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LOC130062452 ATAC-STARR-seq lymphoblastoid silent region 9435 [ Homo sapiens (human) ]

Gene ID: 130062452, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130062452
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9435
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 LOC130062452 in Genome Data Viewer
Location:
chromosome: 18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (48540507..48540596)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (48731706..48731795)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (46066878..46066967)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 456 Neighboring gene RNA polymerase III subunit G pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:46046456-46046664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9436 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:46068922-46069698 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:46069699-46070473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46070992-46071557 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46076265-46076766 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46108065-46108701 Neighboring gene cap binding complex dependent translation initiation factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46108702-46109338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46109339-46109974 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46137869-46138684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46141771-46142312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:46145063-46145781 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13288 Neighboring gene uncharacterized LOC105372107 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46202169-46202793 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13291 Neighboring gene microRNA 4743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46225014-46225804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:46225805-46226594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13293

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_195344.1 

    Range
    101..190
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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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    48540507..48540596
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_013171814.1 Reference GRCh38.p14 PATCHES

    Range
    25526..25615
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    48731706..48731795
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    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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