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LOC130002063 ATAC-STARR-seq lymphoblastoid silent region 20028 [ Homo sapiens (human) ]

Gene ID: 130002063, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002063
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20028
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 LOC130002063 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 (91950214..91950393)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (104116663..104116842)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (94712496..94712675)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene microRNA 3910-2 Neighboring gene microRNA 3910-1 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94455452-94456013 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20027 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109450 Neighboring gene receptor tyrosine kinase like orphan receptor 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94544427-94544926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94561969-94562469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94605877-94606451 Neighboring gene uncharacterized LOC124902210 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94619147-94619806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94619807-94620466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94647759-94648342 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94648343-94648926 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94648927-94649508 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94656806-94657388 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr9:94660754-94661368 and GRCh37_chr9:94661369-94661982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94667938-94668501 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:94670331-94670937 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:94683071-94683911 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr9:94683912-94684752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94696982-94697815 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:94702261-94702775 Neighboring gene NANOG hESC enhancer GRCh37_chr9:94707493-94707994 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94711301-94711802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:94711803-94712302 Neighboring gene Sharpr-MPRA regulatory region 183 Neighboring gene Sharpr-MPRA regulatory region 9366 Neighboring gene uncharacterized LOC105376148 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_109489 Neighboring gene uncharacterized LOC107987094

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_181509.1 

    Range
    101..280
    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
    91950214..91950393
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    104116663..104116842
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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