Personal Genome Explorer internally deals with genotypes oriented with respect to the reference human genome build 36.2. The genotype/orientation shown in the SNP lookup widget doesn’t necessarily match dbSNP’s alleles for the refSNP, as the refSNP may be oriented opposite the reference human genome.
To translate a genotype into the same orientation as the dbSNP data on the refSNP, you need to find the orientation of refSNP relative to the reference human genome. You can find that in the “Integrated Maps” section of the refSNP report, in the “Hit orientation” column for the row that has “reference” in the “Group label” column. If the refSNP’s orientation doesn’t match the genotype’s orientation as reported by Personal Genome Explorer, then the genotype oriented to the refSNP is the complementary nucleotide of the genotype displayed by Personal Genome Explorer.
For example, assume that Personal Genome Explorer displays a genotype of C and an orientation of plus for rs708393. The map for rs708393 shows that it maps to the reference human genome with an orientation of minus. Since that doesn’t match the orientation of Personal Genome Explorer’s genotype, the genotype oriented to the refSNP is the component of C: G.
Most literature and SNPedia pages refer to genotypes in the same orientation as the refSNP.
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