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LOC130006071 ATAC-STARR-seq lymphoblastoid active region 5011 [ Homo sapiens (human) ]

Gene ID: 130006071, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006071
Gene description
ATAC-STARR-seq lymphoblastoid active region 5011
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 LOC130006071 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 (65852833..65852882)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65847302..65847351)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (65620304..65620353)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65544816-65545720 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65547529-65548431 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65549161-65549818 Neighboring gene adaptor related protein complex 5 subunit beta 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65553239-65554220 Neighboring gene uncharacterized LOC124902693 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5005 Neighboring gene OVOL1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65563211-65563711 Neighboring gene ovo like transcriptional repressor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65565291-65565814 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65568897-65569617 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3557 Neighboring gene Sharpr-MPRA regulatory region 4974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3558 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:65601289-65601501 Neighboring gene sorting nexin 32 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5009 Neighboring gene Sharpr-MPRA regulatory region 3467 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65618925-65619786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5010 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:65625223-65625763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5014 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5016 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:65627927-65628466 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3562 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65629159-65629672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:65632825-65633326 Neighboring gene cofilin 1 Neighboring gene MUS81 structure-specific endonuclease subunit Neighboring gene EGF containing fibulin extracellular matrix protein 2

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_185516.1 

    Range
    101..150
    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
    65852833..65852882
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65847302..65847351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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