Table S1 Minor allele frequencies (MAF) of 211 tagging single nucleotide polymorphisms (SNPs) in the Xhosa and Cape Mixed Ancestry (CMA) populations

ABCB1

rs2229109

A

1

0.0

0.0

NA

NA

ABCB1

rs1202185

G

1

0.187

0.216

0.789

0.242

ABCB1

rs10233247

G

1

0.075

0.101

2.22E-16

0.0

ABCB1

rs2235046

A

1

0.254

0.211

0.84

0.624

ABCB1

rs4148743

A

1

0.41

0.358

0.248

0.691

ABCB1

rs2373589

A

1

0.373

0.339

0.0551

0.297

ABCB1

rs6946119

G

1

0.067

0.041

0.556

0.653

ABCB1

rs10275831

A

1

0.037

0.05

0.751

0.579

ABCB1

rs1858923

G

1

0.239

0.128

0.428

0.863

ABCB1

rs2235033

G

1

0.463

0.472

0.25

0.898

ABCB1

rs2157926

T

1

0.537

0.413

0.0328

0.574

ABCB1

rs1922242

T

1

0.448

0.491

0.779

0.629

ABCB1

rs2032588

A

1

0.127

0.197

0.931

0.453

ABCB1

rs10267099

G

1

0.09

0.11

0.421

0.197

ABCB1

rs7787082

G

1

0.396

0.317

0.0048

0.0708

ABCB1

rs4148740

G

1

0.179

0.142

0.48

0.532

ABCB1

rs1211152

A

1

0.0

0.0

NA

NA

ABCB1

rs7796247

A

1

0.037

0.05

0.751

0.579

ABCB1

rs1202175

G

1

0.187

0.216

0.789

0.242

ABCB1

rs1922241

A

1

0.216

0.193

0.535

0.52

ABCB1

rs6465118

A

1

0.224

0.229

0.652

0.493

ABCB1

rs4728705

A

1

0.134

0.133

0.826

0.44

ABCB1

rs13229143

G

1

0.239

0.124

0.428

0.772

ABCB1

rs6950978

T

1

0.0

0.0

NA

NA

ABCB1

rs1202172

C

1

0.351

0.362

0.505

0.776

ABCB1

rs4148732

G

1

0.0

0.0

NA

NA

ABCB1

rs10274587

A

1

0.134

0.128

0.826

0.304

ABCB1

rs3789243

A

1

0.396

0.372

0.205

0.0968

ABCB1

rs4437575

G

1

0.418

0.353

0.881

0.557

ABCB1

rs4728709

G

1

0.522

0.408

0.108

0.261

ABCB1

rs4728707

A

1

0.209

0.188

0.0306

0.928

ABCB1

rs2032583

G

1

0.187

0.147

0.591

0.618

ABCB1

rs17149866

G

1

0.03

0.028

2.22E-16

0.0

ABCB1

rs1882479

G

1

0.119

0.106

0.959

0.0698

ABCB1

rs1055302

A

1

0.231

0.33

0.687

0.211

ABCB1

rs12334183

G

1

0.246

0.317

0.202

0.395

ABCB1

rs10264990

G

1

0.299

0.275

0.25

0.902

ABCB1

rs17149699

A

1

0.284

0.321

0.713

0.917

ABCB1

rs1882478

G

1

0.425

0.399

0.289

0.0243

ABCB1

rs10248420

A

1

0.448

0.413

0.00595

0.339

ABCB1

rs10236274

G

1

0.254

0.289

0.136

0.327

ABCB1

rs3213619

G

1

0.224

0.193

0.652

0.977

ABCB1

rs10225473

G

1

0.127

0.119

0.931

0.186

ABCB1

rs17327442

A

1

0.478

0.459

2.22E-16

0.0

ABCB1

rs17149792

A

1

0.119

0.266

0.959

0.529

ABCB1

rs1202169

G

1

0.261

0.225

0.718

