Table 3.
All polymorphic sites identified in an 8063bp CYP3A5 region re-sequenced in five Ethiopian populations
| Afar | Amhara | Anuak | Maale | Oromo | Total | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Region of CYP3A5 |
Position on chromosome 7 |
Position relative to the translation initiation codon (A of ATG is +1) |
dbSNP database refSNP ID |
Effect |
f |
n |
f |
n |
f |
n |
f |
n |
f |
n |
f |
n |
|
Promoter |
99278314 |
−795 T>A |
rs3823812 |
|
0.00 |
3 |
0.00 |
3 |
0.01 |
4 |
0.01 |
10 |
0.01 |
5 |
0.0331 |
25 |
|
Promoter |
99278267 |
−748 C>G |
|
|
0.01 |
5 |
0.00 |
2 |
0.00 |
1 |
0.00 |
1 |
0.01 |
6 |
0.0198 |
15 |
|
Promoter |
99278224 |
−705 3 base pair deletion |
|
|
0.00 |
1 |
0.00 |
1 |
0.01 |
5 |
0.00 |
1 |
0.00 |
3 |
0.0146 |
11 |
|
Promoter |
99278223 |
−704 A>G |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.0013 |
1 |
|
Promoter |
99278152 |
−633 C>A |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.0013 |
1 |
|
Promoter |
99278146 |
−627 G>A |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Promoter |
99278144 |
−625 A>G |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.0013 |
1 |
|
Promoter |
99278070 |
−551 C>A |
rs28365079 |
|
0.01 |
4 |
0.01 |
5 |
0.02 |
15 |
0.01 |
8 |
0.01 |
4 |
0.0476 |
36 |
|
Promoter |
99277988 |
−469 G>A |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.0013 |
1 |
|
UTR of exon 1 |
99277593 |
−74 C>T |
rs28371764 |
|
0.00 |
2 |
0.01 |
6 |
0.00 |
0 |
0.00 |
2 |
0.00 |
2 |
0.0158 |
12 |
|
UTR of exon 1 |
99277544 |
−25 A>C |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.0013 |
1 |
|
Intron 1 |
99277392 |
127 G>A |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
2 |
0.00 |
0 |
0.0040 |
3 |
|
Intron 1 |
99277337 |
182 C>A |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
3 |
0.00 |
0 |
0.00 |
0 |
0.0040 |
3 |
|
Intron 2 |
99272310 |
5209 C>T |
rs28365067 |
|
0.01 |
11 |
0.02 |
12 |
0.01 |
5 |
0.01 |
8 |
0.01 |
8 |
0.0580 |
44 |
|
Intron 2 |
99272290 |
5229 G>A |
rs41301652 |
|
0.00 |
0 |
0.00 |
0 |
0.00 |
2 |
0.00 |
0 |
0.00 |
0 |
0.0026 |
2 |
|
Intron 2 |
99272275 |
5244 C>T |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
2 |
0.0026 |
2 |
|
Intron 3 |
99272103 |
5416 C>T |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
2 |
0.0026 |
2 |
|
Intron 3 |
99272009 |
5510 T>A |
rs28969392 |
|
0.01 |
6 |
0.01 |
4 |
0.01 |
10 |
0.01 |
9 |
0.00 |
3 |
0.0422 |
32 |
|
Intron 3 |
99271928 |
5591 C>T |
rs41301655 |
|
0.00 |
0 |
0.01 |
4 |
0.00 |
1 |
0.00 |
0 |
0.00 |
2 |
0.0092 |
7 |
|
Intron 3 |
99271853 |
5666 A>G |
rs41301658 |
|
0.00 |
1 |
0.00 |
1 |
0.00 |
3 |
0.01 |
7 |
0.00 |
2 |
0.0185 |
14 |
|
Intron 3 |
99271808 |
5711 A>G |
rs41258334 |
|
0.01 |
11 |
0.01 |
11 |
0.01 |
5 |
0.01 |
9 |
0.01 |
8 |
0.0580 |
44 |
|
Intron 3 |
99271778 |
5741 A>G |
|
|
0.01 |
6 |
0.00 |
3 |
0.01 |
4 |
0.01 |
8 |
0.00 |
3 |
0.0317 |
24 |
|
Intron 3 |
99270539 |
6980 A>G |
rs776746 |
Defines the variant CYP3A5*3 |
0.13 |
95 |
0.14 |
102 |
0.06 |
44 |
0.10 |
75 |
0.13 |
97 |
0.5581 |
413 |
|
Intron 3 |
99270504 |
7015 3 base pair deletion |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.0014 |
1 |
|
Intron 3 |
99270318 |
7201 C>T |
rs8175345 |
|
0.00 |
0 |
0.00 |
1 |
0.01 |
9 |
0.00 |
0 |
0.00 |
1 |
0.0149 |
11 |
|
Exon 4 |
99270249 |
7270 G>A |
|
