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Table 1 Statistically significant enrichment for natural selection and functional annotations in SNP-based heritability of complex traits in East Asian and European populations. Details of all traits and annotations tested are available in Supplemental Table 4

From: Denisovan and Neanderthal archaic introgression differentially impacted the genetics of complex traits in modern populations

Trait

Annotation

East Asian

European

EAS-EUR Difference

Fold-enrichment

SE

P-value

Fold-enrichment

SE

P-value

Z score

P-value

Alanine aminotransferase

B top1

0.855

0.349

0.983

2.728

0.614

0.005

−2.652

0.008

B top2

−13.622

9.421

0.958

2.159

0.366

0.001

−1.674

0.094

Genic

1.237

0.081

0.002

1.315

0.034

2.48E−18

−0.885

0.376

LoF intolerant

1.272

0.232

0.227

1.615

0.121

2.18E−07

−1.311

0.190

Albumin

B top05

−1.971

2.266

0.718

3.950

1.484

0.049

−2.186

0.029

B top1

1.135

0.675

0.983

3.158

0.947

0.024

−1.740

0.082

B top2

8.223

7.181

0.958

3.734

0.670

6.11E−05

0.622

0.534

Genic

1.380

0.092

1.82E−05

1.297

0.027

2.97E−19

0.866

0.386

LoF intolerant

1.532

0.284

0.053

1.648

0.110

1.59E−09

−0.381

0.704

Albumin/globulin ratio

B top05

2.151

2.822

0.718

4.159

1.164

0.006

−0.658

0.511

B top1

1.597

0.453

0.849

2.719

0.597

0.004

−1.498

0.134

B top2

1.794

1.880

0.953

2.943

0.632

0.002

−0.579

0.563

Genic

1.437

0.079

1.35E−09

1.310

0.030

2.07E−16

1.502

0.133

LoF intolerant

2.056

0.283

5.44E−05

1.661

0.117

3.37E−09

1.294

0.196

Aspartate aminotransferase

B top05

−1.507

1.256

0.718

3.323

1.120

0.033

−2.870

0.004

B top1

2.930

2.220

0.983

2.985

0.647

0.002

−0.024

0.981

B top2

−12.232

6.942

0.958

2.742

0.496

0.000285

−2.152

0.031

Genic

1.287

0.067

2.26E−06

1.314

0.030

2.39E−22

−0.371

0.711

LoF intolerant

1.503

0.213

0.010

1.596

0.120

7.26E−08

−0.381

0.703

Asthma

B top05

−2.439

3.102

0.950

2.329

0.629

0.034

−1.506

0.132

B top1

3.842

2.358

0.983

2.486

0.524

0.004

0.561

0.575

B top2

−8.241

1.204

0.961

2.096

0.459

0.016

−8.020

1.06E−15

Genic

1.008

0.085

0.928

1.123

0.040

0.001

−1.235

0.217

LoF intolerant

0.869

0.236

0.575

1.223

0.095

0.016

−1.394

0.163

Blood sugar

B top2

−1.152

1.446

0.953

2.446

0.533

0.003

−2.334

0.020

Genic

1.368

0.089

2.51E−05

1.293

0.065

2.09E−09

0.682

0.495

LoF intolerant

1.324

0.274

0.217

1.635

0.192

2.06E−04

−0.930

0.352

Blood urea nitrogen

Genic

1.237

0.073

3.28E−04

NA

NA

NA

NA

NA

LoF intolerant

1.471

0.238

0.043

NA

NA

NA

NA

NA

Body mass index

Genic

1.167

0.065

0.007

1.125

0.017

7.18E−12

0.628

0.530

LoF intolerant

2.086

0.236

2.05E−07

1.682

0.069

1.46E−20

1.643

0.100

Chloride

Genic

1.361

0.105

3.80E−05

NA

NA

NA

NA

NA

LoF intolerant

1.722

0.338

0.019

NA

NA

NA

NA

NA

Coronary artery disease

B top05

1.338

1.226

0.718

3.230

0.968

0.020

−1.211

0.226

B top2

1.051

1.058

0.953

2.400

0.473

0.002

−1.164

0.244

Denisovan

1.691

0.877

0.003

2.149

1.522

0.449

−0.261

0.794

Genic

1.232

0.047

5.47E−08

1.250

0.040

1.48E−09

−0.282

0.778

LoF intolerant

1.575

0.181

3.36E−04

1.681

0.141

3.07E−07

−0.460

0.645

Diastolic blood pressure

B top05

2.871

2.759

0.718

2.907

0.913

0.039

−0.012

0.990

B top1

1.124

0.341

0.983

2.532

0.479

0.001

−2.394

