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LOC130065419 ATAC-STARR-seq lymphoblastoid active region 17543 [ Homo sapiens (human) ]

Gene ID: 130065419, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065419
Gene description
ATAC-STARR-seq lymphoblastoid active region 17543
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 LOC130065419 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (10435019..10435248)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (10478023..10478252)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (10415667..10415896)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene SDA1 domain containing 1 pseudogene 2 Neighboring gene uncharacterized LOC128706665 Neighboring gene uncharacterized LOC128706666 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:10399946-10401145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12671 Neighboring gene NANOG hESC enhancer GRCh37_chr20:10412265-10412766 Neighboring gene MKKS centrosomal shuttling protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17544 Neighboring gene SLX4 interacting protein Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:10447220-10447919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17545 Neighboring gene Sharpr-MPRA regulatory region 2397 Neighboring gene Sharpr-MPRA regulatory region 8388 Neighboring gene Sharpr-MPRA regulatory region 5326 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:10529678-10530178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17547 Neighboring gene Sharpr-MPRA regulatory region 6934 Neighboring gene Sharpr-MPRA regulatory region 11569 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:10578661-10579860 Neighboring gene DNAJC9 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:10617378-10618174 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:10618175-10618971 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:10621299-10622074 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:10622075-10622850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12672 Neighboring gene jagged canonical Notch ligand 1 Neighboring gene microRNA 6870

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_199836.1 

    Range
    101..330
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    10435019..10435248
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    10478023..10478252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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