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LOC130004693 ATAC-STARR-seq lymphoblastoid silent region 2810 [ Homo sapiens (human) ]

Gene ID: 130004693, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130004693
Gene description
ATAC-STARR-seq lymphoblastoid silent region 2810
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 LOC130004693 in Genome Data Viewer
Location:
chromosome: 10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (110214595..110214644)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (111098463..111098512)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (111974353..111974402)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:111910896-111911890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:111911891-111912883 Neighboring gene small nuclear ribonucleoprotein polypeptide G pseudogene 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:111924423-111924922 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:111928634-111929601 Neighboring gene Sharpr-MPRA regulatory region 9707 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:111933901-111934496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:111965444-111965944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2808 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:111969909-111970887 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4005 Neighboring gene uncharacterized LOC105378480 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2812 Neighboring gene MAX interactor 1, dimerization protein Neighboring gene NANOG hESC enhancer GRCh37_chr10:112045143-112045644 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2813 Neighboring gene survival motor neuron domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4009 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4010 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:112116377-112117576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4017 Neighboring gene Sharpr-MPRA regulatory region 10815 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr10:112169725-112170924 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr10:112174002-112175201 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:112177315-112177815 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2814 Neighboring gene uncharacterized LOC105378482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4020 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4021 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:112190742-112191347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4022

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_184138.1 

    Range
    101..150
    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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    110214595..110214644
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    111098463..111098512
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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