Orientation

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Some genes are read in the reverse direction, and as a result SNPs are sometimes reported reversed. This happens quite often, as 23andMe will report genotypes on the minus, while SNPedia and dbSNP tend to only report genotypes relative to the plus strand. Making it even more confusing, occasionally snps are flipped between genome versions (ie rs17602729).

https://customercare.23andme.com/entries/21272593-Which-DNA-strand-does-23andMe-report-for-SNP-genotypes-

https://customercare.23andme.com/entries/21252301-Which-reference-genome-does-23andMe-use-or-Why-is-the-strand-different-than-what-is-reported-by-dbSN

Each rs# in SNPedia has a field along the right side called 'Orientation.

If the value is 'plus' you don't need to do anything, 23andMe agrees with dbSNP.

If the value is 'minus' you need to change:

  • A->T
  • T->A
  • C->G
  • G->C

This leads to some ambiguous flips.

When needed, Promethease correctly flips genotypes from 23andMe's minus orientation into SNPedia's plus orientation.


  Orientation
MYH6 c.2161 minus
Rs10 plus
Rs1000113 plus
Rs100012
Rs10002492 plus
Rs1000283 minus
Rs10004195 plus
Rs10004839 plus
Rs10005603 plus
Rs1000579 plus
… further results