0.017

B top2

3.116

1.191

0.958

2.323

0.298

9.33E−06

0.646

0.519

Genic

1.271

0.084

3.07E−04

1.230

0.024

5.69E−18

0.472

0.637

LoF intolerant

2.050

0.288

5E−05

1.751

0.093

4.46E−15

0.988

0.323

Estimated glomerular filtration rate

B top05

1.234

1.484

0.718

4.724

1.209

0.002

−1.823

0.068

B top1

2.184

0.471

0.983

3.960

0.848

4.97E−04

−1.830

0.067

B top2

9.394

6.212

0.006

2.955

0.444

8.23E−06

1.034

0.301

Genic

1.277

0.050

1.33E−08

1.306

0.031

2.23E−21

−0.483

0.629

LoF intolerant

1.931

0.203

3.96E−07

1.853

0.135

3.09E−09

0.320

0.749

Hematocrit

Genic

1.342

0.072

1.45E−07

NA

NA

NA

NA

NA

LoF intolerant

2.193

0.280

1.99E−06

NA

NA

NA

NA

NA

Hemoglobin

Genic

1.397

0.092

2.85E−07

NA

NA

NA

NA

NA

LoF intolerant

2.336

0.342

4.79E−06

NA

NA

NA

NA

NA

Lymphocyte count

B top1

1.392

0.437

0.960

3.024

0.742

0.006

−1.896

0.058

B top2

2.193

1.216

0.293

2.722

0.484

3.32E−04

−0.404

0.686

Genic

1.178

0.079

0.015

1.316

0.028

2.70E−20

−1.636

0.102

LoF intolerant

1.523

0.246

0.024

1.671

0.110

5.54E−09

−0.549

0.583

Mean arterial pressure

B top05

1.536

2.312

0.950

2.550

0.766

0.045

−0.416

0.677

B top1

1.085

0.372

0.983

2.220

0.436

0.005

−1.980

0.048

B top2

1.833

1.321

0.958

2.083

0.280

7.84E−05

−0.185

0.853

Genic

1.314

0.076

6.07E−06

1.219

0.024

2.03E−16

1.189

0.234

LoF intolerant

2.092

0.260

2.57E−06

1.784

0.096

7.51E−16

1.112

0.266

Mean corpuscular hemoglobin

B top05

3.948

6.980

0.718

4.182

1.496

0.030

−0.033

0.974

B top1

2.015

0.836

0.849

3.802

1.055

0.007

−1.327

0.184

B top2

2.520

2.993

0.953

4.056

0.734

1.64E−05

−0.498

0.618

Genic

1.303

0.075

8.83E−06

1.348

0.046

1.19E−12

−0.515

0.607

LoF intolerant

1.723

0.278

0.006

1.705

0.167

6.71E−06

0.056

0.955

Mean corpuscular volume

B top1

1.893

0.630

0.849

3.790

1.064

0.009

−1.534

0.125

B top2

3.423

3.146

0.953

3.715

0.666

4.42E−05

−0.091

0.928

Genic

1.311

0.061

2.22E−07

3.715

0.666

4.42E−05

−3.591

3.29E−04

LoF intolerant

1.657

0.243

0.006

1.699

0.154

4.14E−06

−0.143

0.886

Monocyte count

B top05

1.967

2.920

0.718

5.248

2.118

0.045

−0.910

0.363

B top1

2.456

1.347

0.849

3.793

1.004

0.005

−0.796

0.426

B top2

1.348

0.975

0.013

2.773

0.628

0.005

−1.228

0.219

Genic

1.255

0.086

0.002

1.318

0.040

7.53E−13

−0.660

0.509

LoF intolerant

1.548

0.240

0.018

1.557

0.150

8.76E−05

−0.030

0.976

Neutrophil count

B top05

1.800

1.885

0.950

4.148

1.106

0.004

−1.074

0.283

B top1

1.096

0.381

0.983

3.184

0.750

0.003

−2.483

0.013

B top2

4.964

0.986

0.958

2.751

0.518

0.001

1.985

0.047

Genic

1.235

0.080

0.002

1.256

0.025

3.62E−21

−0.248

0.804

LoF intolerant

1.471

0.210

0.021

1.766

0.107

4.15E−11

−1.255

0.210

Non-albumin protein

B top05

4.440

5.075

0.718

4.291

1.014

0.001

0.029

0.977

B top1

1.817

0.620

0.849

2.675

0.549

0.002

−1.036

0.300

B top2

2.184

2.456

0.953

2.847

0.540

0.001

−0.264

0.792

Genic

1.468

0.094

2.72E−09

1.315

0.033

6.72E−16

1.532

0.125

LoF intolerant

2.373

0.301

9.41E−07

1.714

0.114

1.57E−10

2.043

0.041

Platelet count

B top1

3.575

0.375

0.983

4.781

1.276

0.004

−0.907

0.364

B top2

2.644

0.641

0.958

3.744

0.586

6.10E−06

−1.267

0.205

Genic

1.330

0.044

7.64E−12

1.366

0.026

7.71E−24

−0.710

