How does dbSNP code alleles for SNPs from multiple studies across multiple platforms so that they are comparable?
A submitted SNP has a fixed orientation that is defined by its flanking sequence which allows us to map the alleles to the refSNP, the reference genome, or any number of genomic sequences/assemblies. Top / Bottom orientation can be determined by a simple algorithm applied to the alleles and flanking sequence, however, the algorithm is defined for single base alleles only and may not work with some palendromic flanking sequences. Note: To orient linked SNPs in a haplotype, you cannot use submitted SNP (ss), refSNP (rs) or top/bottom orientations; instead you must use the orientation to a common sequence or assembly.
