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LOC130057259 ATAC-STARR-seq lymphoblastoid silent region 6527 [ Homo sapiens (human) ]

Gene ID: 130057259, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057259
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6527
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 LOC130057259 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 (64046449..64046658)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (61853615..61853824)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (64338648..64338857)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64171093-64171988 Neighboring gene microRNA 422a Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9543 Neighboring gene Sharpr-MPRA regulatory region 4498 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64186155-64186656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9545 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9546 Neighboring gene uncharacterized LOC101928988 Neighboring gene death associated protein kinase 2 Neighboring gene Sharpr-MPRA regulatory region 12240 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64264631-64265378 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64277639-64278140 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64290279-64290780 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6524 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9548 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:64318331-64318496 Neighboring gene NANOG hESC enhancer GRCh37_chr15:64330918-64331419 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6525 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6526 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64342658-64343204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9552 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64385112-64385674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9554 Neighboring gene cytosolic iron-sulfur assembly component 2A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9555 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9556 Neighboring gene Sharpr-MPRA regulatory region 7733 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9557 Neighboring gene sorting nexin 1

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_191680.1 

    Range
    101..310
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    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
    64046449..64046658
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    61853615..61853824
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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