Some useful SNP annotation databases:

• SeattleSeq Annotation
• GEN2PHEN Knowledge Centre
• Duke SequenceVariantAnalyzer, or SVA
• SNP Function Portal from University of Michigan
• PolyPhen (=Polymorphism Phenotyping): prediction of functional effect of human nsSNPs
• SIFT from J.Craig Venter Institute

Related web-tools

• Integrative Genomics Viewer (IGV)

Gene-based test

• VEGAS, or Versatile Gene-based Association Study