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LOC129932857 ATAC-STARR-seq lymphoblastoid silent region 1992 [ Homo sapiens (human) ]

Gene ID: 129932857, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932857
Gene description
ATAC-STARR-seq lymphoblastoid silent region 1992
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 LOC129932857 in Genome Data Viewer
Location:
chromosome: 1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (235867074..235867373)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (235263682..235263981)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (236030374..236030673)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene lysosomal trafficking regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2805 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1991 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2807 Neighboring gene microRNA 1537 Neighboring gene RNA, U5E small nuclear 2, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1993 Neighboring gene uncharacterized LOC105373215 Neighboring gene MPRA-validated peak780 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:236073306-236074505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:236081529-236082028 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2808 Neighboring gene long intergenic non-protein coding RNA 2768 Neighboring gene RNA, U6 small nuclear 968, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1994 Neighboring gene MPRA-validated peak781 silencer Neighboring gene meiotic recombination hotspot NID3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2809 Neighboring gene MPRA-validated peak782 silencer Neighboring gene meiotic recombination hotspot NID2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:236162526-236163725 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:236164752-236165460 Neighboring gene nidogen 1 Neighboring gene meiotic recombination hotspot NID1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:236221449-236221986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1995

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_165882.1 

    Range
    101..400
    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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    235867074..235867373
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    235263682..235263981
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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