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Table 3 Most significant overlap between discovery set (case/controls) and validation set (families)

From: Genome-wide association study of bipolar disorder in Canadian and UK populations corroborates disease loci including SYNE1 and CSMD1

Chr

SNP

bp

MAF

MAF_UK

MAF_CAN

P-value:

P_UK

P_CAN

P-value:

P-value:

Gene

Function/domains?

      

discovery

  

validation

joint

  

1

rs12564407

101581806

0.0372

0.0343

0.04089

5.02E-04

0.03818

0.0034

1.13E-05

0.00004

nr S1PR1

Sphingosine-1-phosphate receptor 1; MIM 601974

1

rs17452017

163951301

0.0708

0.07484

0.066

2.71E-04

0.002292

0.04094

1.00E-03

0.0003

nr TMCO1

Transmembrane and coiled-coil domains 1; MIM 614123

2

rs1564004

17962338

0.310

0.3233

0.295

7.85E-04

0.02767

0.009408

4.09E-03

0.0006

KCNS3

Potassium voltage-gated channel; MIM 603888

2

rs6437044

157852441

0.346

0.3413

0.3516

7.19E-04

0.05345

0.004589

4.18E-03

0.001

GALNT5

N-acetylgalactosaminyltransferase 5

2

rs7597971

166996418

0.314

0.303

0.3254

5.46E-04

0.1141

0.0007991

3.93E-03

0.0007

SCN7A

Sodium channel, voltage-gated, type VII, alpha; MIM 182392

5

rs4594899

1185216

0.446

0.4506

0.441

2.39E-04

0.07997

0.0007831

7.96E-03

0.002

nr SLC12A7

Potassium/chloride transporter MIM 604879

5

rs643502

140565698

0.420

0.4059

0.4357

9.18E-04

0.01301

0.03198

8.52E-03

0.001

nr PCDHB12

Protocadherin B12; MIM 606338

7

rs272706

24119442

0.488

0.4854

0.4906

3.91E-04

0.02933

0.005035

7.06E-03

0.007

nr NPY

Neuropeptide Y; MIM 162640

8

rs1154037

4257636

0.0563

0.05561

0.05744

1.15E-03

3.08E-05

0.6685

6.04E-03

0.003

CSMD1

CUB and Sushi multiple domains 1; MIM 608397

12

rs17041209

94684987

0.3276

0.3352

0.3189

5.86E-03

0.006487

0.2539

4.68E-03

0.002

NTN4

Promotes neurite elongation from olfactory bulb explants; MIM 610401

14

rs179524

30312602

0.223

0.2157

0.2307

3.33E-04

0.002542

0.04466

8.09E-03

0.001

nr SCFD1

Sec1 family domain containing 1

16

rs12443910

72711976

0.2943

0.316

0.2699

3.05E-03

0.002753

0.2762

9.82E-03

0.005

nr PSMD7

Proteasome 26S subunit, non-ATPase, 7; MIM 157970

20

rs13039978

57581000

0.0490

0.04626

0.05205

5.45E-04

0.1359

0.0007083

3.08E-03

0.001

nr PHACTR3

Phosphatase and actin regulator 3; MIM 608725

1

rs12564407

101581806

0.0372

0.0343

0.04089

5.02E-04

0.03818

0.0034

1.13E-05

0.00004

nr S1PR1

Sphingosine-1-phosphate receptor 1; MIM 601974

  1. SNPs close to rs1154037, highlighted in bold, were positive in several other BD GWA studies [37, 50], with no overlap in subjects. Where the SNP does not lie within a gene, the nearest coding gene is given (Nr = near). Chr = chromosome; SNP = single nucleotide polymorphism; bp (base pair) indicates coordinates according to build hg18/NCBI36; MAF = minor allele frequency, (also for UK and Canadian (CAN) sets). Mendelian Inheritance in Man (MIM) number, where available, is included with “function/domains?”, as a source of reference.