Odds Ratio Confidence Intervals in SNP Test

Question

[LauferVA]

Hello, I am using SNP Test to do association testing and generate relevant statistics. One of my SNPs appeared strongly associated, p=1.09*10-6; OR = 1.16, 95% CI 0.99 -1.35.

I was just wondering what is being used to calculate the OR CI since it crosses 1, but the p-value appears highly significant.

Can anyone explain this to me?

[Randel]

Which OR do you refer to? het_OR, hom_OR, or all_OR? Can you provide more information, like genotype counts for that SNP?

[Đạt]

Hi, Did you have a question for this answer? I use the imputed variant with method is expected and frequentist is 2 ( dominant). The P-value is 5.7962 e-06 but all_OR is 0.79807 and the CI 99 is: 0.49-1.28 while the hom_OR is 0.02 and CI: 0.0005 -1.18. Could you share the experience? Thank you