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Table 1 Basic characteristics of the selected VIP variants from the PharmGKB database and genotype frequencies in the Wa population

From: Genetic analysis of pharmacogenomic VIP variants in the Wa population from Yunnan Province of China

SNP ID Chromosome BP Functional Consequence Annotation Molecules Paper Discusses Genes Level of Evidence Allele MAF Genotype
Mutation Homozygote Heterozygote Wild Homozygote
rs11572325 1 59896030 intron_variant     CYP2J2   T/A 0.043 0 17 183
rs10889160 1 59896449 intron_variant     CYP2J2   C/T 0.108 0 43 157
rs1760217 1 97137438 genic_downstream_transcript_variant,intron_variant Genotypes AA + AG are associated with decreased survival when treated with antineoplastic agents in people with Pancreatic Neoplasms as compared to genotype GG. antineoplastic agents Efficacy DPYD 3 G/A 0.330 24 84 92
rs1801159 1 97515839 coding_sequence_variant,genic_downstream_transcript_variant,intron_variant,missense_variant Genotype TT is not associated with increased risk of Neutropenia when treated with cyclophosphamide, doxorubicin and fluorouracil in women with Breast Neoplasms as compared to genotypes CC + CT. capecitabine/fluorouracil Toxicity DPYD 1A C/T 0.265 10 85 103
rs1801265 1 97883329 non_coding_transcript_variant,intron_variant,coding_sequence_variant,5_prime_UTR_variant,missense_variant Genotypes AA + AG is associated with decreased Drug Toxicity when treated with capecitabine or fluorouracil in people with Colorectal Neoplasms as compared to genotype GG. fluorouracil/capecitabine Toxicity DPYD 1A G/A 0.095 1 36 163
rs5275 1 186673926 3_prime_UTR_variant Genotype AA is associated with increased progression-free survival and overall survival when treated with capecitabine and oxaliplatin in people with Colorectal Neoplasms as compared to genotypes AG + GG. capecitabine oxaliplatin Efficacy PTGS2 3 G/A 0.175 3 64 133
rs20417 1 186681189 upstream_transcript_variant,non_coding_transcript_variant Allele C is not associated with response to cetuximab or panitumumab in people with Colorectal Neoplasms as compared to allele G. aspirin/ibuprofen/rofecoxib Efficacy PTGS2 3 G/C 0.003 0 1 199
rs12139527 1 201040054 missense_variant,coding_sequence_variant,intron_variant     CACNA1S   G/A 0.040 0 16 184
rs3850625 1 201047168 coding_sequence_variant,missense_variant     CACNA1S   A/G 0.003 0 1 199
rs2306238 1 237550803 intron_variant     RYR2   A/G 0.223 9 71 120
rs2231142 4 88131171 coding_sequence_variant,missense_variant Genotypes GT + TT are not associated with increased likelihood of statin-related myopathy when treated with atorvastatin or simvastatin as compared to genotype GG. rosuvastatin/rosuvastatin Efficacy/Metabolism/PK ABCG2 2A T/G 0.196 7 64 128
rs2231137 4 88139962 coding_sequence_variant,missense_variant Genotypes CT + TT is not associated with increased risk of Neutropenia when treated with valganciclovir in people with Kidney Transplantation as compared to genotype CC. dasatinib imatinib nilotinib/irinotecan/imatinib Other/Toxicity/Dosage ABCG2 3 C/T 0.538 55 103 40
rs698 4 99339632 coding_sequence_variant,non_coding_transcript_variant,missense_variant Genotype CT is associated with decreased likelihood of complete response when treated with cisplatin and cyclophosphamide in women with Ovarian Neoplasms as compared to genotypes CC + TT. cisplatin cyclophosphamide Efficacy ADH1C 3 C/T 0.108 9 25 166
rs776746 7 99672916 intron_variant,splice_acceptor_variant,genic_downstream_transcript_variant,downstream_transcript_variant Genotype CC is associated with decreased dose of tacrolimus in people with Kidney Transplantation as compared to genotypes CT + TT. tacrolimus Metabolism/PK CYP3A5 1A T/C 0.150 29 2 169
rs2242480 7 99763843 intron_variant CYP3A4 *1G/*1G is associated with decreased metabolism of fentanyl in human liver microsomes as compared to CYP3A4 *1/*1 + *1/*1G. tacrolimus Metabolism/PK CYP3A4 1B T/C 0.337 18 98 83
rs1805123 7 150948446 missense_variant,coding_sequence_variant,genic_downstream_transcript_variant Allele G is associated with decreased QT interval as compared to genotype TT.    KCNH2 3 G/T 0.095 0 38 162
rs4646244 8 18390208 upstream_transcript_variant,genic_upstream_transcript_variant,intron_variant Allele A is associated with increased risk of Hepatitis when treated with ethambutol, isoniazid, pyrazinamide and rifampin in people with Tuberculosis. ethambutol isoniazid pyrazinamide rifampin Toxicity/Metabolism/PK NAT2 3 A/T 0.223 13 62 122
