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LOC130067822 ATAC-STARR-seq lymphoblastoid silent region 13956 [ Homo sapiens (human) ]

Gene ID: 130067822, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130067822
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13956
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 LOC130067822 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 (50200331..50201270)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (50707091..50708031)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (50638760..50639699)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50609993-50610685 Neighboring gene pannexin 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50622054-50622629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19298 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50628084-50628698 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:50628699-50629313 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19303 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13955 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19304 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19305 Neighboring gene TraB domain containing Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13957 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19306 Neighboring gene TRABD antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50644205-50644771 Neighboring gene selenoprotein O Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50644772-50645337 Neighboring gene SELENOO antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50645905-50646469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50658024-50658666 Neighboring gene tubulin gamma complex component 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50676935-50677436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50677437-50677936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19307 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:50682041-50682971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19309

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_202237.1 

    Range
    101..1040
    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
    50200331..50201270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    50707091..50708031
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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