0.781

ABCB1

rs6949448

A

1

0.187

0.151

0.591

0.708

ABCB1

rs1202184

A

1

0.269

0.106

0.919

0.218

ABCB1

rs4148745

A

1

0.127

0.138

0.309

0.39

ABCB1

rs1002205

C

0.994

0.276

0.292

0.947

0.025

ABCB1

rs17327624

A

0.994

0.209

0.185

0.956

0.85

ABCB1

rs1202181

G

0.994

0.187

0.213

0.789

0.276

ABCB1

rs2235023

A

0.994

0.269

0.333

0.919

1.0

ABCB1

rs4148734

A

0.994

0.067

0.032

0.174

0.728

ABCB1

rs13233308

A

0.994

0.182

0.018

0.328

0.845

ABCB1

rs1045642

T

0.994

0.205

0.11

0.349

0.754

ABCB1

rs4148738

G

0.989

0.194

0.164

0.683

0.922

ABCB1

rs7779562

G

0.983

0.4

0.444

0.179

0.153

ABCB1

rs9282564

G

0.977

0.008

0.0

0.95

NA

ABCB1

rs10808071

G

0.977

0.164

0.194

0.0379

0.0732

ABCB1

rs2235041

A

0.977

0.077

0.126

0.282

0.256

ABCB1

rs2235074

NA

0.665

NA

NA

NA

NA

ABCB1

rs1002204

NA

0.119

NA

NA

NA

NA

ABCC2

rs2073337

G

1

0.403

0.491

0.34

0.387

ABCC2

rs7476245

A

1

0.097

0.092

0.606

0.0167

ABCC2

rs8187707

A

1

0.082

0.083

0.374

0.347

ABCC2

rs17216282

G

1

0.194

0.161

0.248

0.198

ABCC2

rs8187674

G

1

0.045

0.055

0.701

0.543

ABCC2

rs2180989

C

1

0.276

0.317

0.586

0.684

ABCC2

rs11595888

A

1

0.0

0.0

NA

NA

ABCC2

rs4148396

A

1

0.321

0.303

0.537

0.997

ABCC2

rs4148399

C

1

0.045

0.133

0.701

0.44

ABCC2

rs4148398

A

1

0.187

0.101

0.591

0.907

ABCC2

rs17112266

A

1

0.052

0.078

0.652

0.377

ABCC2

rs7067971

G

1

0.201

0.138

0.832

0.39

ABCC2

rs2804398

A

1

0.269

0.317

0.469

0.684

ABCC2

rs3740065

G

1

0.313

0.445

0.812

0.822

ABCC2

rs3740063

A

1

0.5

0.477

0.903

0.647

ABCC2

rs2273697

A

1

0.187

0.11

0.591

0.101

ABCC2

rs7898096

A

1

0.09

0.211

0.421

0.0702

ABCC2

rs2002042

A

0.994

0.201

0.185

0.832

0.408

ABCC2

rs2756109

A

0.983

0.47

0.448

0.691

0.779

ABCC2

rs4148391

T

0.977

0.0

0.0

NA

NA

ABCC2

rs717620

T

0.898

0.04

0.037

0.743

0.709

ABCC2

rs8187710

NA

0.341

NA

NA

NA

NA

ABCC2

rs2756112

NA

0

NA

NA

NA

NA

CYP2A7P1

rs7250597

A

1

0.082

0.165

0.464

0.499

CYP2A7P1

rs7249735

C

1

0.06

0.092

2.22E-16

0.0

CYP2A7P1

rs7255146

A

0.994

0.227

0.339

0.774

0.128

CYP2A7P1

rs11666982

A

0.994

0.433

0.227

0.471

0.161

CYP2B6

rs1042389

G

1

0.231

0.271

0.0138

0.633

CYP2B6

rs8192719

A

1

0.306

0.317

0.464

0.0294

CYP2B6

rs28399499

G

1

0.09

0.174

2.22E-16

0.0

CYP2B6

rs35773040

A

1

0.0

