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LOC130002060 ATAC-STARR-seq lymphoblastoid silent region 20026 [ Homo sapiens (human) ]

Gene ID: 130002060, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002060
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20026
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 LOC130002060 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 (91423770..91424169)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (103589908..103590307)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (94186052..94186451)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:93979563-93980163 Neighboring gene Sharpr-MPRA regulatory region 15085 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109225 Neighboring gene AU RNA binding methylglutaconyl-CoA hydratase Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109279 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr9:94076941-94077442 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr9:94077443-94077942 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94106111-94106766 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20025 Neighboring gene MPRA-validated peak7289 silencer Neighboring gene uncharacterized LOC124902209 Neighboring gene synapsin-1 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:94188762-94188958 Neighboring gene nuclear factor, interleukin 3 regulated Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:94251258-94252457 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109428 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr9:94277032-94278231 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94334217-94334753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28587 Neighboring gene phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase pseudogene 2 Neighboring gene microRNA 3910-1 Neighboring gene microRNA 3910-2

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_181506.1 

    Range
    101..500
    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
    91423770..91424169
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    103589908..103590307
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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