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LOC130063296 ATAC-STARR-seq lymphoblastoid silent region 9956 [ Homo sapiens (human) ]

Gene ID: 130063296, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063296
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9956
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 LOC130063296 in Genome Data Viewer
Location:
chromosome: 19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (6502296..6502565)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (6491793..6492062)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (6502307..6502576)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 25 member 41 Neighboring gene solute carrier family 25 member 23 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9951 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9950 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6464149-6464690 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6475606-6476345 Neighboring gene DENN domain containing 1C Neighboring gene crumbs cell polarity complex component 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6479893-6480392 Neighboring gene Sharpr-MPRA regulatory region 5032 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13825 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9954 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9955 Neighboring gene CRISPRi-validated cis-regulatory element chr19.1358 Neighboring gene tubulin beta 4A class IVa Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6506805-6507716 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6516143-6516683 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13827 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13831 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9959 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13832 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532416-6532916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6532917-6533417 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13833 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13837 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13838 Neighboring gene TNF superfamily member 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13839 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13840 Neighboring gene TGFBR1 pseudogene 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

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_197713.1 

    Range
    101..370
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    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
    6502296..6502565
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    6491793..6492062
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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