Table 3 All polymorphic sites identified in an 8063bp CYP3A5 region re-sequenced in five Ethiopian populations
From: Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa
| Â | Â | Â | Â | Â | 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 | Â | Â | 0.00 | 0 | 0.00 | 0 | 0.00 | 1 | 0.00 | 2 | 0.00 | 0 | 0.0040 | 3 |
Intron 1 | 99277337 | 182 C>A | Â | Â | 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 | Â | 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 | Â | 0.00 | 0 | 0.00 | 0 | 0.00 | 2 | 0.00 | 0 | 0.00 | 0 | 0.0026 | 2 |
Intron 2 | 99272275 | 5244 C>T | Â | Â | 0.00 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | 2 | 0.0026 | 2 |
Intron 3 | 99272103 | 5416 C>T | Â | Â | 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 | Â | 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 | Â | 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 | Â | 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 | Â | 0.01 | 11 | 0.01 | 11 | 0.01 | 5 | 0.01 | 9 | 0.01 | 8 | 0.0580 | 44 |
Intron 3 | 99271778 | 5741 A>G | Â | Â | 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 | Â | Â | 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 | Â | 0.00 | 0 | 0.00 | 1 | 0.01 | 9 | 0.00 | 0 | 0.00 | 1 | 0.0149 | 11 |
Exon 4 | 99270249 | 7270 G>A | Â | 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 | Â | 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 | Â | 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 | Â | 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 | Â | Â | 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 | Â | 0.01 | 5 | 0.01 | 4 | 0.01 | 9 | 0.01 | 9 | 0.00 | 3 | 0.0396 | 30 |
Exon 8 | 99261651 | 15868 A>G | Â | 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 | Â | Â | 0.00 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | 2 | 0.00 | 0 | 0.0026 | 2 |
Intron 8 | 99260546 | 16973 G>A | Â | Â | 0.00 | 0 | 0.00 | 1 | 0.00 | 0 | 0.00 | 0 | 0.00 | 0 | 0.0013 | 1 |
Exon 9 | 99260502 | 17017 C>T | Â | 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 | Â | 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 | Â | 0.00 | 3 | 0.00 | 3 | 0.01 | 4 | 0.01 | 10 | 0.01 | 5 | 0.0331 | 25 |
Intron 9 | 99260282 | 17237 T>G | Â | Â | 0.00 | 0 | 0.00 | 0 | 0.00 | 1 | 0.00 | 0 | 0.00 | 0 | 0.0013 | 1 |
Intron 9 | 99260170 | 17349 T>G | Â | Â | 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 | Â | 0.00 | 0 | 0.00 | 2 | 0.02 | 12 | 0.01 | 7 | 0.00 | 1 | 0.0291 | 22 |
Intron 9 | 99258320 | 19199 G>A | Â | Â | 0.00 | 0 | 0.00 | 0 | 0.00 | 1 | 0.00 | 0 | 0.00 | 0 | 0.0013 | 1 |
Intron 9 | 99258316 | 19203 T>C | Â | Â | 0.00 | 0 | 0.00 | 0 | 0.00 | 0 | 0.00 | 2 | 0.00 | 0 | 0.0026 | 2 |
Exon 10 | 99258124 | 19395 A>C | Â | 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 | Â | 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 | Â | Â | 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 | Â | 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 | Â | 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 | Â | 0.14 | 105 | 0.14 | 109 | 0.09 | 69 | 0.11 | 84 | 0.14 | 107 | 0.6253 | 474 |