Please Help Me Understand GWAS Results

Question

[chloek88]

Hi there,

It's my first time working with GWAS so please bare with me. I've used both GAPIT and rMVP to run some GWAS analysis. My phenotype is categorical ordinal, (ie. a 1 to 5 scale). I've gotten significant SNPs but I don't quite understand how to interpret the results. How do I know if it is significant because it had higher associations to a rating of '1' vs '5'?

[GenoMax]

Post a result example. Not sure if this description is going to be sufficient for people to give you an answer. You can redact gene names/sample info if you are worried about that.

[chloek88]

Example of my phenotypic data input

Example of the results table

The phenotypic data + genomic data (.vcf) were used as the inputs for the analysis in rMVP.

Thank you.