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LOC129999865 ATAC-STARR-seq lymphoblastoid silent region 18923 [ Homo sapiens (human) ]

Gene ID: 129999865, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129999865
Gene description
ATAC-STARR-seq lymphoblastoid silent region 18923
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 LOC129999865 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 (11200317..11200786)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (8538252..8538721, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (11057826..11058295)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene XK related 6 Neighboring gene uncharacterized LOC101929269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:10926551-10927368 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:10930301-10930846 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:10938390-10939589 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26998 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26999 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:10996613-10997114 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27001 Neighboring gene ribosomal protein L17 pseudogene 29 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18925 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27002 Neighboring gene Sharpr-MPRA regulatory region 9232 Neighboring gene long intergenic non-protein coding RNA 529 Neighboring gene ribosomal protein L19 pseudogene 13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27004 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:11141809-11142310 Neighboring gene uncharacterized LOC101929290 Neighboring gene myotubularin related protein 9

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_179311.1 

    Range
    101..570
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    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
    11200317..11200786
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654717.1 Reference GRCh38.p14 PATCHES

    Range
    2146137..2146605 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    8538252..8538721 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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