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LOC129933177 ATAC-STARR-seq lymphoblastoid silent region 11196 [ Homo sapiens (human) ]

Gene ID: 129933177, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129933177
Gene description
ATAC-STARR-seq lymphoblastoid silent region 11196
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 LOC129933177 in Genome Data Viewer
Location:
chromosome: 2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (18560073..18560582)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (18592187..18592696)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (18741339..18741848)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373451 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:18513234-18513870 Neighboring gene uncharacterized LOC105373454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11195 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:18633458-18633722 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:18637372-18637948 Neighboring gene MPRA-validated peak3612 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr2:18727890-18728410 Neighboring gene Sharpr-MPRA regulatory region 12735 Neighboring gene NT5C1B-RDH14 readthrough Neighboring gene uncharacterized LOC105373456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15357 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15358 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15359 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15360 Neighboring gene RNA, U6 small nuclear 1215, pseudogene Neighboring gene 5'-nucleotidase, cytosolic IB Neighboring gene retinol dehydrogenase 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:18820604-18821104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:18821105-18821605 Neighboring gene Sharpr-MPRA regulatory region 8729 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:18845994-18847193 Neighboring gene NANOG hESC enhancer GRCh37_chr2:18958528-18959297 Neighboring gene long intergenic non-protein coding RNA 1376

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_166202.1 

    Range
    101..610
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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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    18560073..18560582
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    18592187..18592696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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