Table 2.
Top 1% of associated single nucleotide polymorphisms across fine-mapping region
| Name | Position | Highlighted in Fig.1a | Minor allele | MAF | Case-control comparison |
Maternal case-control comparison |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OR | Cl_low | Cl_up | LRTpval | PERMp | ORmatb | Cl_low | Cl_up | LRTpval | PERMp | |||||
| rs1325251 | 52,918,572 | PRKG1 | A | 0.12 | 0.53 | 0.37 | 0.77 | 6.19E-04 | 2.00E-04 | 0.53 | 0.32 | 0.88 | 1.49E-02 | 1.50E-02 |
| rs6588761 | 48,219,815 | R1 | A | 0.03 | 0.28 | 0.11 | 0.62 | 1.10E-03 | 6.67E-04 | 0.19 | 0.07 | 0.48 | 5.57E-04 | <0.001 |
| rs2382748 | 48,228,985 | R1 | C | 0.03 | 3.86 | 0.67 | 10.50 | 1.05E-03 | 6.67E-04 | 6.24 | 2.34 | 18.42 | 2.38E-04 | <0.001 |
| rs17581623 | 52,030,619 | A | 0.10 | 0.56 | 0.37 | 0.83 | 3.58E-03 | 1.33E-03 | 0.67 | 0.39 | 1.16 | 1.50E-01 | 1.89E-01 | |
| rs7477069 | 54,212,144 | A | 0.34 | 0.69 | 0.54 | 0.87 | 2.03E-03 | 1.56E-03 | 0.69 | 0.49 | 0.97 | 3.31E-02 | 3.50E-02 | |
| rs7901053 | 50,473,548 | A | 0.41 | 1.43 | 1.14 | 1.80 | 2.11E-03 | 1.78E-03 | 1.74 | 1.24 | 2.46 | 1.08E-03 | <0.001 | |
| rs4922536 | 48,168,383 | R1 | A | 0.47 | 1.39 | 1.12 | 1.74 | 3.13E-03 | 2.22E-03 | 1.56 | 1.12 | 2.20 | 8.78E-03 | 7.00E-03 |
| rs7899656 | 54,219,374 | A | 0.28 | 1.47 | 1.15 | 1.90 | 2.33E-03 | 2.44E-03 | 1.48 | 1.02 | 2.18 | 3.76E-02 | 3.20E-02 | |
| rs9421758 | 48,153,610 | R1 | A | 0.29 | 1.43 | 1.12 | 1.82 | 3.97E-03 | 4.44E-03 | 1.89 | 1.29 | 2.81 | 8.21E-04 | 2.00E-03 |
| rs6481440 | 60,262,929 | G | 0.05 | 0.46 | 0.26 | 0.78 | 4.06E-03 | 4.89E-03 | 0.43 | 0.16 | 0.96 | 3.99E-02 | 3.70E-02 | |
| rs17698900 | 49,616,272 | G | 0.13 | 0.64 | 0.46 | 0.89 | 7.17E-03 | 5.11E-03 | 0.74 | 0.46 | 1.17 | 2.06E-01 | 2.15E-01 | |
| rs4922522 | 48,173,807 | R1 | C | 0.03 | 2.98 | 1.39 | 7.14 | 4.16E-03 | 5.33E-03 | 3.45 | 1.28 | 9.49 | 1.50E-02 | 1.10E-02 |
| rs2393352 | 58,941,770 | A | 0.49 | 1.40 | 1.12 | 1.75 | 2.88E-03 | 5.33E-03 | 1.20 | 0.86 | 1.66 | 2.79E-01 | 2.69E-01 | |
| rs4326728 | 48,283,860 | R1 | G | 0.02 | 3.92 | 1.44 | 13.69 | 6.03E-03 | 5.56E-03 | 6.11 | 1.87 | 23.45 | 2.76E-03 | 1.00E-03 |
| rs10763176 | 56,478,812 | R2/PCDH15 | A | 0.41 | 0.73 | 0.58 | 0.91 | 5.59E-03 | 5.56E-03 | 0.63 | 0.45 | 0.88 | 6.31E-03 | 6.00E-03 |
| rs12356013 | 51,791,236 | A | 0.07 | 0.55 | 0.34 | 0.84 | 5.92E-03 | 5.78E-03 | 0.88 | 0.45 | 1.86 | 7.33E-01 | 7.43E-01 | |
| rs10888205 | 48,186,564 | R1 | A | 0.24 | 1.43 | 1.11 | 1.83 | 5.06E-03 | 6.00E-03 | 1.77 | 1.21 | 2.67 | 2.90E-03 | 3.00E-03 |
| rs11101409 | 49,507,785 | G | 0.01 | 0.20 | 0.05 | 0.65 | 5.71E-03 | 6.00E-03 | 0.25 | 0.01 | 1.29 | 1.09E-01 | 1.17E-01 | |
| rs1922166 | 56,465,084 | R2/PCDH15 | C | 0.41 | 1.38 | 1.10 | 1.73 | 5.70E-03 | 6.00E-03 | 1.58 | 0.14 | 2.22 | 6.57E-03 | 8.00E-03 |
