Table 5.
Comparisons of polymorphisms identified in this study with those reported in HapMap/Perlegen
| A | |||||||||||
| HAPMAP | Perlegen | ||||||||||
| CHB | CEPH | CHB | EA | ||||||||
| # common polymorphisms | 19 | 19 | 14 | 14 | |||||||
| This Study | # non-common polymorphisms | polymorphisms found in HapMap/Perlegen but not in this study | 25 (22) | 23 (22) | 1 (0) | 1 (0) | |||||
| polymorphisms found in this study but not in HapMap/Perlegen | 41 (26) | 41 (26) | 46 (28) | 46 (26) | |||||||
| () refers to number of monomorphic SNPs in that category in that population | |||||||||||
| B | |||||||||||
| SNP ID | dbSNP ID | Popu | N | Our data | N | HapMap | n | Perlegen | |||
| I2/26 G>A | rs8187843 | A | G | A | G | ||||||
| CH | 36 | 0.00 | 100.00 | 45 | 0.00 | 100.00 | |||||
| CAU | 35 | 7.14 | 92.86 | 60 | 5.83 | 94.17 | |||||
| I7/31 G>T | rs8187850 | G | T | G | T | ||||||
| CH | 35 | 100.00 | 0.00 | 45 | 100.00 | 0.00 | |||||
| CAU | 36 | 98.61 | 1.39 | 60 | 100.00 | 0.00 | |||||
| I7/54 C>A | rs903880 | A | C | A | C | ||||||
| CH | 34 | 1.47 | 98.53 | 45 | 4.44 | 95.56 | |||||
| CAU | 36 | 13.89 | 86.11 | 60 | 25.00 | 75.00 | |||||
| I7/64 C>G | rs246232 | C | G | C | G | C | G | ||||
| CH | 34 | 61.76 | 38.24 | 44 | 55.68 | 44.32 | 21 | 50.00 | 50.00 | ||
| CAU | 35 | 80.00 | 20.00 | 60 | 66.67 | 33.33 | 24 | 52.08 | 47.92 | ||
| E8/825 T>C | rs246221 | C | T | C | T | C | T | ||||
| CH | 36 | 36.11 | 63.89 | 45 | 46.67 | 53.33 | 24 | 56.25 | 43.75 | ||
| CAU | 36 | 13.89 | 86.11 | 60 | 28.33 | 71.67 | 22 | 45.45 | 54.55 | ||
| E9/1062 T>C | rs35587 | C | T | C | T | C | T | ||||
| CH | 36 | 38.89 | 61.11 | 45 | 46.67 | 53.33 | 24 | 58.33 | 41.67 | ||
| CAU | 36 | 31.94 | 68.06 | 60 | 28.33 | 71.67 | 24 | 45.83 | 54.17 | ||
| I11/-78 G>A | rs35595 | A | G | A | G | ||||||
| CH | 36 | 20.83 | 79.17 | 45 | 31.11 | 68.89 | |||||
| CAU | 36 | 13.89 | 86.11 | 60 | 13.33 | 86.67 | |||||
| I11/-48 C>T | rs3765129 | C | T | C | T | C | T | ||||
| CH | 36 | 88.89 | 11.11 | 45 | 88.89 | 11.11 | 24 | 93.75 | 6.25 | ||
| CAU | 36 | 90.28 | 9.72 | 58 | 85.34 | 14.66 | 24 | 85.42 | 14.58 | ||
| I12/56 C>T | rs17265551 | C | T | C | T | C | T | ||||
| CH | 35 | 98.57 | 1.43 | 45 | 95.56 | 4.44 | 24 | 97.92 | 2.08 | ||
| CAU | 36 | 97.22 | 2.78 | 60 | 90.83 | 9.17 | 24 | 89.58 | 10.42 | ||
| I12/-85 G>A | rs4148348 | A | G | A | G | ||||||
| CH | 36 | 8.33 | 91.67 | 45 | 4.44 | 95.56 | |||||
| CAU | 36 | 8.33 | 91.67 | 60 | 7.50 | 92.50 | |||||
| I12/-37 A>G | rs35604 | A | G | A | G | A | G | ||||
