Table 4

The Ten Independent*Association Signals Exhibiting the Lowest Uncorrected p-values for Any Test of NTD Association
Gene/SNP Risk Allele Frequency** Cohort*** Model OR 95% CI (LL) 95% CI (UL) P
1 MFTC
rs17803441 0.07 Combined LR CC Continuous 1.61 1.23 2.08 0.0003
MFTC
rs3134260 0.07 Combined LR CC Continuous 1.56 1.22 2.04 0.0006
2 CDKN2A LL Maternal effect,
rs3218009 0.13 Primary Dominant 2.32 1.45 3.71 0.0004
3 ADA
rs2299686 0.45 Combined LR MC Dominant 1.56 1.22 2.04 0.0005
ADA
rs406383 0.25 Combined LR MC Continuous 1.12 1.58
ADA
rs427483 0.33 Combined LR MC Continuous 1.28 1.10 1.52 0.0018
4 PEMT
rs1108579 0.52 Combined TDT 1.47 1.18 1.82 0.0006
PEMT
rs11656215 0.49 Combined LL Case effect, recessive 1.68 1.24 2.28 0.0008
PEMT
rs4646402 0.57 Combined LL Case effect, dominant 1.67 1.25 2.17 0.0005
5 CUBN
rs7070148 0.90 Combined LR MC Continuous 1.64 1.22 2.17 0.0010
CUBN
rs2273737 0.89 Combined LR MC Continuous 1.54 1.18 2.04 0.0021
6 GART
rs2070388 0.91 Combined TDT 1.89 1.28 2.78 0.0012
GART
rs2070388 0.91 Combined LL Case effect, dominant 1.96 1.30 2.94 0.0012
7 ADA rs6031682 0.16 Combined LR CC Dominant 1.49 1.16 1.92 0.0016
8 DNMT3A rs7560488 0.42 Primary LL Case effect, recessive 2.10 1.31 3.38 0.0021
9 MTHFD1 rs2236225 0.40 Primary LR MC Dominant 1.96 1.28 3.03 0.0022
10 T (Brachyury) rs10806845 0.51 Combined LR MC Recessive 1.54 1.16 2.00 0.0023

* LD between SNPs within an association signal are as follows: MFTC (D’ = 1, r2 = 0.993), ADA (D’ > 0.822, r2 > 0.394), PEMT (D’ > 0.693, r2 > 0.428) and CUBN (D’ = 0.935, r2 = 0.823). ADA rs6031682 was designated as an independent association signal because it shares very little LD (D’ < 0.206, r2 < 0.016) with the other ADA SNPs (rs2299686, rs406383, rs427483).

**Frequency of the risk allele was calculated using control sample genotypes.

*** Primary: 320 triads, 341 controls. Combined: 570 triads, 999 controls.

Pangilinan et al.

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

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