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LOC130000033 ATAC-STARR-seq lymphoblastoid silent region 19024 [ Homo sapiens (human) ]

Gene ID: 130000033, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130000033
Gene description
ATAC-STARR-seq lymphoblastoid silent region 19024
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 LOC130000033 in Genome Data Viewer
Location:
chromosome: 8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (23457181..23457860)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (23732065..23732744)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (23314694..23315373)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19023 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23159094-23159594 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23159595-23160095 Neighboring gene R3H domain and coiled-coil containing 1 Neighboring gene lysyl oxidase like 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23177410-23177975 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23182003-23182503 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23195830-23196330 Neighboring gene LOXL2 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:23209911-23210493 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23236632-23237224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23237225-23237815 Neighboring gene Sharpr-MPRA regulatory region 9444 Neighboring gene Sharpr-MPRA regulatory region 13358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23273382-23273902 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:23279735-23280235 Neighboring gene ectonucleoside triphosphate diphosphohydrolase 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:23308148-23308855 Neighboring gene Sharpr-MPRA regulatory region 8456 Neighboring gene NANOG hESC enhancer GRCh37_chr8:23312327-23312828 Neighboring gene ENTPD4 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23326741-23327240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:23339113-23340081 Neighboring gene DnaJ heat shock protein family (Hsp40) member C5 pseudogene Neighboring gene uncharacterized LOC105379327

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_179479.1 

    Range
    101..780
    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_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    23457181..23457860
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    23732065..23732744
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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