Discovery of SNPs in the CETP Gene
|
|
Base-specific cleavage results |
Public SNPsa |
||||||
|---|---|---|---|---|---|---|---|---|
| Amplicon |
# |
Type |
Positionb |
Allele freq |
SNP ID |
|||
| Amplicon 1 | 1 | C to T | 11594/11597/11598 | 0.93/0.07 | rs5883 | |||
| 2 | T to G | 11690 | 0.85/0.15c | |||||
| 3 | G to A | 11693/11694/11695 | 0.86/0.14c | rs289714 | ||||
| 4 | G to A | 11854/11855 | 0.47/0.53 | rs158477 | ||||
| Amplicon 2 | 5 | C to T | 11967 | 0.99/0.01 | ||||
| 6 | A to C | 11978 | 0.46/0.54 | rs158478 | ||||
| 7 | G to A | 12292 | 0.46/0.54 | rs158479 | ||||
| Amplicon 3 | 8 | G to A | 12469/12471 | 0.13/0.87 | rs158480 | |||
| 9 | A to G | 12530/12531 | 0.13/0.87 | rs158617 | ||||
| 10 | A to T | 12752 | 0.12/0.88 | rs289715 | ||||
| Amplicon 4 | T to G | 13439 | rs2303789d | |||||
| 11 | A to G | 13490 | 0.995/0.005 | |||||
| Amplicon 5 | 12 | T to A | 13620 | 0.29/0.71 | rs289716 | |||
| 13 | G to A | 13632 | 0.63/0.37 | rs289717 | ||||
| 14 | T to A | 14013 | 0.99/0.01c | rs736274 | ||||
| Amplicon 6 | 15 | C to T | 14176 | 0.30/0.70 | rs289718 | |||
| T to C | 14185 | rs289719d | ||||||
| 16 | T to C | 14229 | 0.67/0.33 | rs2033254 | ||||
| 17 | G to A | 14361 | 0.995/0.005 | |||||
| 18 | C to T | 14476 | 0.89/0.11 | |||||
| Amplicon 7 | 19 | T to G | 14626 | 0.92/0.08c | ||||
| 20 | C to T | 14730 | 0.98/0.02 | |||||
| Amplicon 8 | 21 | A to G | 15072 | 0.68/0.32c | ||||
| 22 | T to G | 15192 | 0.10/0.90 | rs1968905 | ||||
| 23 | T to G | 15238 | 0.96/0.04 | |||||
| Amplicon 9 | 24 | G to A | 15429/15430 | 0.63/0.37 | ||||
| 25 | G to A | 15696 | 0.63/0.37 | rs291044 | ||||
| Amplicon 10 | 26 | C to T | 16128/16131/16132 | 0.99/0.01 | ||||
| 27 | C to T | 16177/16179/16180 | 0.99/0.01 | rs891144 | ||||
|
|
|
G to A
|
16256
|
|
rs5881d
|
|||
-
↵a The reader is referred to http://www.ncbi.nlm.nih.gov/ for information on the public SNPs
-
↵b Positional ambiguity was resolved by the MassEXTEND assay; the SNP position is underlined
-
↵c The marked allele frequencies were calculated using the Hardy-Weinberg equation; in these cases, heterozygotes could not be distinguished from either wild-type or mutant homozygous samples
-
↵d Three public SNPs (italics) were not identified using the base-specific cleavage assay. SNPs rs2303789 (found in an Asian population) and rs5881 (allele frequency = 0.025) are absent from our sample collection. rs289719 was missed because of its genetic linkage with and close proximity to rs289718; concurrence of the two SNPs is mass-neutral
