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LOC130067693 ATAC-STARR-seq lymphoblastoid silent region 13889 [ Homo sapiens (human) ]

Gene ID: 130067693, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130067693
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13889
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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Location:
chromosome: 22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45978535..45978684)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (46463136..46463285)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105373071 Neighboring gene uncharacterized LOC107985535 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46275792-46276707 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46276708-46277622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46291489-46292372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46292373-46293254 Neighboring gene Wnt family member 7B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46331075-46331575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46358809-46359309 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46362863-46363759 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr22:46364456-46365655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46382740-46383240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46383241-46383741 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46388443-46388942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46391059-46391977 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13891 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:46392941-46393610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19230 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:46402157-46403148 Neighboring gene uncharacterized LOC124905134 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13893 Neighboring gene dynein heavy chain -like pseudogene

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 across the chromatin accessible human genome. Hansen TJ, et al. Genome Res, 2022 Jul 20. 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

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_202108.1 

    Range
    101..250
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    45978535..45978684
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    46463136..46463285
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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