**80**wrote:

Hi,

I am using a post-gwas analysis tools to test genetic overlap between different traits based on summary level data, and it requires the effect size(beta) and SE.

So for summary stats that has the Z score measures, beta and SE are estimated by using the following formula that was published in a large scale study on Alzheimers.

```
SE~=sqrt(VP/(ES×2pq))
Beta=SE×Z
```

where:

- VP: phenotypic variance approximated to 1;
- ES: effective sample size
- pq: allele frequencies (p allele, q allele)
- Z: Z scores

The summary stats that I currently have access to does not have allele frequency information.

head of the summary stats:

```
> Chr Pos MarkerName EffectAllele OtherAllele Z P.value TotalSampleSize
> 1 744055 rs3131000 a g -1.60 0.10 23546
```

Is there a way to calculate the Betas and SE without contacting the study, with just relying on the information that is currently publicly available.

**0**• written 3.9 years ago by muralinmars •

**80**

Hi, Would it be possible to send the link of the Alzheimers paper you found the equation in please?

0I am somewhat pressed for time but it's not 100% clear which data-points you have. Please take a look here and see if you can work back from the Z-score calculation: A: SNP dataset and Z Score

Do you have the allele tallies?

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