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.

Bains et al.

Bains et al. BMC Genetics 2013 14:34   doi:10.1186/1471-2156-14-34

Open Data