0.0

NA

NA

CYP2B6

rs35303484

G

1

0.0

0.0

NA

NA

CYP2B6

rs2279345

A

1

0.216

0.161

0.18

0.398

CYP2B6

rs7260329

A

1

0.209

0.106

0.956

0.218

CYP2B6

rs3211371

G

1

0.0

0.0

NA

NA

CYP2B6

rs16974799

A

1

0.306

0.335

0.464

0.0694

CYP2B6

rs7255374

A

1

0.366

0.399

0.614

0.18

CYP2B6

rs36060847

A

1

0.0

0.0

NA

NA

CYP2B6

rs8100458

G

1

0.336

0.252

0.394

0.136

CYP2B6

rs2113103

A

1

0.261

0.151

0.104

0.0626

CYP2B6

rs35979566

A

1

0.0

0.0

NA

NA

CYP2B6

rs36079186

G

1

0.0

0.0

NA

NA

CYP2B6

rs34223104

G

1

0.007

0.005

0.951

0.962

CYP2B6

rs2279342

A

1

0.015

0.018

0.901

0.845

CYP2B6

rs8192712

G

1

0.03

0.009

0.801

0.923

CYP2B6

rs2054675

G

1

0.306

0.339

0.464

0.0514

CYP2B6

rs3745274

C

1

0.231

0.202

0.0138

0.00829

CYP2B6

rs11882450

G

0.994

0.06

0.079

0.603

0.66

CYP2B6

rs4803417

C

0.994

0.159

0.115

0.0321

0.683

CYP2B6

rs6508963

A

0.994

0.007

0.023

0.951

0.805

CYP2B6

rs34097093

A

0.983

0.0

0.0

NA

NA

CYP2B6

rs2306606

G

0.983

0.201

0.184

0.0389

0.0203

CYP2B6

rs2279343

NA

0

NA

NA

NA

NA

CYP2C18

rs11188059

A

1

0.03

0.0

0.801

NA

CYP2C18

rs932809

A

1

0.224

0.248

0.801

0.5

CYP2C18

rs12243416

A

1

0.09

0.151

0.421

0.711

CYP2C18

rs1326830

A

1

0.067

0.0

0.174

NA

CYP2C18

rs7896133

A

1

0.201

0.202

0.832

0.128

CYP2C18

rs2296680

A

1

0.209

0.234

0.956

0.277

CYP2C18

rs2296684

A

1

0.067

0.119

0.174

0.682

CYP2C18

rs2860840

A

1

0.09

0.005

0.421

0.962

CYP2C18

rs10509675

A

1

0.09

0.151

0.421

0.711

CYP2C18

rs1409656

G

1

0.112

0.151

0.302

0.708

CYP2C18

rs7917985

A

1

0.157

0.266

0.551

0.889

CYP2C18

rs7085563

A

0.994

0.333

0.404

0.0648

0.0581

CYP2C18

rs1010570

A

0.994

0.485

0.495

0.114

0.564

CYP2C18

rs1409655

A

0.994

0.098

0.064

0.375

0.38

CYP2C18

rs11188067

G

0.983

0.1

0.148

0.37

0.778

CYP2C19

rs10509677

G

1

0.022

0.014

0.851

0.884

CYP2C19

rs4917623

G

1

0.209

0.115

0.427

0.683

CYP2C19

rs1322179

A

1

0.201

0.211

0.832

0.509

CYP2C19

rs12248560

A

1

0.09

0.151

0.421

0.711

CYP2C19

rs4244285

A

1

0.201

0.22

0.832

0.339

CYP2C19

rs7101258

C

1

0.172

0.183

0.378

0.395

CYP2C19

rs7915414

A

0.994

0.418

0.44

0.0309

0.966

CYP2D6

rs5758589

A

1

0.321

0.335

0.537

0.339

CYP2D6

rs9623531

G

0.983

0.408

0.338

0.259

0.151

CYP3A4

rs4986910

G

1

0.0

0.0

NA

NA

CYP3A4

rs28371759

G

