Question about imputation

Hi, can you help me with a imputation question.
My collaborators and I performed imputation using Michigan Server. I came across this common SNP below, which I could not impute I used Ilumina OmniExpressExome for the genotyping array. I am wondering if anyone has problem to impute the SNP below?

rs2417879
chr12:21109552 (hg19)
chr12:20956618 (hg38)

This is interesting – I looked at another dataset (genotyped with the GSA v2) that was also imputed using the Michigan Server (using the HRC reference panel), and this variant was also not present in this data.

Perhaps you could try and perform the imputation again using another reference panel.

Another option would be to find a proxy for this variant, using LDproxy in LDlink and use this variant in your analyses.

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