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LOC130064275 ATAC-STARR-seq lymphoblastoid silent region 10544 [ Homo sapiens (human) ]

Gene ID: 130064275, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064275
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10544
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 LOC130064275 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 (35959120..35959169)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38504910..38504959)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36450022..36450071)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36398209-36398362 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14505 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14506 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14507 Neighboring gene transmembrane immune signaling adaptor TYROBP Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14508 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14509 Neighboring gene leucine rich repeat and fibronectin type III domain containing 3 Neighboring gene uncharacterized LOC105372383 Neighboring gene Sharpr-MPRA regulatory region 3529 Neighboring gene Sharpr-MPRA regulatory region 1826 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10543 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14510 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36453209-36453373 Neighboring gene MPRA-validated peak3453 silencer Neighboring gene MPRA-validated peak3454 silencer Neighboring gene MPRA-validated peak3455 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36485053-36485552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14512 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14513 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10545 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10546 Neighboring gene succinate dehydrogenase complex assembly factor 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36498887-36499428 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36499429-36499968 Neighboring gene spectrin repeat containing nuclear envelope family member 4

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_198692.1 

    Range
    101..150
    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
    35959120..35959169
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    38504910..38504959
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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