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LOC130065232 ATAC-STARR-seq lymphoblastoid silent region 11087 [ Homo sapiens (human) ]

Gene ID: 130065232, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065232
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11087
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 LOC130065232 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (58514064..58514263)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (61610057..61610256)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (59025431..59025630)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 693, pseudogene Neighboring gene uncharacterized LOC105372485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15206 Neighboring gene solute carrier family 27 member 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:59017967-59018180 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:59023062-59023576 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:59029424-59030084 Neighboring gene zinc finger and BTB domain containing 45 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15207 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:59049840-59050470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:59050471-59051099 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:59054606-59055110 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11091 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11092 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11093 Neighboring gene RNA, 7SL, cytoplasmic 525, pseudogene Neighboring gene tripartite motif containing 28 Neighboring gene microRNA 6807

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_199649.1 

    Range
    101..300
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    58514064..58514263
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    61610057..61610256
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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