| CH | 36 | 83.33 | 16.67 | 45 | 72.22 | 27.78 | 24 | 81.25 | 18.75 | ||
| CAU | 36 | 79.17 | 20.83 | 60 | 82.50 | 17.50 | 24 | 91.67 | 8.33 | ||
| E13/1684 C>T | rs35605 | C | T | C | T | C | T | ||||
| CH | 36 | 83.33 | 16.67 | 45 | 72.22 | 27.78 | 24 | 81.25 | 18.75 | ||
| CAU | 36 | 80.56 | 19.44 | 60 | 82.50 | 17.50 | 24 | 91.67 | 8.33 | ||
| E13/1704 C>T | rs8187858 | C | T | C | T | C | T | ||||
| CH | 36 | 100.00 | 0.00 | 45 | 100.00 | 0.00 | 24 | 100.00 | 0.00 | ||
| CAU | 36 | 98.61 | 1.39 | 60 | 90.83 | 9.17 | 24 | 95.83 | 4.17 | ||
| E16/2001 C>T | rs8187863 | C | T | T | C | T | |||||
| CH | 36 | 100.00 | 0.00 | 45 | 100.00 | 0.00 | 24 | 100.00 | 0.00 | ||
| CAU | 36 | 98.61 | 1.39 | 60 | 98.33 | 1.67 | 24 | 95.83 | 4.17 | ||
| E16/2007 C>T | rs2301666 | C | T | C | T | C | T | ||||
| CH | 36 | 98.61 | 1.39 | 45 | 97.78 | 2.22 | 24 | 97.92 | 2.08 | ||
| CAU | 36 | 100.00 | 0.00 | 60 | 100.00 | 0.00 | 24 | 100.00 | 0.00 | ||
| I18/-30 G>C | rs2074087 | C | G | C | G | ||||||
| CH | 36 | 15.28 | 84.72 | 24 | 14.58 | 85.42 | |||||
| CAU | 36 | 18.06 | 81.94 | 24 | 4.17 | 95.83 | |||||
| I21/26 T>C | rs11075296 | C | T | C | T | C | T | ||||
| CH | 36 | 0.00 | 100.00 | 45 | 0.00 | 100.00 | 24 | 0.00 | 100.00 | ||
| CAU | 36 | 0.00 | 100.00 | 60 | 0.00 | 100.00 | 24 | 0.00 | 100.00 | ||
| I22/62 T>C | rs3887893 | G | A | G | A | ||||||
| CH | 36 | 58.33 | 41.67 | 45 | 50.00 | 50.00 | |||||
| CAU | 36 | 43.06 | 56.94 | 59 | 37.29 | 62.71 | |||||
| E28/4002 G>A | rs2239330 | A | G | A | G | A | G | ||||
| CH | 36 | 8.33 | 91.67 | 45 | 11.11 | 88.89 | 24 | 16.67 | 83.33 | ||
| CAU | 36 | 37.50 | 62.50 | 60 | 29.17 | 70.83 | 24 | 31.25 | 68.75 | ||
| I28/-45 G>A | rs212087 | A | G | A | G | A | G | ||||
| CH | 36 | 18.06 | 81.94 | 45 | 20.00 | 80.00 | 24 | 18.75 | 81.25 | ||
| CAU | 36 | 58.33 | 41.67 | 60 | 39.17 | 60.83 | 24 | 43.75 | 56.25 | ||
| C | |||||||||||
| P-value | Our data | HapMap | Perlegen | ||||||||
| CH | EA | Both | CH | EA | Both | CH | EA | Both | |||
| Average difference between datasets | |||||||||||
| Our data | - | - | - | 0.77 | 0.24 | 0.26 | 0.28 | 0.83 | 0.71 | ||
| HapMap | 0.42 | 2.11 | 1.27 | - | - | - | 0.03 | 0.16 | 0.02 | ||
| Perlegen | 2.54 | 0.83 | 0.85 | 3.48 | 3.57 | 3.67 | - | - | - | ||
Note: Cells in the top right triangular section indicate p values of paired-samples t test, whereas those in the lower triangular section contain the average differences in allele frequencies between comparable SNPs between the respective data sets.