I have a list of significant SNP-gene pairs after using SNOs genotyped on Illumina platform and using gene expression data. I used MatrixeQTL to obtain this. I am kind of stuck as to how to proceed with understanding these results and would like your views on them. I thought i can check the where the SNP in this significant pair map to in the genome and also do a simple GO analysis for the genes. I was looking up at some papers who have carried out a GO analysis for SNPS (Gowinda and SNP2GO). I thought of trying these but then, what I have is not a typical GWAS study and all I have is a list of SNPS and their position in the genome and gene expression and position of the genes on the genome. Any advice as to how to interpret this result will be appreciate as I am new to this field.
Thanks in advance.