0.478

LoF intolerant

1.998

0.166

1.98E−08

1.984

0.142

5.76E−11

0.064

0.949

Potassium

B top1

1.112

0.363

0.983

2.387

0.390

3.54E−04

−2.393

0.017

B top2

2.507

1.948

0.958

2.326

0.292

2.99E−06

0.092

0.927

Genic

1.306

0.078

1.36E−05

1.103

0.032

0.002

2.425

0.015

LoF intolerant

1.944

0.284

5.48E−05

1.641

0.115

7.51E−08

0.992

0.321

Pulse pressure

Genic

1.393

0.094

3.91E−07

NA

NA

NA

NA

NA

LoF intolerant

2.304

0.306

2.14E−06

NA

NA

NA

NA

NA

Red blood cell count

B top05

1.639

2.885

0.718

4.790

1.325

0.004

−0.993

0.321

B top1

2.173

0.691

0.849

3.476

0.724

0.001

−1.303

0.193

B top2

5.614

1.771

0.958

3.033

0.487

1.83E−05

1.405

0.160

Genic

1.353

0.066

4.87E−08

1.130

0.025

4.54E−07

3.159

0.002

LoF intolerant

2.077

0.255

1.00E−05

1.561

0.092

1.19E−09

1.901

0.057

Serum creatinine

B top05

8.840

5.950

0.021

4.724

1.209

0.002

0.678

0.498

B top1

3.121

1.461

0.983

3.960

0.848

4.97E−04

−0.497

0.619

B top2

1.492

1.396

0.718

2.955

0.444

8.23E−06

−0.998

0.318

Genic

1.289

0.052

7.98E−09

1.306

0.031

2.23E−21

−0.277

0.782

LoF intolerant

1.865

0.194

9.85E−07

1.853

0.135

3.09E−09

0.050

0.960

Smoking behaviors: Smoking initiation

Genic

1.041

0.129

0.754

NA

NA

NA

NA

NA

LoF intolerant

1.379

0.324

0.248

NA

NA

NA

NA

NA

Sodium

B top05

3.381

4.513

0.718

2.171

0.552

0.036

0.266

0.790

B top1

1.362

0.715

0.983

1.953

0.329

0.003

−0.750

0.453

B top2

−1.750

1.570

0.958

1.700

0.209

0.001

−2.178

0.029

Genic

1.426

0.138

1.07E−04

1.130

0.025

4.54E−07

2.111

0.035

LoF intolerant

2.193

0.485

0.006

1.561

0.092

1.19E−09

1.283

0.200

Systolic blood pressure

B top05

1.752

2.069

0.718

2.296

0.515

0.013

−0.255

0.799

B top1

1.014

0.389

0.985

2.035

0.334

0.002

−1.991

0.047

B top2

3.253

1.345

0.958

2.055

0.244

9.62E−06

0.876

0.381

Genic

1.341

0.070

8.58E−08

1.234

0.024

3.92E−18

1.439

0.150

LoF intolerant

2.143

0.241

8.95E−08

1.795

0.087

3.96E−18

1.356

0.175

Total cholesterol

B top1

4.831

2.371

0.983

4.722

1.431

0.008

0.039

0.969

B top2

−7.322

9.190

0.953

2.873

0.781

0.012

−1.105

0.269

Genic

1.359

0.086

2.71E−05

1.308

0.034

3.49E−13

0.553

0.580

LoF intolerant

1.287

0.303

0.308

1.432

0.174

0.011

−0.414

0.679

Total protein

B top05

5.388

5.538

0.718

4.096

0.826

2.83E−04

0.231

0.818

B top1

1.956

0.514

0.849

2.736

0.520

0.001

−1.066

0.286

B top2

1.610

1.907

0.953

2.825

0.405

5.76E−06

−0.623

0.533

Genic

1.395

0.093

2.96E−07

1.310

0.027

5.72E−18

0.874

0.382

LoF intolerant

2.111

0.278

2.98E−05

1.745

0.129

1.75E−10

1.197

0.231

Type 2 diabetes

B top05

2.218

1.431

0.718

2.204

0.501

0.016

0.009

0.993

B top1

1.085

0.292

0.983

2.109

0.392

0.005

−2.092

0.036

B top2

5.468

3.974

0.293

2.090

0.254

6.08E−06

0.848

0.396

Genic

1.171

0.034

8.13E−07

1.147

0.032

8.17E−06

0.523

0.601

LoF intolerant

1.955

0.179

1.56E−07

1.608

0.123

2.03E−06

1.596

0.110

White blood cell count

B top05

5.024

3.190

0.718

5.029

1.350

0.003

−0.001

0.999

B top1

1.200

0.354

0.983

3.307

0.666

0.001

−2.793

0.005

B top2

−5.583

7.351

0.953

2.757

0.479

2.79E−04

−1.132

0.258

Genic

1.340

0.073

5.24E−07

1.253

0.023

3.31E−23

1.148

0.251

LoF intolerant

1.728

0.204

1.59E−04

1.730

0.100

8.96E−12

−0.007

0.995