring gene VISTA enhancer hs1858 Neighboring gene Sharpr-MPRA regulatory region 12713 Neighboring gene Sharpr-MPRA regulatory region 9356 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:34011296-34011867 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34018010-34018510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:34018511-34019011 Neighboring gene uncharacterized LOC101929918 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:34072933-34073132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4589 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4591 Neighboring gene uncharacterized LOC124902660 Neighboring gene cell cycle associated protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4592 Neighboring gene N-acetyltransferase 10 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4594

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_184972.1 

    Range
    101..170
    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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    34052945..34053014
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    34189975..34190044
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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