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LOC130006217 ATAC-STARR-seq lymphoblastoid active region 5114 [ Homo sapiens (human) ]

Gene ID: 130006217, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130006217
Gene description
ATAC-STARR-seq lymphoblastoid active region 5114
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 LOC130006217 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 (67606885..67607014)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (67601573..67601702)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (67374356..67374485)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr11:67351053-67351195 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3646 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5110 Neighboring gene glutathione S-transferase pi 1 Neighboring gene MPRA-validated peak1312 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5112 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:67370959-67371644 Neighboring gene NDUFV1 divergent transcript Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67372331-67373016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5113 Neighboring gene NADH:ubiquinone oxidoreductase core subunit V1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:67379204-67380403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:67380373-67380888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5116 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67381921-67382434 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67382435-67382950 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67382951-67383466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:67383983-67384496 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:67384509-67385123 Neighboring gene double C2 domain gamma, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67386492-67387365 Neighboring gene uncharacterized LOC124902696 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:67388663-67389245 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:67389246-67389827 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:67393084-67393613

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_185662.1 

    Range
    101..230
    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
    67606885..67607014
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    67601573..67601702
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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