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LOC130001523 ATAC-STARR-seq lymphoblastoid silent region 19757 [ Homo sapiens (human) ]

Gene ID: 130001523, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001523
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19757
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 LOC130001523 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 (5853832..5853881)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (5858985..5859034)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (5853832..5853881)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28170 Neighboring gene programmed cell death 1 ligand 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28173 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28174 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28175 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:5629427-5629927 Neighboring gene RIC1 homolog, RAB6A GEF complex partner 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28176 Neighboring gene uncharacterized LOC124902115 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:5762408-5763607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19756 Neighboring gene endoplasmic reticulum metallopeptidase 1 Neighboring gene Sharpr-MPRA regulatory region 2314 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28177 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28178 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28179 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:5879621-5880122 Neighboring gene small nucleolar RNA U13 Neighboring gene adenylate kinase 4 pseudogene 4 Neighboring gene bromodomain containing 10

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_180969.1 

    Range
    101..150
    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
    5853832..5853881
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    5858985..5859034
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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