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LOC129996957 ATAC-STARR-seq lymphoblastoid silent region 17458 [ Homo sapiens (human) ]

Gene ID: 129996957, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129996957
Gene description
ATAC-STARR-seq lymphoblastoid silent region 17458
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 LOC129996957 in Genome Data Viewer
Location:
chromosome: 6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (109381925..109382204)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (110559962..110560241)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109703128..109703407)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene coiled-coil domain containing 162, pseudogene Neighboring gene RNY3 pseudogene 11 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:109649788-109650315 Neighboring gene ribosomal protein L7 pseudogene 28 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109703563-109704072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24923 Neighboring gene CD164 molecule Neighboring gene Sharpr-MPRA regulatory region 15445 Neighboring gene peptidylprolyl isomerase like 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109761883-109762088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17460 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24926 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109775979-109776487 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24928 Neighboring gene microtubule associated monooxygenase, calponin and LIM domain containing 1 Neighboring gene sphingomyelin phosphodiesterase 2 Neighboring gene zinc finger and BTB domain containing 24

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_176403.1 

    Range
    101..380
    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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    109381925..109382204
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    110559962..110560241
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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