<p>Negative beta means that the trait under test is negatively correlated with the allele. What this actually means in relation to your specific question will depend on how the trait is coded and how the allele is coded.</p>
<p>It might, for example, be the case that &quot;yes&quot; is coded as 0 and &quot;no&quot; as 1, in which case a &quot;no&quot; answer would be associated with a high allele count for allele 2. You will need to check the algorithm to find that out, or (better) do your own manual / independent checking of alleles to discover the direction of association.</p>
<p>Take care when interpreting the results of these association tests, especially when deviating from statements beyond what the results actually say. You should also pay attention to is meaningless, whereas a beta value of -3.43 means there is a strong correlation between the trait and allele.</p>

CC BY-SA 4.0
2022-06-03T03:17:45.347Z
2022-06-07T23:13:03.903Z
2022-06-07T23:13:03.903Z
gringer
<p>I have run a GWAS on a binary trait - &quot;Are you following a carnivore diet?&quot; - so the cases are individuals who follow this diet, and the controls are individuals who do not follow this diet. I have a genome-wide significant SNP, with a negative beta in reference to Allele 2. Does this imply that individuals with Allele 2 are less likely to follow this diet?</p>

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2022-06-02T17:13:38.833Z
Can you provide some outputs and provide some details about exactly how you performed your GWAS and estimation? What is your statistical test, is there e.g. a logistic/logit transform involved?
Maximilian Press
<gwas><genetics>
How to interpret a negative beta within a binary GWAS?
# How to interpret a negative beta within a binary GWAS?

(Asked by: username_0 on 2022-06-02)

I have run a GWAS on a binary trait - "Are you following a carnivore diet?" - so the cases are individuals who follow this diet, and the controls are individuals who do not follow this diet. I have a genome-wide significant SNP, with a negative beta in reference to Allele 2. Does this imply that individuals with Allele 2 are less likely to follow this diet?

**Tags:** gwas, genetics
> **Comments:**
> **username_1**: Can you provide some outputs and provide some details about exactly how you performed your GWAS and estimation? What is your statistical test, is there e.g. a logistic/logit transform involved?  

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## 1 answers

### Answer by username_2 on 2022-06-03. Score: 1 | Accepted answer

Negative beta means that the trait under test is negatively correlated with the allele. What this actually means in relation to your specific question will depend on how the trait is coded and how the allele is coded.

It might, for example, be the case that "yes" is coded as 0 and "no" as 1, in which case a "no" answer would be associated with a high allele count for allele 2. You will need to check the algorithm to find that out, or (better) do your own manual / independent checking of alleles to discover the direction of association.

Take care when interpreting the results of these association tests, especially when deviating from statements beyond what the results actually say. You should also pay attention to is meaningless, whereas a beta value of -3.43 means there is a strong correlation between the trait and allele.


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