The mechanisms that underlie the association between obesity and type-2 diabetes have yet to be fully understood. Here we interpreted the combined impacts of diabetes and obesity associated single nucleotide polymorphisms (SNPs) by integrating data on the genes with which they physically interact and the functional (i.e. expression quantitative trait loci [eQTL]) outcomes associated with these interactions. We identified enrichment for spatially regulated genes involved in lipid metabolism in adipose, skeletal muscle, and pancreas (p-value = 1.57 x 10-2). The spatial eQTL SNP-gene interactions occur in a tissue and disease specific manner. For example, obesity associated eQTL SNP-gene interactions occurred most frequently in the thyroid (23.16%) and tibial nerve (17.90%) while those associated with type-2 diabetes occurred most frequently in the thyroid (22.16%) and subcutaneous adipose (19.32%). Our results are consistent with differential regulation of genes by spatially connected regions that are marked by disease associated SNPs in tissues involved in regulating energy homoestasis and adiposity. Investigating these putative spatial SNP-gene interactions may shed more light on the development of obesity and type 2-diabetes.