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LOC130006818 ATAC-STARR-seq lymphoblastoid active region 5570 [ Homo sapiens (human) ]

Gene ID: 130006818, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130006818
Gene description
ATAC-STARR-seq lymphoblastoid active region 5570
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 LOC130006818 in Genome Data Viewer
Location:
chromosome: 11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (117231871..117231920)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (117247169..117247218)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3932 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5566 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5567 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117052141-117052936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117058437-117058937 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5568 Neighboring gene SID1 transmembrane family member 2 Neighboring gene uncharacterized LOC100652768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117066811-117067310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117068643-117069306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117072631-117073294 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117076473-117077103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117077104-117077734 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117077735-117078365 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117079206-117079706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117079707-117080207 Neighboring gene transgelin Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:117088224-117089423 Neighboring gene proprotein convertase subtilisin/kexin type 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117089878-117090378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5569 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3934 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3935 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:117106511-117107012 Neighboring gene Sharpr-MPRA regulatory region 1788 Neighboring gene ring finger protein 214 Neighboring gene small Cajal body-specific RNA 11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:117139693-117140239 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:117159860-117161059 Neighboring gene beta-secretase 1 Neighboring gene BACE1 antisense RNA

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_186263.1 

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    117231871..117231920
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    117247169..117247218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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