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LOC130002761 ATAC-STARR-seq lymphoblastoid silent region 20384 [ Homo sapiens (human) ]

Gene ID: 130002761, updated on 14-Oct-2023

Summary

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Gene symbol
LOC130002761
Gene description
ATAC-STARR-seq lymphoblastoid silent region 20384
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 LOC130002761 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 (129610678..129610727)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141815278..141815327)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132252097-132252756 Neighboring gene extensin-like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132252757-132253416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132253417-132254075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132256099-132256899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132256900-132257699 Neighboring gene long intergenic non-protein coding RNA 963 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132257700-132258500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132258501-132259299 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132259614-132260182 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132260183-132260750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132287329-132287829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132310394-132310894 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132317282-132317929 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132318577-132319224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132319225-132319870 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132320519-132321164 Neighboring gene HNF1 motif-containing MPRA enhancer 89 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332093-132332956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132332957-132333820 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132333821-132334682 Neighboring gene uncharacterized LOC105376292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29113 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132346053-132346610 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132349961-132350644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132362549-132363048 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29115 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132366575-132367074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132369161-132369798 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20385 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373341-132373842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132373843-132374342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132382842-132383492 Neighboring gene chromosome 9 open reading frame 50 Neighboring gene N-terminal Xaa-Pro-Lys N-methyltransferase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29118 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132388415-132388953 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132393630-132394420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132402376-132402933 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132402934-132403490 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20387 Neighboring gene ankyrin repeat and SOCS box containing 6

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

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_182207.1 

    Range
    101..150
    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
    129610678..129610727
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    141815278..141815327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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