Hello Everyone, I'm new to GWAS so forgive me for asking naive question. I have my summary statistics(From Linear mixed model) looks like below:

```
CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ INFO N TEST BETA SE CHISQ LOG10P
```

Allele0 is the reference allele and allele1 is the alternative allele. I wonder how to calculate R^2 from this summary. The GWAS model used normal approximation, 𝜒^2 chi-square to estimate the P-value.

I saw different equations such as `SNP (PVE)=2p(1-p)*beta^2`

, and `SNP (PVE) = [2*(beta^2)*MAF*(1-MAF)]/[2*(beta^2)*MAF(1-MAF)+((se(beta))^2)*2*N*MAF*(1-MAF)]`

What's the best software to analyze the percentage of phenotypic variation explained by the identified SNPs?

Thank you very much!

I am not sure about where the second expression comes from.

You can read the response I gave in the following related post, which motivates the first expression. Note however that your trait has to have unit variance.

How to estimate the percent phenotypic variation explained by the significant SNP from a GWAS study?