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LOC130055911 ATAC-STARR-seq lymphoblastoid active region 8587 [ Homo sapiens (human) ]

Gene ID: 130055911, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130055911
Gene description
ATAC-STARR-seq lymphoblastoid active region 8587
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 LOC130055911 in Genome Data Viewer
Location:
chromosome: 14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (67817022..67817121)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (62024126..62024225)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (68283739..68283838)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 213, pseudogene Neighboring gene zinc finger FYVE-type containing 26 Neighboring gene DnaJ heat shock protein family (Hsp40) member C9 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8586 Neighboring gene Sharpr-MPRA regulatory region 13811 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:68286883-68287644 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:68335343-68335842 Neighboring gene RAD51 paralog B Neighboring gene MPRA-validated peak2182 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:68395137-68396136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:68552975-68553525 Neighboring gene centrosomal protein 170kDa pseudogene Neighboring gene uncharacterized LOC105370546 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:68604367-68605351 Neighboring gene RNA, 7SL, cytoplasmic 706, pseudogene

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_190332.1 

    Range
    101..200
    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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    67817022..67817121
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    62024126..62024225
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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