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LOC130059159 ATAC-STARR-seq lymphoblastoid silent region 7562 [ Homo sapiens (human) ]

Gene ID: 130059159, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059159
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7562
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 LOC130059159 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 (66605489..66605708)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72399784..72400003)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene CKLF-CMTM1 readthrough Neighboring gene CKLF like MARVEL transmembrane domain containing 1 Neighboring gene CKLF like MARVEL transmembrane domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7561 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66642903-66643714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66653785-66654286 Neighboring gene CKLF like MARVEL transmembrane domain containing 4 Neighboring gene CKLF like MARVEL transmembrane domain containing 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:66677635-66677813 Neighboring gene Sharpr-MPRA regulatory region 8452 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:66708833-66709036 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:66710611-66711112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66725551-66726230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66726231-66726910 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66726911-66727590 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:66729849-66730688 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7565 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7566 Neighboring gene dynein cytoplasmic 1 light intermediate chain 2 Neighboring gene MPRA-validated peak2616 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:66785153-66785868 Neighboring gene DYNC1LI2 divergent transcript Neighboring gene telomere repeat binding bouquet formation protein 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

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_193580.1 

    Range
    101..320
    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
    66605489..66605708
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    72399784..72400003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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