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Short report
Linkage disequilibrium analysis of global populations confirms presence of regulatory SNP rs11615992 of human P2RX7 gene and uncovers rs61083578 as potential alternative in fixed allele populations
Mauro Chavez
Johns Hopkins University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9126-8608
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The P2RX7 gene is ubiquitously expressed throughout the human body and encodes for ligand-gated ion channels. P2RX7 also contains the non-synonymous single nucleotide polymorphism (SNP) rs3751143 which has been linked to decreased ion channel function and diseases such as prostate cancer, tuberculosis, bipolar disorder, inflammation and Parkinson's disease amongst others. While there have been many studies on this gene, few dive into the allele-specific expression (ASE) of P2RX7. Previous research has shown over-expression of the rs3751143 wild-type A allele over the C allele in lung tissues of heterozygous individuals correlated with the presence of downstream SNP variant rs11615992. Linkage disequilibrium was demonstrated between these two SNPs in populations in China. This article aims to expand current knowledge for which SNPs near the P2RX7 gene are in linkage disequilibrium with rs3751143; expanding upon findings of Peng et al (2019). By using various bioinformatic tools on variant data gleaned from the 1000 Genomes Project, this analysis confirms that the downstream SNP rs11615992 is in strong LD with rs3751143 in populations across the world, outside of the initially studied Chinese groups. Furthermore, in the case of African populations, where rs11615992 seems fixed, rs61083578 was identified as a potential downstream regulatory element to P2RX7 allele-specific expression. The goal of this study is to contribute to the understanding of P2RX7 gene expression on a global scale with respect to regulation by SNPs surrounding the P2RX7 gene itself, strengthening the relevance of the research performed by Peng et al (2019).
Keywords
P2RX7, Allele-specific expression (ASE), linkage disequilibrium (LD), single nucleotide polymorphism (SNP), rs3751143, rs11615992, rs61083578
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This is a preprint. It has not completed peer review.
Short report
Linkage disequilibrium analysis of global populations confirms presence of regulatory SNP rs11615992 of human P2RX7 gene and uncovers rs61083578 as potential alternative in fixed allele populations
Mauro Chavez
Johns Hopkins University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9126-8608
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 14 May, 2020
No community comments so far
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Bioinformatics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The P2RX7 gene is ubiquitously expressed throughout the human body and encodes for ligand-gated ion channels. P2RX7 also contains the non-synonymous single nucleotide polymorphism (SNP) rs3751143 which has been linked to decreased ion channel function and diseases such as prostate cancer, tuberculosis, bipolar disorder, inflammation and Parkinson's disease amongst others. While there have been many studies on this gene, few dive into the allele-specific expression (ASE) of P2RX7. Previous research has shown over-expression of the rs3751143 wild-type A allele over the C allele in lung tissues of heterozygous individuals correlated with the presence of downstream SNP variant rs11615992. Linkage disequilibrium was demonstrated between these two SNPs in populations in China. This article aims to expand current knowledge for which SNPs near the P2RX7 gene are in linkage disequilibrium with rs3751143; expanding upon findings of Peng et al (2019). By using various bioinformatic tools on variant data gleaned from the 1000 Genomes Project, this analysis confirms that the downstream SNP rs11615992 is in strong LD with rs3751143 in populations across the world, outside of the initially studied Chinese groups. Furthermore, in the case of African populations, where rs11615992 seems fixed, rs61083578 was identified as a potential downstream regulatory element to P2RX7 allele-specific expression. The goal of this study is to contribute to the understanding of P2RX7 gene expression on a global scale with respect to regulation by SNPs surrounding the P2RX7 gene itself, strengthening the relevance of the research performed by Peng et al (2019).