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LOC130059917 ATAC-STARR-seq lymphoblastoid silent region 7983 [ Homo sapiens (human) ]

Gene ID: 130059917, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059917
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7983
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 LOC130059917 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (2058697..2058786)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1945972..1946061)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1954503-1955398 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7974 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7976 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7978 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7981 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1961456-1961958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7984 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7985 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11464 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1968405-1969158 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11466 Neighboring gene microRNA 212 Neighboring gene microRNA 132 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:1974493-1975692 Neighboring gene uncharacterized LOC107984988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1978509-1979198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1979199-1979889 Neighboring gene HIC ZBTB transcriptional repressor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11468 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11469 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1987859-1988771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11470 Neighboring gene SMG6 nonsense mediated mRNA decay factor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11471 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11472 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11473 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11474 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11475 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11476 Neighboring gene MCUR1 pseudogene 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 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_194338.1 

    Range
    101..190
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    2058697..2058786
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1945972..1946061
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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