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LOC130056975 ATAC-STARR-seq lymphoblastoid active region 9344 [ Homo sapiens (human) ]

Gene ID: 130056975, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130056975
Gene description
ATAC-STARR-seq lymphoblastoid active region 9344
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 LOC130056975 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (44663957..44664126)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (42471929..42472098)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44828013-44828800 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6397 Neighboring gene EIF3J divergent transcript Neighboring gene eukaryotic translation initiation factor 3 subunit J Neighboring gene SPG11 vesicle trafficking associated, spatacsin Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44874604-44874775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6398 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44879793-44880004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9341 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:44936676-44936780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9342 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:44955204-44956160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9347 Neighboring gene PAT1 homolog 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:45003536-45004198 Neighboring gene microRNA 10393 Neighboring gene beta-2-microglobulin

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

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_191396.1 

    Range
    101..270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    44663957..44664126
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    42471929..42472098
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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