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LOC130067569 ATAC-STARR-seq lymphoblastoid silent region 13811 [ Homo sapiens (human) ]

Gene ID: 130067569, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067569
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13811
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 LOC130067569 in Genome Data Viewer
Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (41919600..41920069)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (42398465..42398934)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (42315604..42316073)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13802 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13803 Neighboring gene shisa family member 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42310379-42311304 Neighboring gene uncharacterized LOC124905125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13810 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19139 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42315058-42315561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19141 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19142 Neighboring gene TNF receptor superfamily member 13C Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42321037-42321538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42321539-42322038 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13813 Neighboring gene microRNA 378i Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19143 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42324809-42325419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42325420-42326029 Neighboring gene centromere protein M Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:42328573-42329080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19144 Neighboring gene CAGE-defined B cell enhancer downstream of CENPM Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:42335612-42336579 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19151 Neighboring gene small integral membrane protein 45

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_201984.1 

    Range
    101..570
    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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    41919600..41920069
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    42398465..42398934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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