Table 2 Imputation performance at known pathogenic repeats

From: A reference haplotype panel for genome-wide imputation of short tandem repeats

Locus Motif Disordera Length r2 LOO Observed concordance Naive concordance Random concordance Best tag SNP r 2 bestSNP
3:63898362 CAG SCA7 0.75 92.0% 75.6% 63.9% rs58676857 0.57
4:3076604 CAG HD 0.47 64.3% 39.4% 27.5% rs762855 0.11
5:146258292 CAG SCA12 0.88 93.8% 59.9% 46.3% rs2082405 0.64
6:16327867 CAG SCA1 0.72 85.3% 55.0% 33.8% rs17860797 0.04
6:170870996 CAG SCA17 0.51 80.0% 39.8% 31.5% rs9472489 0.15
12:112036755 CAG SCA2 0.49 96.2% 88.2% 80.2% rs148019457 0.28
12:7045892 CAG DRPLA 0.86 81.2% 38.8% 24.9% rs34199021 0.69
13:70713516 CTG/CAG SCA8 0.87 84.7% 27.0% 24.0% rs9564660 0.39
14:92537355 CAG SCA3 0.88 86.4% 33.8% 27.5% rs7144492 0.27
16:87637894 CAG HDL 0.55 88.2% 55.2% 46.5% rs2434850 0.34
19:46273463 CTG DM1 0.87 86.9% 39.4% 30.8% rs7254351 0.44
19:13318673 CAG SCA6 0.81 92.0% 44.1% 39.2% rs2070737 0.63