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LOC129929550 ATAC-STARR-seq lymphoblastoid silent region 346 [ Homo sapiens (human) ]

Gene ID: 129929550, updated on 12-Sep-2024

Summary

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Gene symbol
LOC129929550
Gene description
ATAC-STARR-seq lymphoblastoid silent region 346
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 LOC129929550 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 (18902322..18902541)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (18722130..18722349)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (19228816..19229035)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene aldehyde dehydrogenase 4 family member A1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19210623-19210854 Neighboring gene microRNA 4695 Neighboring gene uncharacterized LOC124903866 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:19229285-19230102 Neighboring gene microRNA 1290 Neighboring gene intermediate filament family orphan 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19248832-19249412 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 283 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19253369-19253995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 285 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 286 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19259223-19260210 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr1:19261862-19262407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19262408-19262952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19262953-19263498 Neighboring gene Sharpr-MPRA regulatory regions 2400 and 6542 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19268377-19268894 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 287 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19276675-19277594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 289 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 347 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 293 Neighboring gene uncharacterized LOC105376815 Neighboring gene MPRA-validated peak97 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19334779-19335422 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:19337151-19338350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19338425-19339336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19354797-19355297 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19362307-19362878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19370112-19371086

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_162607.1 

    Range
    101..320
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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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    18902322..18902541
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    18722130..18722349
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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