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LOC130059489 ATAC-STARR-seq lymphoblastoid silent region 7748 [ Homo sapiens (human) ]

Gene ID: 130059489, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059489
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7748
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 LOC130059489 in Genome Data Viewer
Location:
chromosome: 16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (81006623..81006992)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (87068158..87068527)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80641586-80642086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80642087-80642587 Neighboring gene chromodomain Y like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11170 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr16:80700312-80701272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80760822-80761322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:80761323-80761823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7743 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7747 Neighboring gene androgen receptor regulated long noncoding RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11172 Neighboring gene Sharpr-MPRA regulatory region 7727 Neighboring gene NANOG hESC enhancer GRCh37_chr16:81032399-81032965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11175 Neighboring gene C-X9-C motif containing 2 Neighboring gene CENPN antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7750 Neighboring gene centromere protein N Neighboring gene ATM interactor

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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_193910.1 

    Range
    101..470
    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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    81006623..81006992
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791800.1 Reference GRCh38.p14 PATCHES

    Range
    54862..55231
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    87068158..87068527
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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