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LOC130064064 ATAC-STARR-seq lymphoblastoid silent region 10440 [ Homo sapiens (human) ]

Gene ID: 130064064, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064064
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10440
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 LOC130064064 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 (19385927..19386066)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19523411..19523550)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19496736..19496875)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene SURP and G-patch domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19431454-19432425 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:19446492-19447691 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19447717-19448218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19452846-19453354 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10437 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10438 Neighboring gene MAU2 sister chromatid cohesion factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19459741-19460241 Neighboring gene uncharacterized LOC124904656 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14348 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14349 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr19:19481673-19482872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19489171-19489816 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10439 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14350 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19505798-19506651 Neighboring gene GATA zinc finger domain containing 2A Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr19:19515640-19516548 and GRCh37_chr19:19516549-19517455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14352 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19538881-19539384 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19546839-19547444 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14354 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19563343-19563843 Neighboring gene microRNA 640 Neighboring gene Sharpr-MPRA regulatory region 5941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14356 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14357 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19573083-19573864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19583474-19584166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19584167-19584858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10444 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19585552-19586243 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19593349-19593956 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19595063-19595847 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:19599635-19600834 Neighboring gene Sharpr-MPRA regulatory region 10818/8147 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:19602420-19603619 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19615802-19616302 Neighboring gene testis specific serine kinase 6

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_198481.1 

    Range
    101..240
    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
    19385927..19386066
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19523411..19523550
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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