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LOC130056931 ATAC-STARR-seq lymphoblastoid silent region 6376 [ Homo sapiens (human) ]

Gene ID: 130056931, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056931
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6376
Gene type
biological region
Feature type(s)
regulatory: silencer
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 a silencer based on its ability to repress 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 LOC130056931 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (42736355..42736644)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (40543487..40543776)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (43028553..43028842)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9306 Neighboring gene eukaryotic translation initiation factor 4E binding protein 2 pseudogene 2 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:42892996-42893612 Neighboring gene StAR related lipid transfer domain containing 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9307 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42911331-42912096 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr15:42912097-42912861 Neighboring gene NANOG hESC enhancer GRCh37_chr15:42957961-42958533 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:43022854-43023381 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6377 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6378 Neighboring gene TTBK2 antisense RNA 1 Neighboring gene codanin 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:43051195-43051957 Neighboring gene tau tubulin kinase 2 Neighboring gene Sharpr-MPRA regulatory region 5629 Neighboring gene keratin 8 pseudogene 50

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_191352.1 

    Range
    101..390
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    42736355..42736644
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    40543487..40543776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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