Genetic variants and risk of gastric cancer: a pathway analysis of a genome-wide association study

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Table 1 Candidate causal SNPs and pathways

Candidate SNP	Functional class	Gene	Candidate causal pathway*	-log ₁₀ ( P )†	In LD with	r ²	D’	-log ₁₀ ( P )‡
rs4745	Nonsynonymous coding	EFNA1	1	-	rs4460629	1.0	1.0	6.472
rs12904	Regulatory region	EFNA1	1	-	rs4460629	1.0	1.0	6.472
rs1801019	Nonsynonymous coding	UMPS	2,3	-	rs4234221	0.824	1.0	4.087
rs364897	Nonsynonymous coding	GBA	4,11	-	rs4460629	0.924	1.0	6.472
rs11187870	Regulatory region	PLCE1	5,6,7,8,9,10,12	-	rs3781264	0.857	1.0	10.405
rs2274223	Nonsynonymous coding	PLCE1	5,6,7,8,9,10,12	8.633	rs2274223	-	-	8.633
rs3765524	Nonsynonymous coding	PLCE1	5,6,7,8,9,10,12	8.556	rs3765524	-	-	8.556

SNP; single nucleotide polymorphism, LD; linkage disequilibrium.
*numbers indicate the indexes of pathway ranked significance (false discovery rate).
†-log₁₀ (P) values of candidate causal SNPs in the original genome wide association studies (GWAS), - denotes that this SNP is not represented in the original GWAS.
‡-log₁₀ (P) values of SNPs in LD with candidate causal SNPs in the original GWAS.