Illumina Zhonghua Chip Two Snp The Same Position

Question

[Liyf]

I am very confused about illumina Zhonghua, why different SNPs have the same chrosome position, take one for example, rs28456011 and kgp4449990, both chr1:1567206(hg19)???

[Sean Davis]

When you contacted Illumina, what did they say, just out of curiosity?

[Liyf]

I just contacted illumina, and not get reply. I am waiting.

Answer 1

[JC]

One simple explanation (besides duplicate entries with different IDs) is they represent an unique variation at the same position, chr1:1567206 in the reference is a G, the rs28456011 is reported as A, maybe kgp4449990 is a T or C (I didn't find the genotype).

[Liyf]

Thank you！I am still confused about this, I think may be you are right. In fact, I felt that if I use all the SNPs, I will not miss any important SNPs