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LOC130065586 ATAC-STARR-seq lymphoblastoid silent region 12752 [ Homo sapiens (human) ]

Gene ID: 130065586, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130065586
Gene description
ATAC-STARR-seq lymphoblastoid silent region 12752
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 LOC130065586 in Genome Data Viewer
Location:
chromosome: 20
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (25390545..25390964)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (25455649..25456068)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (25371181..25371600)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17665 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12746 Neighboring gene glycogen phosphorylase B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25274716-25275238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25276284-25276805 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25280703-25281254 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25281255-25281805 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:25289826-25291025 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25297613-25298222 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17668 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12747 Neighboring gene abhydrolase domain containing 12, lysophospholipase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:25310906-25311427 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25337131-25337731 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25337732-25338331 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12749 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12751 Neighboring gene uncharacterized LOC105372581 Neighboring gene peptidylprolyl isomerase A pseudogene 2 Neighboring gene MPRA-validated peak4176 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17669 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:25388698-25389455 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25418017-25418688 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25418689-25419360 Neighboring gene GINS complex subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25457461-25457961 Neighboring gene ninein like Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25483989-25484500 Neighboring gene Sharpr-MPRA regulatory region 10548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25506669-25507224 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25507225-25507779 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25513199-25514199 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25529495-25530318 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:25541385-25541914 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:25545021-25545520 Neighboring gene Sharpr-MPRA regulatory region 10614 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12753

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_200003.1 

    Range
    101..520
    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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    25390545..25390964
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    25455649..25456068
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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