Hi, I am doing allelic imbalance analysis (or allele-specific expression analysis) and have a question.
I want to see the association between marker SNP and nearby exon SNPs.
My data shows that for all three types of status of marker SNP (AA, AB, BB), AI ratios of exon SNPs are all nearly 1.
So, almost all exon SNPs should be removed as usual criteria for exclusion is 0.8 (SNPs with extreme major allele fraction above 0.8 are excluded).
So my question is, how can I conclude from this data? Does it show there is no association between the marker SNP and expression of nearby genes?