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LOC130008150 ATAC-STARR-seq lymphoblastoid silent region 4592 [ Homo sapiens (human) ]

Gene ID: 130008150, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130008150
Gene description
ATAC-STARR-seq lymphoblastoid silent region 4592
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 LOC130008150 in Genome Data Viewer
Location:
chromosome: 12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (57755546..57755645)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (57723897..57723996)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (58149329..58149428)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:58120605-58121240 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:58121241-58121874 Neighboring gene AGAP2 antisense RNA 1 Neighboring gene ArfGAP with GTPase domain, ankyrin repeat and PH domain 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:58127413-58128612 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:58131678-58131897 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6551 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6553 Neighboring gene tetraspanin 31 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4588 Neighboring gene microRNA 6759 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:58145719-58146452 Neighboring gene cyclin dependent kinase 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4591 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4593 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6554 Neighboring gene membrane associated ring-CH-type finger 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6555 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:58158104-58158882 Neighboring gene cytochrome P450 family 27 subfamily B member 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr12:58164747-58165946 Neighboring gene methyltransferase 1, tRNA methylguanosine

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_188676.1 

    Range
    101..200
    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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    57755546..57755645
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    57723897..57723996
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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