G77S |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.0014 |
1 |
|
Intron 4 |
99270164 |
7355 C>T |
rs28365074 |
|
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
2 |
0.0041 |
3 |
|
Intron 5 |
99264352 |
13167 T>C |
rs68178885 |
|
0.00 |
3 |
0.00 |
2 |
0.00 |
1 |
0.00 |
3 |
0.00 |
1 |
0.0132 |
10 |
|
Intron 6 |
99264149 |
13370 G>A |
rs41301670 |
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
2 |
0.0027 |
2 |
|
Exon 7 |
99262835 |
14684 G>A |
rs10264272 |
Defines the variant CYP3A5*6 |
0.04 |
28 |
0.03 |
23 |
0.05 |
39 |
0.03 |
23 |
0.03 |
21 |
0.1763 |
134 |
|
Exon 7 |
99262793 |
14726 A>G |
rs2838372 |
Synonymous |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Intron 7 |
99262642 |
14877 A>G |
|
|
0.00 |
1 |
0.01 |
5 |
0.02 |
12 |
0.01 |
9 |
0.00 |
2 |
0.0382 |
29 |
|
Intron 7 |
99261737 |
15782 T>C |
rs28969393 |
|
0.01 |
5 |
0.01 |
4 |
0.01 |
9 |
0.01 |
9 |
0.00 |
3 |
0.0396 |
30 |
|
Exon 8 |
99261651 |
15868 A>G |
|
K266R |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Intron 8 |
99261583 |
15936 C>A |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
2 |
0.00 |
0 |
0.0026 |
2 |
|
Intron 8 |
99260546 |
16973 G>A |
|
|
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Exon 9 |
99260502 |
17017 C>T |
|
R268Stop |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Intron 9 |
99260407 |
17112 C>T |
rs28383478 |
|
0.00 |
0 |
0.00 |
2 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.0026 |
2 |
|
Intron 9 |
99260362 |
17157 G>T |
rs4646453 |
|
0.00 |
3 |
0.00 |
3 |
0.01 |
4 |
0.01 |
10 |
0.01 |
5 |
0.0331 |
25 |
|
Intron 9 |
99260282 |
17237 T>G |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Intron 9 |
99260170 |
17349 T>G |
|
|
0.00 |
3 |
0.00 |
2 |
0.01 |
7 |
0.01 |
7 |
0.00 |
3 |
0.0291 |
22 |
|
Intron 9 |
99258524 |
18995 C>T |
rs10247580 |
|
0.00 |
0 |
0.00 |
2 |
0.02 |
12 |
0.01 |
7 |
0.00 |
1 |
0.0291 |
22 |
|
Intron 9 |
99258320 |
19199 G>A |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Intron 9 |
99258316 |
19203 T>C |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
2 |
0.00 |
0 |
0.0026 |
2 |
|
Exon 10 |
99258124 |
19395 A>C |
|
K342T |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.0013 |
1 |
|
Exon 11 |
99250397 |
27125-27126 T insertion |
rs41303343 |
Defines the variant CYP3A5*7 |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
1 |
0.00 |
0 |
0.0026 |
2 |
|
Exon 11 |
99250381 |
27138 A>G |
|
V350M |
0.00 |
0 |
0.00 |
0 |
0.00 |
1 |
0.00 |
0 |
0.00 |
0 |
0.0013 |
1 |
|
Intron 12 |
99247647 |
29872 G>T |
|
|
0.00 |
0 |
0.00 |
0 |
0.00 |
0 |
0.00 |
2 |
0.00 |
0 |
0.0026 |
2 |
|
Intron 12 |
99247503 |
30016 1 base pair deletion |
rs28365093 |
|
0.00 |
3 |
0.01 |
4 |
0.02 |
15 |
0.01 |
8 |
0.01 |
4 |
0.0450 |
34 |
|
Intron 12 |
99246026 |
31493 T>C |
rs28365069 |
|
0.01 |
4 |
0.01 |
11 |
0.01 |
11 |
0.02 |
18 |
0.01 |
9 |
0.0699 |
53 |
| 3' UTR | 99245914 | 31605 C>T | rs15524 | 0.14 | 105 | 0.14 | 109 | 0.09 | 69 | 0.11 | 84 | 0.14 | 107 | 0.6253 | 474 | |
n refers to the total number of chromosomes on which a particular variant was observed. f is the relative frequency of each variant. Total refers to the number of times a variant was observed in the Ethiopian cohort (758 chromosomes) and f is its relative frequency. Position on chromosome 7 is based on NCBI Build 132, February 2009.