Procedure to detect interactions among selected SNPs. a) gene-based method: interaction among SNPs located in the same gene region (including 20 kb up and down stream of the gene) are exhaustively tested. Note that the previous method based on adjacent SNPs  can be considered a special case of this method; b) pathway-based method, part of STAT3 pathway are used to illustrate this method, interactions among SNPs located in different genes in the same pathway are tested; c) network based method: first, a disease-associated subnetwork is generated, then interactions among SNPs positioned in different genes in the subnetwork are tested; d) interactions between eSNPs and SNPs located in the genes whose expression are regulated by the eSNP are tested. Red triangles represent SNPs. Dashed lines represent potential interactions.