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Minor alleles same but the risk alleles different for same SNP in differnt popul

SNP risk alleles minor alleles

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#1 angel0071987



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Posted 05 March 2013 - 02:43 AM

i have found for one SNP that the minor allele (A) is the risk allele in population 1, and yet in population 2 the minor allele is the same (A), but in this case it is protective why is this? (the risk and protection was determined by the odds ratio - OR >1 A1 increases risk of disease compared to A2). the SNP found may not be the causative SNP itself but instead be in linkage disequilibrium with an unidentified SNP which may be different in the 2 populations. Could there have been a crossover in one population - if so how would that make the risk SNPs different but minor allele the same?

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