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LOC130066293 ATAC-STARR-seq lymphoblastoid silent region 13099 [ Homo sapiens (human) ]

Gene ID: 130066293, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130066293
Gene description
ATAC-STARR-seq lymphoblastoid silent region 13099
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 LOC130066293 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 (62143276..62143985)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (63934143..63934852)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (60718332..60719041)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13095 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:60641713-60642226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60662279-60662835 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60662836-60663391 Neighboring gene uncharacterized LOC105372706 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60687696-60688502 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:60697043-60697730 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:60697731-60698419 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60698420-60699107 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60708899-60709398 Neighboring gene LSM family member 14B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13100 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13101 Neighboring gene Sharpr-MPRA regulatory region 1753 Neighboring gene proteasome 20S subunit alpha 7 Neighboring gene SS18L1 subunit of BAF chromatin remodeling complex Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:60735092-60736291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60736587-60737199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13102 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:60757942-60758126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13103 Neighboring gene mitochondrial ribosome associated GTPase 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:60789379-60789879 Neighboring gene histamine receptor H3

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_200710.1 

    Range
    101..810
    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
    62143276..62143985
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    63934143..63934852
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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