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LOC130001318 ATAC-STARR-seq lymphoblastoid silent region 19611 [ Homo sapiens (human) ]

Gene ID: 130001318, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130001318
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19611
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 LOC130001318 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (143246394..143247283)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (144393781..144394670)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (144328564..144329453)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene glycosylphosphatidylinositol anchored high density lipoprotein binding protein 1 Neighboring gene uncharacterized LOC124902036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19610 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19612 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144332854-144333354 Neighboring gene ZFP41 zinc finger protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19613 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19614 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144350631-144351453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28067 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144353055-144353555 Neighboring gene GLI family zinc finger 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:144357207-144357850 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144357851-144358494 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:144361711-144362353 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28068 Neighboring gene MYC-induced long non-coding RNA

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_180764.1 

    Range
    101..990
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    143246394..143247283
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    144393781..144394670
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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