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