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LOC130063547 ATAC-STARR-seq lymphoblastoid silent region 10097 [ Homo sapiens (human) ]

Gene ID: 130063547, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130063547
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10097
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 LOC130063547 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 (10960758..10961177)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (11087765..11088184)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (11071434..11071853)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene coactivator associated arginine methyltransferase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11037946-11038648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:11038649-11039349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10095 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10096 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:11046750-11047081 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:11048011-11048510 Neighboring gene Yip1 domain family member 2 Neighboring gene translocase of inner mitochondrial membrane 29 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14000 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11087822-11088514 Neighboring gene SWI/SNF related BAF chromatin remodeling complex subunit ATPase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11120526-11121026 Neighboring gene RNA, 7SL, cytoplasmic 192, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11138820-11139320 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14002 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14003 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14004 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14005 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:11167289-11167788 Neighboring gene LDLR antisense RNA 1 Neighboring gene low density lipoprotein receptor

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 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_197964.1 

    Range
    101..520
    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
    10960758..10961177
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    11087765..11088184
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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