Table 2

SNPs Selected for Study in the Combined NTD Cohort
RSID Gene Case–control Logistic Regression p-value TDT p-value Mother-Control Logistic Regression p-value Log-Linear Maternal Genotype p-value
rs2428735 PADI4 0.0006 0.2801 0.0229 0.4043
rs942459 PADI4 0.0089 0.3841 0.1002 .*
rs12743862 ARID1A 0.1030 0.0314 0.9124 .
rs12729444 ARID1A 0.1068 0.0314 0.9124 .
rs12726081 ARID1A 0.1030 0.0314 0.9124 .
rs12726287 ARID1A 0.1030 0.0314 0.9276 .
rs11247593 ARID1A 0.0208 0.1294 0.1815 0.1383
rs11247594 ARID1A 0.0257 0.1580 0.2126 0.1331
rs12752833 ARID1A 0.1030 0.0314 0.9124 .
rs12735646 ARID1A 0.1030 0.0290 0.9124 .
rs12737946 ARID1A 0.1030 0.0314 0.9124 .
rs12731749 ARID1A 0.0862 0.0201 0.8813 .
rs11247596 ARID1A 0.7022 0.0311 0.9123 0.9708
rs12733999 CTH 0.0277 1.0000 0.0077 .
rs10889869 CTH 0.9408 0.0436 0.2582 0.9918
rs12723350 CTH 0.0472 0.6803 0.0120 0.0572
rs16834388 MTR 0.1070 0.0225 0.9177 0.8117
rs10733117 MTR 0.1604 0.0207 0.5363 0.1956
rs10925238 MTR 0.0503 0.0139 0.9512 0.5724
rs4077829 MTR 0.0921 0.0170 0.7931 0.6494
rs12060570 MTR 0.0602 0.0201 0.9373 0.6843
rs2789352 MTR 0.2535 0.0348 0.7505 0.1245
rs7367859 MTR 0.2355 0.0444 0.5437 0.0571
rs10925260 MTR 0.1262 0.0328 0.8485 0.1713
rs2853522 MTR 0.1080 0.0449 0.8826 0.1600
rs2853523 MTR 0.2127 0.0418 0.7770 0.0594
rs3944004 LRP2 0.3963 0.0048 0.5667 0.2170
rs4667593 LRP2 0.7913 0.0087 0.3028 0.7203
rs16856530 LRP2 0.1458 0.4352 0.0396 0.7874
rs2024481 LRP2 0.9568 0.0087 0.2889 0.7601
rs10490131 LRP2 0.4348 0.0140 0.8093 0.8201
rs4668123 LRP2 0.1564 0.9379 0.0487 0.9494
rs2268373 LRP2 0.0338 0.0229 0.0718 0.4172
rs11886219 LRP2 0.0491 0.3924 0.0034 .
rs2268365 LRP2 0.6858 0.0312 0.6914 0.8866
rs2673164 LRP2 0.5967 0.7656 0.4009 0.0231
rs700550 LRP2 0.4767 0.2507 0.7529 0.0383
rs853988 LRP2 0.8386 0.6872 0.2807 0.0048
rs2673177 LRP2 0.0095 0.5791 0.0015 0.0279
rs10199676 LRP2 0.0075 0.7290 0.0213 0.9036
rs2389557 LRP2 0.0336 0.6507 0.1005 0.4636
rs16856843 LRP2 0.0075 0.9055 0.0133 0.9035
rs10806845 T (Brachyury) 0.0399 0.6331 0.0010 0.3100
rs3127441 T (Brachyury) 0.0485 0.6215 0.0043 0.8873
rs12200529 T (Brachyury) 0.5867 0.7758 0.0278 0.2407
rs16898752 T (Brachyury) 0.1443 1.0000 0.0412 0.2063
rs7753771 T (Brachyury) 0.5378 1.0000 0.0384 .
rs1001978 T (Brachyury) 0.5378 1.0000 0.0384 .
rs3099280 T (Brachyury) 0.9972 0.5149 0.0199 0.1406
rs4512347 MFTC 0.0344 0.6473 0.2789 .
rs10112450 MFTC 0.1575 0.0196 0.4726 0.3474
rs17803441 MFTC 0.0016 0.0115 0.2911 0.2838
rs3134260 MFTC 0.0016 0.0086 0.2513 0.2919
rs4876902 EHMT1 0.4872 0.0595 0.6710 0.9049
rs4526432 EHMT1 0.0433 0.0251 0.5323 0.4040
rs10752062 CUBN 0.2564 0.8216 0.0254 0.1471
rs17139378 CUBN 0.2113 0.6780 0.0086 0.1051
rs7100290 CUBN 0.4039 0.0269 0.6692 .
rs1276720 CUBN 0.2147 0.0422 0.5445 0.0714
rs1276721 CUBN 0.1737 0.0206 0.5381 0.2471
rs11254284 CUBN 0.4198 0.7175 0.0474 0.0548
rs11254313 CUBN 0.4354 0.4206 0.0277 0.3041
rs12258009 CUBN 0.7700 0.1582 0.6214 0.7119
rs17431655 CUBN 0.1453 0.8474 0.0459 .
rs17139663 CUBN 0.0407 0.8864 0.0579 0.5552
rs11254339 CUBN 0.0490 0.7928 0.0838 0.8621
rs1801228 CUBN 0.1118 0.8474 0.0356 .
rs12254816 CUBN 0.5285 0.6670 0.0407 0.1765
rs7899751 CUBN 0.4747 0.8386 0.0433 0.1183
rs11254375 CUBN 0.7142 0.6682 0.5854 0.0332
rs7070148 CUBN 0.1447 0.9013 0.0029 0.2028
rs2273737 CUBN 0.1136 0.9042 0.0064 0.3337
rs7096079 CUBN 0.0202 0.8897 0.0432 0.3447
rs2073588 FTH1 0.2129 0.0046 0.9390 .
rs17156616 FTH1 0.5455 0.0127 0.8668 .
rs195445 FTH1 0.9840 0.3738 0.8436 0.7908
rs7957531 LRP6 0.4835 0.9068 0.0407 0.2288
rs10845493 LRP6 0.1614 0.0149 0.9106 0.7491
rs17302049 LRP6 0.4464 0.0242 0.8904 0.9593
rs1181334 LRP6 0.2935 0.0211 0.9466 0.9000
rs12309338 LRP6 0.7156 0.6056 0.0329 .
rs3760183 PEMT 0.0146 0.0111 0.2960 .
rs16961845 PEMT 0.2442 0.8788 0.0043 .
rs4646342 PEMT 0.4687 0.6714 0.7126 0.0351
rs2350631 PEMT 0.0641 0.6803 0.0181 0.3410
rs9910090 SHMT1 0.0342 0.1508 0.1370 0.7042
rs9901160 SHMT1 0.5153 0.0153 0.9278 0.4380
rs4911263 DNMT3B 0.0686 0.8332 0.0145 0.0475
rs6058896 DNMT3B 0.0460 0.0016 0.5438 .
rs447833 ADA 0.0832 0.0090 0.3777 0.6497
rs2299686 ADA 0.4258 0.7269 0.0391 0.2794
rs427483 ADA 0.3645 0.5276 0.0275 0.5681
rs6094017 ADA 0.1869 0.5169 0.0088 0.6004

* (.) = Failure to converge (no result).

Pangilinan et al.

Pangilinan et al. BMC Medical Genetics 2012 13:62   doi:10.1186/1471-2350-13-62

Open Data