Comprehensive review and annotation of susceptibility SNPs associated with obesity‐related traits

Comprehensive review and annotation of susceptibility SNPs associated with obesity‐related traits We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non‐coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases. We identified 24,623 functional SNPs, including 4 nonsense SNPs, 479 missense SNPs, 399 untranslated region SNPs which might affect microRNA binding, 262 promoter and 5,492 enhancer SNPs which might affect transcription factor binding, 7 splicing sites, 76 SNPs which might affect gene methylation levels, 1,839 SNPs under natural selection and 17,351 SNPs which might modify histone binding. Expression quantitative trait loci analyses for functional SNPs identified 98 target genes, including 69 protein coding genes, 27 long non‐coding RNAs and 3 processed transcripts. The percentage of protein coding genes that could be correlated with obesity‐related pathways directly or through gene–gene interaction is 75.36 (52/69). Our results may serve as an encyclopaedia of obesity susceptibility SNPs and offer guide for functional experiments. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Obesity Reviews Wiley

Comprehensive review and annotation of susceptibility SNPs associated with obesity‐related traits

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Publisher
Wiley Subscription Services, Inc., A Wiley Company
Copyright
© 2018 World Obesity Federation
ISSN
1467-7881
eISSN
1467-789X
D.O.I.
10.1111/obr.12677
Publisher site
See Article on Publisher Site

Abstract

We aimed to summarize the results of genetic association studies for obesity and provide a comprehensive annotation of all susceptibility single nucleotide polymorphisms (SNPs). A total of 72 studies were summarized, resulting in 90,361 susceptibility SNPs (738 index SNPs and 89,623 linkage disequilibrium SNPs). Over 90% of the susceptibility SNPs are located in non‐coding regions, and it is challenging to understand their functional significance. Therefore, we annotated these SNPs by using various functional databases. We identified 24,623 functional SNPs, including 4 nonsense SNPs, 479 missense SNPs, 399 untranslated region SNPs which might affect microRNA binding, 262 promoter and 5,492 enhancer SNPs which might affect transcription factor binding, 7 splicing sites, 76 SNPs which might affect gene methylation levels, 1,839 SNPs under natural selection and 17,351 SNPs which might modify histone binding. Expression quantitative trait loci analyses for functional SNPs identified 98 target genes, including 69 protein coding genes, 27 long non‐coding RNAs and 3 processed transcripts. The percentage of protein coding genes that could be correlated with obesity‐related pathways directly or through gene–gene interaction is 75.36 (52/69). Our results may serve as an encyclopaedia of obesity susceptibility SNPs and offer guide for functional experiments.

Journal

Obesity ReviewsWiley

Published: Jan 1, 2018

Keywords: ; ; ;

References

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