inconsistent Rsquared values

[scoetzee]

Rsquared values change depending upon biological features:

I analyzed BCa candidate functional SNPs results from FuncSNPi, and realized that there are some errors (?).

For instance,
r^2 value of rs999737 and rs79071597 do not match in spite of the fact that same ethnicity groups were used.
The only difference is a biofeature, so theoretically, r^2, D, LOD values from haploview data should not be changed.
Please check the script to make it 100% correct!

L1 L2 D. LOD r.2 CIlow CIhi Dist T.int tagSNP bioFeature location ethnicity genome1000 TagTRUE1 TagTRUE2
rs999737 rs79071597 0.908 50.97 0.639 0.84 0.95 9872 62.05 rs999737 Galaxy13-[MDAMB231-vs-Input_triangel_subpeaks 14:68534681-69534682 EUR EUR TRUE FALSE
rs999737 rs79071597 0.91 51.96 0.644 0.84 0.95 9872 64.26 rs999737 Galaxy9-[HMEC-vs-Input_triangle_subpeaks 14:68534681-69534682 EUR EUR TRUE FALSE