Which allele is the effect allele after SVT (b.wald)?

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Carmen F. Bjurstrom

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Apr 16, 2020, 3:02:02 AM4/16/20
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Hi!
Does anybody know which of the alleles is the effect allele, after running a single variant test (b.wald) on EPACT?
The marker_Id column provides information about the SNP, example (A/T), A being the reference allele and T being the alternative allele, but
it is unclear to me, which of the two alleles causes the effect?
Grateful for any input. Thank you in advance!

Hyun Min Kang

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Apr 16, 2020, 9:31:03 AM4/16/20
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The non-reference allele (T in the example) is always the effect allele.

Hyun.
-----------------------------------------------------
Hyun Min Kang, Ph.D.
Associate Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu


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Carmen F. Bjurstrom

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Apr 16, 2020, 9:46:50 AM4/16/20
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Thank you very much!


On Thursday, April 16, 2020 at 3:31:03 PM UTC+2, Hyun Min Kang wrote:
The non-reference allele (T in the example) is always the effect allele.

Hyun.
-----------------------------------------------------
Hyun Min Kang, Ph.D.
Associate Professor of Biostatistics
University of Michigan, Ann Arbor
Email : hmk...@umich.edu


On Thu, Apr 16, 2020 at 3:02 AM Carmen F. Bjurstrom <cflbju...@gmail.com> wrote:
Hi!
Does anybody know which of the alleles is the effect allele, after running a single variant test (b.wald) on EPACT?
The marker_Id column provides information about the SNP, example (A/T), A being the reference allele and T being the alternative allele, but
it is unclear to me, which of the two alleles causes the effect?
Grateful for any input. Thank you in advance!

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