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LOC130063095 ATAC-STARR-seq lymphoblastoid silent region 9805 [ Homo sapiens (human) ]

Gene ID: 130063095, updated on 27-Aug-2024

Summary

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Gene symbol
LOC130063095
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9805
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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Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (2739789..2740188)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (2715075..2715474)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene G protein subunit gamma 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2643435-2643934 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2650512-2650687 Neighboring gene microRNA 7850 Neighboring gene GNG7 intron CAGE-defined B cell enhancer Neighboring gene MPRA-validated peak3237 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2678080-2678228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13713 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9804 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2723575-2724487 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13715 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2734868-2735368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2735369-2735869 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13716 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:2739111-2739378 Neighboring gene DIRAS family GTPase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13717 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9806 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9807 Neighboring gene solute carrier family 39 member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2768763-2769263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9808 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13719 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9809 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2786765-2787291 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2787292-2787818 Neighboring gene small glutamine rich tetratricopeptide repeat co-chaperone alpha Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13720 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:2796022-2796522 Neighboring gene thimet oligopeptidase 1

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

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_197512.1 

    Range
    101..500
    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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    2739789..2740188
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    2715075..2715474
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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