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LOC130063328 ATAC-STARR-seq lymphoblastoid silent region 9960 [ Homo sapiens (human) ]

Gene ID: 130063328, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063328
Gene description
ATAC-STARR-seq lymphoblastoid silent region 9960
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 LOC130063328 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 (6671190..6671289)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (6660819..6660918)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (6671201..6671300)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13850 Neighboring gene ribosomal protein L7 pseudogene 50 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13852 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6631163-6631664 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13857 Neighboring gene TNF superfamily member 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6674384-6674960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:6674961-6675535 Neighboring gene Sharpr-MPRA regulatory region 11629 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6697003-6697504 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6697505-6698004 Neighboring gene complement C3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6727893-6728394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6728395-6728894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9961 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:6735174-6735942 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:6736406-6736560 Neighboring gene G protein-coupled receptor 108 Neighboring gene microRNA 6791

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_197745.1 

    Range
    101..200
    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
    6671190..6671289
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    6660819..6660918
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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