rs4271002 8 18390758 upstream_transcript_variant,genic_upstream_transcript_variant,intron_variant Allele C is associated with increased risk of intolerance of aspirin in people with Asthma as compared to allele G. aspirin Toxicity NAT2 3 C/G 0.241 9 77 111
rs1041983 8 18400285 coding_sequence_variant,synonymous_variant NAT2 *6A/*7B is associated with increased likelihood of Toxic liver disease when treated with isoniazid and rifampin in people with Tuberculosis. ethambutol isoniazid pyrazinamide rifampin Toxicity NAT2 1B T/C 0.455 42 96 60
rs1801280 8 18400344 missense_variant,coding_sequence_variant NAT2 *5A is associated with increased risk of severe cutaneous adverse reactions when treated with sulfamethoxazole and trimethoprim in people with Acquired Immunodeficiency Syndrome. ethambutol isoniazid pyrazinamide rifampin Toxicity NAT2 1B C/T 0.043 0 17 183
rs1799929 8 18400484 coding_sequence_variant,synonymous_variant Allele T is not associated with increased risk of hepatotoxicity when treated with ethambutol, isoniazid, pyrazinamide and rifampin in people with Tuberculosis as compared to allele C. ethambutol isoniazid pyrazinamide rifampin Toxicity NAT2 1B T/C 0.043 0 17 183
rs1799930 8 18400593 missense_variant,coding_sequence_variant NAT2 *6/*7 is associated with increased likelihood of Toxic liver disease when treated with ethambutol, isoniazid, pyrazinamide and rifampin in people with Tuberculosis ethambutol isoniazid pyrazinamide rifampin Toxicity NAT2 1B A/G 0.234 12 69 118
rs1208 8 18400806 missense_variant,coding_sequence_variant NAT2 *5B/*7B + *6A/*6A + *6A/*7B + *7B/*7B are associated with increased risk of Toxic liver disease when treated with ethambutol, isoniazid, pyrazinamide and rifampin in people with Tuberculosis. ethambutol isoniazid pyrazinamide rifampin Toxicity NAT2 1B G/A 0.043 0 17 183
rs1799931 8 18400860 missense_variant,coding_sequence_variant NAT2 *6/*7 is associated with increased likelihood of Toxic liver disease when treated with ethambutol, isoniazid, pyrazinamide and rifampin in people with Tuberculosis. ethambutol isoniazid pyrazinamide rifampin Toxicity NAT2 1B A/G 0.230 10 72 118
rs1495741 8 18415371 None Genotype AA is associated with increased likelihood of Toxic liver disease when treated with Drugs For Treatment Of Tuberculosis as compared to genotypes AG + GG. Drugs For Treatment Of Tuberculosis Toxicity NAT2 3 G/A 0.370 26 93 77
rs2115819 10 45405641 intron_variant Genotype GG is associated with increased FEV1 response when treated with montelukast in people with Asthma as compared to genotypes AA + AG. montelukast Efficacy ALOX5 3 A/G 0.140 9 38 153
rs4244285 10 94781859 coding_sequence_variant,synonymous_variant Allele A is associated with decreased exposure to clopidogrel active metabolite when treated with clopidogrel in healthy individuals as compared to allele G. nelfinavir Metabolism/PK CYP2C19 3 A/G 0.389 31 92 75
rs1057910 10 94981296 missense_variant,coding_sequence_variant CYP2C9 *1/*3 is associated with decreased metabolism of meloxicam in healthy individuals as compared to CYP2C9 *1/*1. piroxicam Metabolism/PK CYP2C9 1A C/A 0.023 0 9 191
rs11572103 10 95058349 missense_variant,coding_sequence_variant CYP2C8 *1/*3 + *3/*3 is associated with increased response to paclitaxel in women with Breast Neoplasms as compared to CYP2C8 *1/*1. rosiglitazone Toxicity CYP2C8 3 A/T 0.010 0 4 196
rs7909236 10 95069673 upstream_transcript_variant Allele T is not associated with concentrations of imatinib in people with Neoplasms as compared to allele G.    CYP2C8   T/G 0.030 0 12 188
rs17110453 10 95069772 upstream_transcript_variant Genotypes AC + CC is not associated with resistance to clopidogrel in people with Stroke as compared to genotype AA.    CYP2C8   C/A 0.363 26 93 81
rs3813867 10 133526101 non_coding_transcript_variant,upstream_transcript_variant CYP2E1 *1/*5B is associated with increased elimination rate of acetaminophen in people with Liver Diseases, Alcoholic as compared to CYP2E1 *1/*1. Drugs For Treatment Of Tuberculosis Toxicity CYP2E1 3 C/G 0.075 3 24 172
rs2031920 10 133526341 non_coding_transcript_variant,upstream_transcript_variant Genotypes CT + TT are associated with increased risk of Toxic liver disease when treated with Drugs For Treatment Of Tuberculosis in people with Tuberculosis as compared to genotype CC. Drugs For Treatment Of Tuberculosis   CYP2E1 3 T/C 0.098 3 33 164
