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LOC130002313 ATAC-STARR-seq lymphoblastoid silent region 20166 [ Homo sapiens (human) ]

Gene ID: 130002313, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130002313
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20166
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 LOC130002313 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 (109320420..109320529)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (121489768..121489877)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (112082700..112082809)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene erythrocyte membrane protein band 4.1 like 4B Neighboring gene RNA, U6 small nuclear 984, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20165 Neighboring gene MT-ND2 pseudogene 11 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28759 Neighboring gene protein tyrosine phosphatase non-receptor type 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28761 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28763 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:112193017-112193518 Neighboring gene Sharpr-MPRA regulatory region 2753 Neighboring gene HNF1 motif-containing MPRA enhancer 98 Neighboring gene microRNA 3927 Neighboring gene Y-box binding protein 1 pseudogene 6

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_181759.1 

    Range
    101..210
    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
    109320420..109320529
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    121489768..121489877
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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