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LOC130002773 ATAC-STARR-seq lymphoblastoid silent region 20391 [ Homo sapiens (human) ]

Gene ID: 130002773, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130002773
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20391
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 LOC130002773 in Genome Data Viewer
Location:
chromosome: 9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (129835207..129835556)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142039778..142040127)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20388 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20389 Neighboring gene Sharpr-MPRA regulatory region 13743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29121 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29122 Neighboring gene torsin family 1 member B Neighboring gene Sharpr-MPRA regulatory region 5710 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132597987-132598487 Neighboring gene torsin family 1 member A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132601680-132602180 Neighboring gene chromosome 9 open reading frame 78 Neighboring gene ubiquitin specific peptidase 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29123 Neighboring gene Sharpr-MPRA regulatory region 12255 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132632499-132632998 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132636644-132637144 Neighboring gene Sharpr-MPRA regulatory region 12063 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132647083-132647764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29125 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20393 Neighboring gene microRNA 6855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132651249-132652136 Neighboring gene Sharpr-MPRA regulatory region 3297 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29128 Neighboring gene Sharpr-MPRA regulatory region 1290 Neighboring gene formin binding protein 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29129 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29131 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29132 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20394 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29133 Neighboring gene Sharpr-MPRA regulatory region 9235 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29136 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29138 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29140 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29142 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29143 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29144 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:132786300-132786450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29146 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132796970-132797470 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132797471-132797971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29148 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20395 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20396 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132811133-132811633

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_182219.1 

    Range
    101..450
    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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    129835207..129835556
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    142039778..142040127
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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