rs6413432 10 133535040 intron_variant Genotype TT is associated with increased progression-free survival when treated with cisplatin and cyclophosphamide in women with Ovarian Neoplasms as compared to genotype AT. cisplatin cyclophosphamide Efficacy CYP2E1 3 A/T 0.025 0 10 190
rs2070676 10 133537633 intron_variant Genotype CG is associated with increased risk of severe emesis when treated with cisplatin and cyclophosphamide in women with Ovarian Neoplasms as compared to genotype CC. cisplatin cyclophosphamide Efficacy/Toxicity CYP2E1 3 G/C 0.175 3 64 133
rs5219 11 17388025 missense_variant,stop_gained,5_prime_UTR_variant,intron_variant,coding_sequence_variant Allele T is associated with decreased activity of KCNJ11 when treated with glibenclamide pancreatic islet cells. gliclazide Efficacy KCNJ11 3 T/C 0.340 9 118 73
rs1801028 11 113412762 missense_variant,coding_sequence_variant Genotypes CG + GG are not associated with response to antipsychotics in people with Schizophrenia as compared to genotype CC.    DRD2   C/G 0.005 0 2 198
rs2306283 12 21176804 missense_variant,coding_sequence_variant Genotype AA is associated with decreased response to rocuronium as compared to genotypes AG + GG. pitavastatin Metabolism/PK SLCO1B1 3 A/G 0.168 5 57 138
rs4516035 12 47906043 upstream_transcript_variant Allele T is associated with increased jejunal CYP3A4 protein levels as compared to allele C. midazolam Metabolism/PK VDR 3 C/T 0.025 0 10 190
rs762551 15 74749576 intron_variant CYP1A2 *1K is associated with decreased transcription of CYP1A2 when exposed to xenobiotics in B1642 cells. caffeine Toxicity CYP1A2 3 C/A 0.321 17 91 87
rs2472304 15 74751897 intron_variant Allele A is associated with increased likelihood of remission when treated with paroxetine in people with Depressive Disorder, Major as compared to allele G. paroxetine/erlotinib Efficacy/Metabolism/PK CYP1A2 3 A/G 0.083 0 33 167
rs750155 16 28609251 5_prime_UTR_variant,intron_variant,genic_upstream_transcript_variant,upstream_transcript_variant Allele T is not associated with ABT-751 pharmacokinetic parameters when treated with ABT-751 in people with Neoplasms as compared to allele C.    SULT1A1   T/C 0.406 22 112 58
rs1800764 17 63473168 None     ACE   C/T 0.269 14 79 106
rs4291 17 63476833 upstream_transcript_variant Genotypes AT + TT are associated with increased risk of aspirin intolerance when exposed to aspirin in people with Asthma as compared to genotype AA. captopril/aspirin/amlodipine chlorthalidone lisinopril Efficacy/Toxicity/Efficacy ACE 3 T/A 0.500 0 200 0
rs4267385 17 63506395 None Genotypes CC + CT are associated with same protective properties against angiotensin-converting enzyme inhibitors-induced cough when treated with Ace Inhibitors, Plain in people with homozygous GG genotype for rs4343 as compared to genotype TT. Ace Inhibitors Plain Toxicity ACE 3 T/C 0.260 16 71 111
rs2108622 19 15879621 missense_variant,coding_sequence_variant CYP4F2 *1/*3 + *3/*3 are associated with increased exposure to Vitamin K1 in healthy individuals as compared to CYP4F2 *1/*1. warfarin Dosage CYP4F2 1A T/C 0.173 6 57 137
rs3093105 19 15897578 missense_variant,coding_sequence_variant Allele C is associated with increased catalytic activity of CYP4F2 when treated with vitamin e in Sf9 insect cells transfected with CYP4F2 as compared to allele A. vitamin e Metabolism/PK CYP4F2 3 C/A 0.497 1 198 0
rs8192726 19 40848591 intron_variant Genotypes AC + CC are associated with increased plasma concentration (p=0.028) of efavirenz in people with HIV Infections as compared to genotype AA. efavirenz Other CYP2A6 4 A/C 0.163 8 49 143
rs1051298 21 45514912 intron_variant,3_prime_UTR_variant Allele G is associated with increased progression-free survival when treated with bevacizumab and pemetrexed in people with Lung Neoplasms as compared to allele A. pemetrexed Efficacy SLC19A1 3 G/A 0.431 8 152 35
rs1051296 21 45514947 intron_variant,3_prime_UTR_variant     SLC19A1   A/C 0.469 44 95 56
rs1131596 21 45538002 missense_variant,5_prime_UTR_variant,synonymous_variant,genic_upstream_transcript_variant,coding_sequence_variant Allele G is not associated with response to methotrexate in children with Precursor Cell Lymphoblastic Leukemia-Lymphoma as compared to allele A.    SLC19A1   G/A 0.490 33 129 37
rs1065852 22 42130692 intron_variant,missense_variant,coding_sequence_variant Allele A is associated with decreased clearance of alpha-hydroxymetoprolol in healthy individuals as compared to allele G. paroxetine Metabolism/PK CYP2D6 1A G/A 0.430 29 170 1
  1. SNP Single nucleotide polymorphism, BP Base pair, MAF Minor allele frequency