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KMID : 0613820210310060568
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Journal of Life Science
2021 Volume.31 No. 6 p.568 ~ p.573
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The Association of Long Noncoding RNA LOC105372577 with Endoplasmic Reticulum Protein 29 Expression: A Genome-wide Association Study
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Lee So-Yeon
Kwon Ki-Sang
Ko Young-Hwa
Kwon O-Yu
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Abstract
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This study identified genomic factors associated with endoplasmic reticulum protein (ERp)29 gene expression in a genome-wide association study (GWAS) of genetic variants, including single-nucleotide polymorphisms (SNPs). In total, 373 European genes from the 1000 Genomes Project were analyzed. SNPs with an allelic frequency of less than or more than 5% were removed, resulting in 5,913,563 SNPs including in the analysis. The following expression quantitative trait loci (eQTL) from the long noncoding RNA LOC105372577 were strongly associated with ERp29 expression: rs6138266 (p<4.172e10), rs62193420 (p<1.173e10), and rs6138267 (p<2.041e10). These were strongly expressed in the testis and in the brain. The three eQTL were identified through a transcriptome-wide association study (TWAS) and showed a significant association with ERp29 and osteosarcoma amplified 9 (OS9) expression. Upstream sequences of rs6138266 were recognized by ChIP-seq data, while HaploReg was used to demonstrate how its regulatory DNA binds upstream of transcription factor 1 (USF1). There were no changes in the expression of OS9 or USF1 following ER stress.
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KEYWORD
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Endoplasmic reticulum protein (ERp)29, expression quantitative trait loci (eQTL), genome- wide association study (GWAS), osteosarcoma amplified 9 (OS9), single-nucleotide polymorphisms (SNPs)
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