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LOC130007103 ATAC-STARR-seq lymphoblastoid active region 5761 [ Homo sapiens (human) ]

Gene ID: 130007103, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130007103
Gene description
ATAC-STARR-seq lymphoblastoid active region 5761
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 LOC130007103 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 (132093900..132094109)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (132131181..132131390)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene neurotrimin Neighboring gene uncharacterized LOC107984413 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:131758747-131759640 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5760 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4084 Neighboring gene Sharpr-MPRA regulatory region 6145 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:131801564-131801730 Neighboring gene NANOG hESC enhancer GRCh37_chr11:131824673-131825174 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:131847321-131847831 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:131851053-131852006 Neighboring gene VISTA enhancer hs335 Neighboring gene uncharacterized LOC124902795 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:131958013-131959212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5762 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr11:131992888-131993886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132115578-132116078 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132154202-132154771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132154772-132155340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5764 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:132188093-132189292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132199915-132200414 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:132204500-132205000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5765 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:132324306-132324486 Neighboring gene NTM intronic transcript Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:132340747-132341946 Neighboring gene uncharacterized LOC124902819 Neighboring gene opioid binding protein/cell adhesion molecule like

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_186547.1 

    Range
    101..310
    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
    132093900..132094109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    132131181..132131390
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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