TABLE 4.
SNPs identified and genotyped in CYP3A4 and transcription factors
| Position in Ref Seq | Position Relative to ATG | rs Number | SNP and Flanking Sequence | Str a | MAF(MA) All | Het F | Het M | Hom Var F | Hom Var M |
|---|---|---|---|---|---|---|---|---|---|
| NC_000019 b | FoxA3 (HNF3γ) | ||||||||
| 51067448 | 7894 | ccctggcac(C>T)gccaagccac | (+) | 0.01(T) | 1 | 2 | 0 | 0 | |
| 51067619 | 8065 | rs16980091 | tgtctttca(C>T)gactgcttcg | (+) | 0.13(T) | 12 | 17 | 1 | 1 |
| 51068057 | 8503 | rs3810327 | cagcacctcc(C>A)aaactggacg | (+) | 0.1(A) | 10 | 15 | 0 | 0 |
| NT_011362 c | HNF4α | ||||||||
| 8036502 | −858 | rs11508796 | ccagaggag(C>T)gccagacagg | (+) | 0.13(T) | 12 | 15 | 2 | 0 |
| 8038170 | 811 | ttcttcagtg(T>G)accgttttca | (−) | 0.03(G) | 2 | 6 | 0 | 0 | |
| 8038270 | 911 | rs6031546 | tattgtgtc(T>C)tccacgaatt | (−) | 0.21(C) | 17 | 24 | 3 | 1 |
| 8038389 | 1030 | tgtgtgattt(G>T)aacaggttta | (−) | 0.004(T) | 1 | 0 | 0 | 0 | |
| 8038632 | 1273 | rs2144908 | attccctggc(C>T)ctctgtcctc | (−) | 0.18(T) | 15 | 18 | 3 | 2 |
| 8052201 | 14842 | taggctgtct(T>C)gtcccctgct | (+) | 0.02(C) | 1 | 3 | 0 | 0 | |
| 8052545 | 15186 | rs6103716 | gaaagttgtc(A>C)aaacaggcatga | (+) | 0.33(C) | 23 | 37 | 3 | 6 |
| 8052558 | 15199 | rs6031558 | acaggcatg(G>C)gaagggcaga | (+) | 0.31(C) | 27 | 31 | 4 | 4 |
| 8078452 | 41093 | gaataaacc(C>T)agaccttgtg | (−) | 0.004(T) | 1 | 0 | 0 | 0 | |
| 8078520 | 41161 | rs717248 | tgtcgtgaag(A>G)ttaaatgaga | (−) | 0.06(G) | 3 | 11 | 0 | 0 |
| 8078699 | 41340 | rs717247 | aaaaatatt(A>G)gcttctttct | (−) | 0.31(G) | 23 | 29 | 4 | 9 |
| 8115620 | 78261 | atgcctacat(A>G)tggggacatc | (+) | 0.005(G) | 1 | 0 | 0 | 0 | |
| 8115852 | 78493 | gagagctccc(G>A)ttacatgagg | (+) | 0.005(A) | 1 | 0 | 0 | 0 | |
| 8115972 | 78613 | ggccgctccc(G>A)ccttcccctg | (+) | 0.28(A) | 21 | 21 | 2 | 7 | |
| 8115985 | 78626 | ttcccctgtg(C>T)cttccctcca | (+) | 0.005(T) | 0 | 1 | 0 | 0 | |
| 8116201 | 78842 | rs6017341 | agggcaaagg(G>C)ctgatgaggt | (−) | 0.04(C) | 5 | 4 | 0 | 0 |
| NC_000012 d | SMRT (Ncor2) | ||||||||
| 123568072 | −22322 | rs6488932 | gcgtgggctc(A>G)ggcaggggag | (−) | 0.02(G) | 1 | 3 | 0 | 0 |
| 123568276 | −22526 | agcctcaccc(C>T)ggcctgcccg | (+) | 0.02(T) | 1 | 4 | 0 | 0 | |
| 123568478 | −22728 | rs837948 | cgacagaact(G>A)gggctctttc | (+) | 0.37(A) | 15 | 39 | 9 | 10 |
| 123568845 | −23095 | gcagaggggc(G>A)gccccagagg | (+) | 0.004(A) | 0 | 1 | 0 | 0 | |
| 123568894 | −23144 | ctcccatccc(G>A)gccctggagg | (+) | 0.01(A) | 1 | 1 | 0 | 0 | |
| 123569005 | −23255 | rs12426064 | ccgcctgacc(C>T)cacggctggg | (+) | 0.01(T) | 1 | 1 | 0 | 0 |
| NG_000004 e , f | CYP3A4 | ||||||||
| 135607 | −392 | rs2740574 | gacaagggc(A>G)gagagaggcg | (+) | 0.07(G) | 4 | 11 | 0 | 1 |
| 124166 | −11833 | cagtgtgtg(C>G)gttcccctcc | (−) | 0.18(G) | 16 | 21 | 1 | 3 | |
| 117722 | −18277 | rs11766150 | ctaagcttct(C>G)ttctcgcttc | (−) | 0.07(G) | 4 | 12 | 0 | 1 |
| 117559 | −18440 | rs12705060 | caaatggct(T>A)actagaataa | (+) | 0.49(A) | 21 | 35 | 14 | 17 |
| 151975 | 15977 | rs2246709 | aatccatag(A/G)gcagaaagtt | (−) | 0.32(G) | 17 | 35 | 7 | 7 |
| 163672 | 27674 | rs12333983 | atatacacgg(T>A)tacatccatt | (−) | 0.14(A) | 10 | 19 | 1 | 2 |
| CYP3A5 | |||||||||
| 247167 | 6986 | rs776746 | ttgtctttc(A>G)tatctcttc | (+) | 0.13(A) | 9 | 17 | 1 | 2 |
| AF364606 g | PXR (NR1I2) | ||||||||
| 63396 | −6993 | rs2472677 | catatttttt(T>C)tgattaaaaa | (+) | 0.35(C) | 27 | 25 | 4 | 10 |
| 46370 | −24019 | rs3842689 | atcaccacag(-/GAGAAG)ccttaactac | (+) | 0.34(Del) | 26 | 30 | 3 | 12 |
| 44477 | −25912 | rs1523130 | tattggaaag(G>A)aaaagagtaa | (+) | 0.38(A) | 24 | 30 | 6 | 14 |
| NT_007933 h | MDR1 (ABCB1) | ||||||||
| 12455162 | 8615 | rs3789243 | acaacgacgc(C>T)ccataaatta | (−) | 0.47(T) | 32 | 31 | 9 | 18 |
| 12394894 | 68883 | rs2032582 | actagaaggt(G>T)ctgggaaggt | (−) | 0.49(T) | 24 | 24 | 11 | 24 |
| 12372921 | 90856 | rs1045642 | aggaagagat(T>C)gtgagggcag | (−) | 0.42(C) | 30 | 24 | 7 | 19 |
MA, minor allele; MAF, minor allele frequency; Gene and ATG positions in the Reference Sequence (Ref Seq): Het, heterozygous; Hom, homozygous; Var, variant.
Strand orientation with respect to GenBank sequence.
FoxA3 = 51059358–51068895, ATG = 51059555–51059557.
HNF4α = 8037356–8112945, ATG = 8037360–8037362.
Ncor2 = 123374914–123568793, ATG = 123545750-48 (compliment).
CYP3A4 = 135895–163090, ATG = 135999–136001.
CYP3A5 = 240080–271889, ATG = 240182–240184.
PXR = 45837–80887, ATG = 70390–70392.
ABCB1 = 12367224–12576840, ATG = 12463776-4 (compliment).