MAGMA

https://ctg.cncr.nl/software/magma

The brower-based version of MAGMA is called FUMA:

https://ctg.cncr.nl/software/fuma_gwas

MAGMA is relatively easy to use (especially in browser version), but what is it actually doing behind the scenes? Here are two papers:

The first is the original MAGMA publication, but I would actually recommend reading the second one instead (or at least, first). Both articles are written by the same primary group of authors; the second provides a better overview of the field, potential approaches, what MAGMA does differently than competing approaches, and why what MAGMA does is better.