The new Ensembl release includes a new view for SNPs and other genomic variations. It shows the alignment of the polymorphic position together with 10 base pairs of sequence up- and downstream. The user can choose among all available multiple alignments. Polymorphic positions in the other species are also shown.
This is very useful for looking at ancestral alleles, especially in combination with our EPO alignments as they include the inferred ancestral sequence. Although dbSNP provide predicted ancestral alleles for human SNPs, these are based on the chimp sequence only. In several cases, the ancestral sequence inferred from the multiple alignment is in disagreement with the chimp sequence like in this example. Using multiple alignments gives better results and more confidence to the calls.