Alcohol dependence (AD) and nicotine dependence (ND) co-occur frequently (AD+ND). We integrated SNP-based, gene-based, and protein-protein interaction (PPI) network analyses to identify shared risk genes or gene subnetworks for AD+ND in African Americans (AAs, N=2094) and European Americans (EAs, N=1207). The DSM-IV criterion counts for AD and ND were modeled as two dependent variables in a multivariate linear mixed model, and analyzed separately for the two populations. The most significant SNP was rs6579845 in EAs (p<1.29×10−8) in GM2A, which encodes GM2 ganglioside activator, and is a cis-expression quantitative locus (eQTL) that affects GM2A expression in blood and brain tissues. However, this SNP was not replicated in another small sample. We identified a subnetwork of 24 genes that contributed to the AD+ND criterion counts. In the gene-set analysis for the subnetwork in an independent sample, the Study of Addiction: Genetics and Environment project (SAGE) (predominately EAs), these 24 genes as a set differed in AD+ND versus control subjects in EAs (p=0.041). Functional enrichment analysis for this subnetwork revealed that the gene enrichment involved primarily nerve growth factor pathways, and cocaine and amphetamine addiction. In conclusion, we identified a genomewide significant variant at GM2A and a gene subnetwork underlying the genetic trait of shared AD+ND. These results increase our understanding of the shared (pleiotropic) genetic risk that underlies AD+ND.