| rs4922505 | 48,042,154 | G | 0.02 | 0.27 | 0.09 | 0.70 | 6.41E-03 | 6.22E-03 | 0.36 | 0.06 | 1.30 | 1.29E-01 | 1.37E-01 | |
| rs10857619 | 49,577,319 | A | 0.43 | 0.74 | 0.59 | 0.93 | 8.61E-03 | 6.89E-03 | 0.82 | 0.60 | 1.13 | 2.21E-01 | 2.09E-01 | |
| rs10508906 | 49,601,155 | G | 0.28 | 1.42 | 1.10 | 1.83 | 6.45E-03 | 6.89E-03 | 1.16 | 0.80 | 1.67 | 4.36E-01 | 4.27E-01 | |
| rs11006267 | 60,233,640 | G | 0.04 | 0.46 | 0.25 | 0.80 | 5.57E-03 | 7.11E-03 | 0.46 | 0.17 | 1.05 | 6.82E-02 | 6.40E-02 | |
| rs12257237 | 45,334,677 | G | 0.09 | 1.79 | 1.17 | 2.76 | 6.52E-03 | 7.33E-03 | 1.61 | 0.87 | 2.92 | 1.26E-01 | 1.27E-01 | |
| rs1838539 | 60,269,468 | G | 0.05 | 0.50 | 0.30 | 0.83 | 7.32E-03 | 7.33E-03 | 0.46 | 0.19 | 1.00 | 5.03E-02 | 5.60E-02 | |
| rs1147967 | 44,322,938 | A | 0.15 | 1.53 | 1.13 | 2.09 | 6.54E-03 | 7.56E-03 | 1.42 | 0.91 | 2.29 | 1.21E-01 | 1.19E-01 | |
| rs7896935 | 49,453,503 | A | 0.12 | 1.58 | 1.12 | 2.23 | 8.78E-03 | 8.00E-03 | 1.72 | 1.04 | 3.02 | 3.53E-02 | 3.30E-02 | |
| rs11005844 | 58,969,302 | A | 0.47 | 0.74 | 0.59 | 0.92 | 7.95E-03 | 9.33E-03 | 0.84 | 0.60 | 1.17 | 2.93E-01 | 3.11E-01 | |
| rs11004683 | 56,454,702 | R2/PCDH15 | C | 0.41 | 1.35 | 1.07 | 1.70 | 9.76E-03 | 9.56E-03 | 1.56 | 1.12 | 2.19 | 9.29E-03 | 8.00E-03 |
| rs7919766 | 44,317,317 | G | 0.17 | 0.68 | 0.50 | 0.91 | 9.46E-03 | 1.07E-02 | 0.74 | 0.47 | 1.13 | 1.72E-01 | 1.93E-01 | |
| rs12570371 | 54,217,463 | A | 0.28 | 1.39 | 1.09 | 1.78 | 8.92E-03 | 1.09E-02 | 1.32 | 0.92 | 1.93 | 1.31E-01 | 1.50E-01 | |
| rs2607872 | 48,051,698 | G | 0.04 | 0.48 | 0.27 | 0.85 | 1.09E-02 | 1.11E-02 | 0.53 | 0.21 | 1.16 | 1.17E-01 | 1.28E-01 | |
| rs10996377 | 52,690,748 | PRKG1 | A | 0.07 | 0.57 | 0.36 | 0.89 | 1.39E-02 | 1.13E-02 | 0.44 | 0.25 | 0.79 | 6.60E-03 | 3.00E-03 |
| rs9421801 | 48,042,861 | A | 0.04 | 2.03 | 1.15 | 3.64 | 1.40E-02 | 1.16E-02 | 1.88 | 0.84 | 4.77 | 1.27E-01 | 1.18E-01 | |
| rs11595808 | 47,034,484 | A | 0.02 | 3.03 | 1.29 | 7.95 | 1.06E-02 | 1.20E-02 | NA | NA | NA | 1.29E-03 | 5.00E-03 | |
| rs885834 | 50,485,518 | G | 0.38 | 1.35 | 1.07 | 1.70 | 1.15E-02 | 1.22E-02 | 1.37 | 0.99 | 1.90 | 6.04E-02 | 5.80E-02 | |
| rs1922158 | 56,494,637 | R2/PCDH15 | A | 0.41 | 0.75 | 0.59 | 0.94 | 1.21E-02 | 1.31E-02 | 0.65 | 0.47 | 0.91 | 1.19E-02 | 1.30E-02 |
| rs10761612 | 52,368,092 | C | 0.44 | 0.76 | 0.60 | 0.94 | 1.39E-02 | 1.33E-02 | 0.86 | 0.62 | 1.18 | 3.50E-01 | 3.76E-01 | |
| rs1922155 | 56,458,141 | R2/PCDH15 | G | 0.41 | 1.33 | 1.06 | 1.68 | 1.31E-02 | 1.36E-02 | 1.55 | 1.11 | 2.18 | 1.00E-02 | 1.40E-02 |
CO controls, CA cases
a
Rl, R2 refer to region 1 or 2 in gray in Fig. 1
b
Italic indicates stronger effect in maternal subsets