1

0.0

0.0

NA

NA

CYP3A4

rs17161829

A

1

0.09

0.22

0.421

0.0669

CYP3A4

rs7801671

C

1

0.328

0.284

6.29E-05

3.33E-05

CYP3A4

rs17161886

C

1

0.104

0.252

0.34

0.0455

CYP3A4

rs2687117

A

1

0.172

0.275

0.403

0.721

CYP3A4

rs12333983

A

1

0.433

0.271

0.471

0.328

CYP3A4

rs2740574

A

1

0.425

0.234

0.575

0.606

CYP3A4

rs4986909

A

1

0.0

0.0

NA

NA

CYP3A4

rs2738258

A

1

0.172

0.358

0.00932

0.691

CYP3A4

rs10267228

C

0.994

0.306

0.333

0.676

0.0833

CYP3A4

rs7811025

A

0.983

0.159

0.341

1.54E-11

0

CYP3A4

rs4987161

G

0.983

0.0

0.0

NA

NA

CYP3A5

rs4646450

C

1

0.172

0.032

0.0817

5.98E-09

CYP3A5

rs1419745

G

1

0.433

0.495

0.00671

0.773

CYP3A5

rs4646446

A

1

0.104

0.046

0.34

0.616

CYP3A5

rs10224569

A

0.994

0.194

0.329

0.248

0.309

CYP3A5

rs10264272

A

0.989

0.179

0.201

0.48

0.427

CYP3A7

rs10211

A

1

0.522

0.358

0.00101

0.663

CYP3A7

rs2687144

A

1

0.53

0.431

0.0024

0.774

CYP3A7

rs2687074

C

1

0.164

0.252

0.0508

0.295

CYP3A7

rs2687136

A

0.994

0.508

0.463

0.0139

0.191

SLC22A6

rs12293966

G

1

0.082

0.193

0.464

0.977

SLC22A6

rs6591722

A

1

0.149

0.083

0.0158

0.112

SLC22A6

rs2276300

A

1

0.0

0.0

NA

NA

SLC22A6

rs4149170

A

1

0.284

0.45

0.404

0.691

SLC22A6

rs955434

A

0.994

0.22

0.234

0.894

0.985

SLC22A6

rs10897310

NA

0.591

NA

NA

NA

NA

UGT1A1

rs4663972

G

1

0.239

0.431

0.143

0.621

UGT1A1

rs28900396

G

1

0.149

0.339

0.625

0.142

UGT1A1

rs4148323

A

1

0

0

NA

NA

UGT1A1

rs3755319

A

1

0.396

0.261

0.806

0.823

UGT1A1

rs10199882

G

1

0.164

0.156

0.288

0.326

UGT1A1

rs11563251

G

1

0.56

0.44

0.996

0.469

UGT1A1

rs1018124

G

1

0.09

0.087

0.421

0.836

UGT1A1

rs4148328

A

1

0.269

0.124

0.469

0.14

UGT1A1

rs9784064

A

1

0.119

0.197

0.267

0.0103

UGT1A1

rs10929303

A

1

0.299

0.381

0.0771

0.465

UGT1A1

rs887829

A

1

0.366

0.353

0.109

0.503

UGT1A1

rs4148329

A

1

0.418

0.216

0.393

0.242

UGT1A1

rs2003569

A

1

0.209

0.367

0.125

0.269

UGT1A1

rs7572563

G

1

0.328

0.147

0.0741

0.0725

UGT1A1

rs3771342

A

1

0.164

0.165

0.00446

0.475

UGT1A1

rs8330

C

1

0.276

0.385

0.586

0.0907

UGT1A1

rs28946889

A

0.994

0.0

0.0

NA

NA

UGT1A1

rs929596

G

0.994

0.333

0.312

0.14

0.0398

UGT1A1

rs1500482

G

0.994

0.144

0.193

0.527

0.208

UGT1A1

rs4663971

C

0.983

0.469

0.477

0.4

0.184

UGT1A1

rs6431630

NA

0

NA

NA

NA

NA