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LOC130057499 ATAC-STARR-seq lymphoblastoid silent region 6639 [ Homo sapiens (human) ]

Gene ID: 130057499, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130057499
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6639
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 LOC130057499 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 (73700405..73700454)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (71517618..71517667)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (73992746..73992795)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene NPTN intronic transcript 1 Neighboring gene neuroplastin Neighboring gene ReSE screen-validated silencer GRCh37_chr15:73879798-73879963 Neighboring gene NANOG hESC enhancer GRCh37_chr15:73909554-73910143 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:73910157-73910718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6634 Neighboring gene uncharacterized LOC105370891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:73975613-73976121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6635 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6636 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6638 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6637 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:73977139-73977645 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:73988434-73988945 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr15:73988946-73989458 and GRCh37_chr15:73989459-73989969 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:73994347-73995068 Neighboring gene CD276 molecule Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74043809-74044582 Neighboring gene inhibitory synaptic factor 1 Neighboring gene INSYN1 antisense RNA 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_191920.1 

    Range
    101..150
    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
    73700405..73700454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    71517618..71517667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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