SNPs3D analysis is only provided for non-synonymous SNPs. Other sorts of SNPs, particularly those affecting transcription, splicing and perhaps RNA message structure will also play a role in susceptibility to complex trait disease. Little data is available on the relative importance of the different SNP types, although for monogenic disease, the role is relatively small. For example, single base variant effects operating through transcription are quite rare, accounting for 0.5% of cases [1]. Whatever the case, it is clearly desirable to include other classes of SNP. It should shortly be possible to extend coverage in this way, using DNA sequence profiles based on the complete genome sequences of higher eukaryotes.
