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LOC130065879 ATAC-STARR-seq lymphoblastoid active region 17885 [ Homo sapiens (human) ]

Gene ID: 130065879, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065879
Gene description
ATAC-STARR-seq lymphoblastoid active region 17885
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 LOC130065879 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 (41011842..41011891)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (42743512..42743561)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (39640482..39640531)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 484 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:39502077-39502280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12911 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:39526059-39526232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:39589576-39590207 Neighboring gene uncharacterized LOC100128988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17881 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17883 Neighboring gene uncharacterized LOC105372621 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:39625651-39626225 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:39631901-39633100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17884 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:39657161-39657512 Neighboring gene origin of replication in promoter of TOP1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12912 Neighboring gene RNA, U2 small nuclear 52, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14849 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:39686360-39687559 Neighboring gene DNA topoisomerase I Neighboring gene t(11;20)(p15;q11) topoisomerase (DNA) I recombination region Neighboring gene PLCG1 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12913

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_200296.1 

    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    41011842..41011891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    42743512..42743561
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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