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LOC130059595 ATAC-STARR-seq lymphoblastoid silent region 7794 [ Homo sapiens (human) ]

Gene ID: 130059595, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130059595
Gene description
ATAC-STARR-seq lymphoblastoid silent region 7794
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 LOC130059595 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 (84700462..84700571)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90766724..90766833)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84605929-84606461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11242 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84617304-84617809 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11243 Neighboring gene coactosin like F-actin binding protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84623933-84624432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84631141-84631642 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84631643-84632142 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84632885-84633706 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11245 Neighboring gene Sharpr-MPRA regulatory region 4329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84637045-84637609 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11249 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84647291-84647792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84647793-84648292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84674539-84675097 Neighboring gene uncharacterized LOC105371376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7789 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11252 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7790 Neighboring gene kelch like family member 36 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84706085-84706586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7791 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7792 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7793 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84745056-84745556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84752587-84753087 Neighboring gene ubiquitin specific peptidase 10 Neighboring gene Sharpr-MPRA regulatory region 11774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11253 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:84760363-84760863 Neighboring gene uncharacterized LOC124903737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84769037-84770002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84770003-84770968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11254 Neighboring gene Sharpr-MPRA regulatory region 6565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11255 Neighboring gene Sharpr-MPRA regulatory region 1784 Neighboring gene uncharacterized LOC105371378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84828009-84828510

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_194016.1 

    Range
    101..210
    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
    84700462..84700571
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    90766724..90766833
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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