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LOC129932922 ATAC-STARR-seq lymphoblastoid silent region 2029 [ Homo sapiens (human) ]

Gene ID: 129932922, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129932922
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2029
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 LOC129932922 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 (245156394..245156933)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (244573860..244574399)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (245319696..245320235)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245316423-245317098 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245317099-245317774 Neighboring gene RNA, U1 small nuclear 132, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245342748-245343248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245343249-245343749 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:245358334-245359141 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:245366003-245366213 Neighboring gene kinesin family member 26B Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:245376557-245377756 Neighboring gene KIF26B antisense RNA 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:245397844-245398363 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:245419187-245420056 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:245420057-245420924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:245421793-245422660 Neighboring gene DnaJ heat shock protein family (Hsp40) member C19 pseudogene 8

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_165947.1 

    Range
    101..640
    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
    245156394..245156933
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    244573860..244574399
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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