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LOC130064339 ATAC-STARR-seq lymphoblastoid silent region 10563 [ Homo sapiens (human) ]

Gene ID: 130064339, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064339
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10563
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 LOC130064339 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 (38223987..38224556)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (41026149..41026718)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (38714627..38715196)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene signal induced proliferation associated 1 like 3 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38656938-38657140 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38661080-38661641 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38666131-38666631 Neighboring gene small nucleolar RNA, C/D box 152 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38693513-38694196 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:38700253-38701236 Neighboring gene RNA, 7SL, cytoplasmic 663, pseudogene Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:38707788-38708987 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38709595-38710094 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38718119-38718889 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10564 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14569 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38729145-38729644 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:38734884-38735760 Neighboring gene double PHD fingers 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:38746806-38746993 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38751829-38752766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38752767-38753703 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:38753844-38754761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10565 Neighboring gene protein phosphatase 1 regulatory inhibitor subunit 14A Neighboring gene serine peptidase inhibitor, Kunitz type 2

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_198756.1 

    Range
    101..670
    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
    38223987..38224556
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    41026149..41026718
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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