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LOC130056800 ATAC-STARR-seq lymphoblastoid silent region 6307 [ Homo sapiens (human) ]

Gene ID: 130056800, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130056800
Gene description
ATAC-STARR-seq lymphoblastoid silent region 6307
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 LOC130056800 in Genome Data Viewer
Location:
chromosome: 15
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (38564571..38564810)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (36369863..36370102)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (38856772..38857011)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene CTD small phosphatase 2 pseudogene Neighboring gene family with sequence similarity 98 member B Neighboring gene uncharacterized LOC105370774 Neighboring gene RAS guanyl releasing protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9204 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6306 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:38857079-38857590 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:38885521-38886720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9210 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9211 Neighboring gene uncharacterized LOC105370775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9212 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9213 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9214 Neighboring gene long intergenic non-protein coding RNA 2694

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_191221.1 

    Range
    101..340
    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_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    38564571..38564810
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    36369863..36370102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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