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LOC130062058 ATAC-STARR-seq lymphoblastoid silent region 9225 [ Homo sapiens (human) ]

Gene ID: 130062058, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130062058
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9225
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 LOC130062058 in Genome Data Viewer
Location:
chromosome: 17
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (82716523..82716762)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (83590910..83591149)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (80674399..80674638)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904093 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:80660456-80661655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80661763-80662564 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80671133-80671632 Neighboring gene uncharacterized LOC101929552 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9226 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80687657-80688157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80692522-80693234 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80693947-80694659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80694660-80695371 Neighboring gene fructosamine 3 kinase related protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80701509-80702145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9229 Neighboring gene Sharpr-MPRA regulatory region 591 Neighboring gene fructosamine 3 kinase Neighboring gene tubulin folding cofactor D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80747669-80748170 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:80751687-80752407 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80786629-80787475 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:80795429-80795930 Neighboring gene zinc finger protein 750

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_197134.1 

    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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    82716523..82716762
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    83590910..83591149
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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