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LOC130061679 ATAC-STARR-seq lymphoblastoid silent region 8978 [ Homo sapiens (human) ]

Gene ID: 130061679, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130061679
Gene description
ATAC-STARR-seq lymphoblastoid silent region 8978
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 LOC130061679 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75755387..75755556)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (76648612..76648781)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73751468..73751637)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene RecQ like helicase 5 Neighboring gene uncharacterized LOC107985013 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:73662359-73663558 Neighboring gene SAP30 binding protein Neighboring gene SAP30BP antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73684215-73684716 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:73684717-73685216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73693087-73693798 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:73695788-73696987 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73702471-73703670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73717282-73717820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73717821-73718359 Neighboring gene ITGB4 intron CAGE-defined low expression enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73724533-73725033 Neighboring gene integrin subunit beta 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73749848-73750621 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73754136-73754662 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73754663-73755189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8979 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8980 Neighboring gene galactokinase 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73769871-73770371 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8981 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8982 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12776 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73774948-73775552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12777 Neighboring gene H3.3 histone B Neighboring gene microRNA 4738

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_196813.1 

    Range
    101..270
    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    75755387..75755556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    76648612..76648781
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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