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LOC130064039 ATAC-STARR-seq lymphoblastoid silent region 10425 [ Homo sapiens (human) ]

Gene ID: 130064039, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064039
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10425
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 LOC130064039 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 (18919120..18919309)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19054878..19055067)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19029929..19030118)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10419 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10421 Neighboring gene NANOG hESC enhancer GRCh37_chr19:18944963-18945515 Neighboring gene UPF1 RNA helicase and ATPase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14333 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18960435-18960659 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10422 Neighboring gene ceramide synthase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10423 Neighboring gene growth differentiation factor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18994867-18995367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10424 Neighboring gene COPI coat complex subunit epsilon Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19028406-19029296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14334 Neighboring gene DEAD-box helicase 49 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19042288-19042799 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19042800-19043310 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19043997-19044615 Neighboring gene homer scaffold protein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10426 Neighboring gene HOMER3 antisense RNA 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_198456.1 

    Range
    101..290
    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
    18919120..18919309
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19054878..19055067
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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