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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.
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