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LOC130064751 ATAC-STARR-seq lymphoblastoid silent region 10809 [ Homo sapiens (human) ]

Gene ID: 130064751, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064751
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10809
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 LOC130064751 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 (46350001..46350060)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (49177447..49177506)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46853258..46853317)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46763899-46764398 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr19:46765735-46766934 Neighboring gene Sharpr-MPRA regulatory region 13463 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46774457-46775170 Neighboring gene IGF like family member 1 pseudogene 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46806397-46806980 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46806981-46807564 Neighboring gene hypoxia inducible factor 3 subunit alpha Neighboring gene RNA, U6 small nuclear 924, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46823333-46823834 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46823835-46824334 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14837 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46854004-46854805 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10811 Neighboring gene protein phosphatase 5 catalytic subunit Neighboring gene uncharacterized LOC105372426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46886025-46886926 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46896972-46897472 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46906697-46907404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46911937-46912461 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46915195-46916028 Neighboring gene coiled-coil domain containing 8

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_199168.1 

    Range
    101..160
    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
    46350001..46350060
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    49177447..49177506
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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