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LOC130002123 ATAC-STARR-seq lymphoblastoid silent region 20060 [ Homo sapiens (human) ]

Gene ID: 130002123, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002123
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20060
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 LOC130002123 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 (95004771..95004960)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (107174130..107174319)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (97767053..97767242)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene aminopeptidase O (putative) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28635 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:97587461-97588134 Neighboring gene microRNA 2278 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28636 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110389 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:97634019-97634518 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110405 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110431 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:97678815-97679315 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:97680413-97680914 Neighboring gene uncharacterized LOC101928119 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:97689588-97690377 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:97690378-97691166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:97691883-97692383 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:97712716-97712894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20058 Neighboring gene Sharpr-MPRA regulatory region 10357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:97741836-97742834 Neighboring gene Sharpr-MPRA regulatory region 2222 Neighboring gene Sharpr-MPRA regulatory region 14176 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20059 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20061 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:97780096-97781295 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:97785561-97786760 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:97791169-97791319 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:97794537-97795036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:97807172-97807937 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:97825060-97825769 Neighboring gene microRNA 6081 Neighboring gene microRNA 23b

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_181569.1 

    Range
    101..290
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    95004771..95004960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    107174130..107174319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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