Table 2.
Linkage disequilibrium between the 11 SNPs of CNOT6 in European populations included in the 1000 Genomes Project and imputation quality scores
| SNP | Position (hg19) |
D' | r2 | Function prediction | Imputation quality | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| SNPinfoa | Regulome DBb | Info ICR |
Rsq MDACC |
Rsq IARC |
Info NCI |
Info Toronto |
Rsq GLC |
||||
| rs2453176 | 179975792 | -- | 1f | 1.000 | 0.999 | 1.000 | 1.000 | 1.000 | 1.000 | ||
| rs780126 | 179963034 | 1.00 | 0.71 | -- | -- | 0.874 | 0.751 | 0.703 | 0.859 | 0.857 | 0.784 |
| rs2387281 | 179988283 | 1.00 | 0.97 | -- | -- | 0.998 | 0.972 | 0.969 | 0.996 | 0.990 | 0.967 |
| rs6877400 | 179996111 | 1.00 | 0.97 | Splicing site | 5 | 0.998 | 0.964 | 0.965 | 0.996 | 0.990 | 0.953 |
| rs2387285 | 179982278 | 1.00 | 0.97 | -- | 4 | 0.990 | 0.966 | 0.923 | 0.988 | 0.981 | 0.964 |
| rs812956 | 179953048 | 1.00 | 0.97 | -- | 6 | 0.991 | 0.961 | 0.962 | 0.988 | 0.978 | 0.976 |
| rs9800264 | 179940091 | 1.00 | 0.99 | -- | -- | 0.999 | 0.970 | 0.977 | 0.998 | 0.993 | 1.000 |
| rs6422334 | 179982151 | 1.00 | 0.99 | -- | 5 | 0.999 | 0.982 | 0.976 | 0.997 | 0.994 | 0.979 |
| rs10052782 | 179975104 | 1.00 | 1.00 | -- | 6 | 1.000 | 0.998 | 1.000 | 1.000 | 1.000 | 1.000 |
| rs76820754 | 179936737 | 1.00 | 1.00 | -- | 6 | 1.000 | 0.970 | 0.971 | 0.999 | 0.998 | 0.999 |
| rs2447734 | 179968674 | 1.00 | 1.00 | -- | -- | 1.000 | 0.994 | 0.999 | 0.999 | 0.997 | 0.999 |
SNP: single nucleotide polymorphism;
Imputation quality: Rsq: MaCH r-squared; Info: IMPUTE2 information score;