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LOC130056873 ATAC-STARR-seq lymphoblastoid silent region 6344 [ Homo sapiens (human) ]

Gene ID: 130056873, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056873
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6344
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 LOC130056873 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 (40844490..40844729)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (38650518..38650757)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (41136688..41136927)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene DnaJ heat shock protein family (Hsp40) member C17 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9266 Neighboring gene zinc finger FYVE-type containing 19 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 14D Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41117412-41117912 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:41117913-41118413 Neighboring gene Sharpr-MPRA regulatory region 7770 Neighboring gene SPINT1 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:41135684-41135866 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:41135819-41136390 Neighboring gene serine peptidase inhibitor, Kunitz type 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9267 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9268 Neighboring gene uncharacterized LOC124903475 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9269 Neighboring gene ras homolog family member V Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9270 Neighboring gene VPS18 core subunit of CORVET and HOPS complexes

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_191294.1 

    Range
    101..340
    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
    40844490..40844729
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    38650518..38650757
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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