Genome-wide association studies and re-sequencing projects are revealing an increasing number of disease-associated SNPs, a large fraction of which are non-coding. Although they could have relevance for disease susceptibility and progression, the lack of information about regulatory regions impedes the assessment of their functionality. Here we present a web server, ChroMoS (Chromatin Modified SNPs), which combines genetic and epigenetic data with the goal of facilitating SNPs classification, prioritization and prediction of their functional consequences. ChroMoS uses a large database of SNPs and chromatin states, but allows a user to provide his/her own genetic information. Based on the SNP classification and interactive prioritization, a user can compute the functional impact of multiple SNPs using two prediction tools, one for differential analysis of transcription factor binding (sTRAP) and another for SNPs with potential impact on binding of miRNAs (MicroSNiPer).