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Table 2 Top SNPs demonstrating gene-environment interactions for mental and motor composite scores

From: Genome-wide gene by lead exposure interaction analysis identifies UNC5D as a candidate gene for neurodevelopment

  

Position

Alleles

Mexico

(n = 390)

Bangladesh

(n = 497)

Meta-analysis

Directiona

 

SNP

Chr

(bp)

Minor/Ref

p

MAF

p

MAF

p

 

Mapped genes

Mental composite scores

 rs9642758

8

35,721,159

A/G

0.0004

0.076

0.0023

0.123

4.35E-06

++

UNC5D

 rs2276102

11

87,013,438

T/C

0.0028

0.411

0.0011

0.330

1.13E-05

++

TMEM135

 rs7952312

11

99,789,888

T/G

0.0031

0.365

0.0019

0.440

2.05E-05

--

CNTN5

 rs7556550

1

89,928,044

T/C

0.0038

0.382

0.0033

0.190

4.26E-05

--

GBP5/GBP6/LRRC8B/LRRC8C

 rs619092

3

173,131,044

T/C

0.0018

0.248

0.0067

0.225

4.69E-05

--

NLGN1

 rs10503970

8

34,866,368

A/G

0.0018

0.077

0.0073

0.116

4.98E-05

++

UNC5D

 rs2020402

11

87,120,819

T/G

0.0017

0.343

0.0090

0.403

5.98E-05

--

LOC101929137/ TMEM135

 rs2483678

1

10,582,047

T/C

0.0045

0.135

0.0043

0.308

6.31E-05

--

PEX14

 rs2480786

1

10,567,658

A/G

0.0057

0.134

0.0037

0.299

6.94E-05

++

PEX14

 rs10270302

7

150,213,019

T/C

0.0021

0.071

0.0095

0.079

7.53E-05

++

GIMAP7

 rs17035156

1

10,585,527

A/C

0.0050

0.133

0.0048

0.302

7.84E-05

--

PEX14

 rs4811754

20

55,392,174

A/C

0.0031

0.423

0.0079

0.245

8.68E-05

--

TFAP2C

 rs1498706

12

93,996,980

A/G

0.0041

0.275

0.0066

0.161

9.04E-05

--

MRPL42/SOCS2/CRADD

 rs10493836

1

90,574,778

T/C

0.0053

0.083

0.0067

0.068

0.00012

--

ZNF326/LRRC8D

 rs10953862

7

79,063,644

A/G

0.0067

0.240

0.0060

0.292

0.00013

--

MAGI2

 rs1335647

1

89,832,464

T/C

0.0093

0.438

0.0048

0.221

0.00014

++

GBP6

 rs12120749

1

52,145,202

A/G

0.0098

0.253

0.0049

0.041

0.00015

--

OSBPL9

 rs4734384

8

99,133,678

A/C

0.0075

0.260

0.0079

0.313

0.00019

--

POP1

 rs1349784

11

99,806,211

T/G

0.0067

0.383

0.0098

0.409

0.00021

--

CNTN5

 rs999995

10

78,735,498

A/G

0.0085

0.485

0.0098

0.419

0.00026

++

KCNMA1

Motor composite scores

 rs3817591

15

33,057,775

T/C

5.54E-05

0.427

0.0031

0.490

1.16E-06

--

FMN1

 rs4308495

5

30,155,798

T/C

0.0016

0.089

0.0019

0.121

1.15E-05

++

 

 rs28694796

7

155,403,168

A/G

0.0006

0.081

0.0093

0.068

2.72E-05

--

EN2/RBM33/CNPY1/SHH

 rs322172

17

25,659,288

A/G

0.0088

0.232

0.0010

0.263

2.97E-05

++

MIR4522/WSB1/KSR1

 rs10015043

4

169,485,237

A/G

0.0040

0.422

0.0025

0.366

3.28E-05

++

PALLD

 rs13353041

1

55,773,756

A/G

0.0080

0.051

0.0015

0.074

3.96E-05

++

USP24/MIR442

 rs170602

20

56,019,162

T/C

0.0082

0.186

0.0016

0.210

4.19E-05

++

SPO11/RAE1/RBM38/CTCFL/PCK1/ZBP1

 rs9945240

18

44,139,893

A/G

0.0067

0.062

0.0021

0.054

4.53E-05

++

LOXHD1

 rs10022111

4

169,484,303

A/G

0.0018

0.459

0.0072

0.297

4.91E-05

--

PALLD

 rs2318817

18

65,494,366

A/C

0.0025

0.048

0.0064

0.119

5.57E-05

++

LOC643542

 rs2552531

2

218,698,323

A/G

0.0050

0.019

0.0038

0.066

6.19E-05

++

TNS1

 rs17075573

3

40,131,246

T/C

0.0027

0.116

0.0086

0.082

8.38E-05

--

MYRIP

 rs30732

5

66,151,551

T/C

0.0058

0.302

0.0052

0.123

9.42E-05

++

MAST4

 rs6458566

6

47,361,788

A/G

0.0053

0.310

0.0056

0.467

9.50E-05

++

TNFRSF21/CD2AP

 rs1647292

8

4,017,692

T/C

0.0031

0.158

0.0091

0.177

9.83E-05

--

CSMD1

 rs1324800

13

48,388,487

A/G

0.0033

0.041

0.0089

0.078

0.00010

++

SUCLA2

 rs16849242

3

162,188,734

T/C

0.0097

0.171

0.0049

0.333

0.00014

++

 

 rs17111847

1

55,749,478

T/C

0.0070

0.052

0.0070

0.067

0.00015

--

USP24/MIR442

 rs11600036

11

81,001,092

A/G

0.0062

0.135

0.0080

0.433

0.00016

++

 

 rs10122848

9

25,368,388

T/G

0.0071

0.073

0.0077

0.229

0.00017

--

 

 rs12593647

15

87,117,255

A/C

0.0090

0.164

0.0090

0.262

0.00024

++

AGBL1

  1. SNP Single-nucleotide polymorphism, MAF minor allele frequency
  2. All models adjusted for child’s gender, child’s age at time of neurodevelopment testing, gestational age, parity, maternal education (binary), environmental tobacco smoke exposure (binary), and first two principal components of population stratification
  3. aEffects of gene-environment interaction on the neurodevelopmental outcomes. “+”: increased risk; “-”: protective effect. The first “+/−” represents the effect observed in Mexico cohort, and the second “+/−” represents the effect observed in Bangladesh cohort