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LOC129930671 ATAC-STARR-seq lymphoblastoid silent region 952 [ Homo sapiens (human) ]

Gene ID: 129930671, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129930671
Gene description
ATAC-STARR-seq lymphoblastoid silent region 952
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 LOC129930671 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 (63774084..63774133)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (63649908..63649957)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (64239755..64239804)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene phosphoglucomutase 1 Neighboring gene uncharacterized LOC105378771 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:64140637-64141138 Neighboring gene RNA, 7SL, cytoplasmic 130, pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr1:64179745-64180246 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:64187597-64188096 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:64197420-64197975 Neighboring gene Sharpr-MPRA regulatory region 14006 Neighboring gene Sharpr-MPRA regulatory region 13784 Neighboring gene Sharpr-MPRA regulatory region 321 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:64246221-64246776 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:64260455-64261114 Neighboring gene ribosomal protein L19 pseudogene 3 Neighboring gene receptor tyrosine kinase like orphan receptor 1 Neighboring gene cofilin 1 pseudogene 3

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_163721.1 

    Range
    101..150
    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
    63774084..63774133
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    63649908..63649957
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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