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LOC130009157 ATAC-STARR-seq lymphoblastoid silent region 5067 [ Homo sapiens (human) ]

Gene ID: 130009157, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130009157
Gene description
ATAC-STARR-seq lymphoblastoid silent region 5067
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 LOC130009157 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 (124863402..124864081)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (124868539..124869218)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (125347948..125348627)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903045 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125234102-125234622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125234623-125235143 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125239799-125240701 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125242645-125243146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125243147-125243646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125245231-125245731 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7300 Neighboring gene Sharpr-MPRA regulatory region 2215 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7303 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7302 Neighboring gene MPRA-validated peak2030 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125268792-125269560 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125270855-125271355 Neighboring gene uncharacterized LOC124903046 Neighboring gene scavenger receptor class B member 1 Neighboring gene MPRA-validated peak2031 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125282050-125282560 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125282561-125283071 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25196 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125301275-125301774 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125309151-125309872 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125309873-125310594 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125323854-125324380 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125324381-125324905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:125346238-125346764 Neighboring gene uncharacterized LOC105370050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7306 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_25236 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:125351043-125352242 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125369125-125369812 Neighboring gene CRISPRi-validated cis-regulatory element chr12.4732 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7308 Neighboring gene RNA, U6 small nuclear 927, pseudogene Neighboring gene Sharpr-MPRA regulatory region 9680 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:125398493-125399450 Neighboring gene ubiquitin C

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_188812.1 

    Range
    101..780
    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
    124863402..124864081
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    124868539..124869218
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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