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Table 1 Candidate causal SNPs and pathways

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

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
  1. SNP; single nucleotide polymorphism, LD; linkage disequilibrium.
  2. *numbers indicate the indexes of pathway ranked significance (false discovery rate).
  3. †-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.
  4. ‡-log10 (P) values of SNPs in LD with candidate causal SNPs in the original GWAS.