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LOC130002150 ATAC-STARR-seq lymphoblastoid silent region 20079 [ Homo sapiens (human) ]

Gene ID: 130002150, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002150
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20079
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 LOC130002150 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (96417537..96417776)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (108589257..108589496)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (99179819..99180058)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene SLC35D2-HSD17B3 readthrough Neighboring gene solute carrier family 35 member D2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:99104760-99105284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:99105285-99105808 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110853 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20077 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20078 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110866 Neighboring gene Sharpr-MPRA regulatory region 10311 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110873 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28652 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28653 Neighboring gene zinc finger protein 367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20080 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99180933-99181466 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99181467-99182000 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:99182517-99183716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:99185787-99186288 Neighboring gene NSA2 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28654 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20083 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20084 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20085 Neighboring gene hyaluronan binding protein 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:99256389-99257179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:99257792-99258292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:99273815-99274314 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:99284685-99285884 Neighboring gene cell division cycle 14B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20087 Neighboring gene MPRA-validated peak7299 silencer Neighboring gene uncharacterized LOC105376163 Neighboring gene MPRA-validated peak7301 silencer

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_181596.1 

    Range
    101..340
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    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    96417537..96417776
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    108589257..108589496
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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