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LOC130064046 ATAC-STARR-seq lymphoblastoid silent region 10431 [ Homo sapiens (human) ]

Gene ID: 130064046, updated on 12-Sep-2024

Summary

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Gene symbol
LOC130064046
Gene description
ATAC-STARR-seq lymphoblastoid silent region 10431
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 LOC130064046 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 (19110431..19110620)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (19246247..19246436)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (19221240..19221429)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene SURP and G-patch domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19162565-19163065 Neighboring gene armadillo repeat containing 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14335 Neighboring gene uncharacterized LOC124904655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10429 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10430 Neighboring gene solute carrier family 25 member 42 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:19198769-19199269 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:19205587-19206086 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:19207400-19208599 Neighboring gene Sharpr-MPRA regulatory region 5014 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:19230026-19230212 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19230180-19230759 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19230760-19231338 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19231339-19231917 Neighboring gene transmembrane protein 161A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19248669-19249530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14337 Neighboring gene BORCS8-MEF2B readthrough Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14338 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14339 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:19271207-19272182 Neighboring gene myocyte enhancer factor 2B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10435

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_198463.1 

    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
    19110431..19110620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    19246247..19246436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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