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LOC130066734 ATAC-STARR-seq lymphoblastoid silent region 13340 [ Homo sapiens (human) ]

Gene ID: 130066734, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066734
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13340
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 LOC130066734 in Genome Data Viewer
Location:
chromosome: 21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 21 NC_000021.9 (42234927..42234996)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 21 NC_060945.1 (40624984..40625053)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 21 NC_000021.8 (43655037..43655106)

Chromosome 21 - NC_000021.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372814 Neighboring gene ATP binding cassette subfamily G member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43640159-43640690 Neighboring gene RNA, 5S ribosomal pseudogene 492 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18508 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18509 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43681218-43681718 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_62106 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18510 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13341 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43726767-43727266 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43732190-43733186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43736619-43737238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43737239-43737857 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr21:43740112-43740766 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43741168-43741668 Neighboring gene trefoil factor 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr21:43755987-43756488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr21:43757967-43758662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18512 Neighboring gene H3K27ac hESC enhancer GRCh37_chr21:43763551-43764050 Neighboring gene trefoil factor 2

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_201150.1 

    Range
    101..170
    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_000021.9 Reference GRCh38.p14 Primary Assembly

    Range
    42234927..42234996
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060945.1 Alternate T2T-CHM13v2.0

    Range
    40624984..40625053
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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