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. 2009 Apr 7;2:16. doi: 10.1186/1755-8794-2-16

Table 3.

Genetic effects that replicated internally, cross-validated, and passed FDR criterion

Main Effects (4) SNP Subset 1 p-value Subset 2 p-value Full Sample p-value R2 × 100 CV R2 × 100
F3_rs3917643 0.0477 0.0270 0.0021 1.58 1.05
KITLG_rs995029 0.0001 0.0921 0.0001 2.33 0.96
CAPN10_rs7571442 0.0856 0.0318 0.0021 1.70 0.59
MMP2_rs9928731 0.0161 0.0383 0.0032 1.48 0.56
SNP-Covariate Interactions (12) SNP Covariate Subset 1 p-value Subset 2 p-value Full Sample p-value R2 × 100 CV R2 × 100
KITLG_rs1492347 Log homocysteine 0.0002 0.0640 0.0003 4.37 1.57
ITGB3_rs3851806 Height 0.0286 0.0101 0.0010 2.54 1.51
TGFB3_rs2284791 Log C-reactive protein 0.0073 0.0173 0.0003 2.92 1.51
TGFB3_rs2284791 Physical activity 0.0885 0.0015 0.0007 2.69 1.46
TGFB3_rs2268622 Log C-reactive protein 0.0026 0.0360 0.0003 2.86 1.42
KITLG_rs995029 Log homocysteine 0.0002 0.0621 0.0003 4.42 1.40
IL28RA_rs11587500 LDL particle size 0.0026 0.0014 0.0004 2.79 1.26
ACCN4_rs1872858 Fibrinogen 0.0494 0.0339 0.0010 2.59 1.24
LTA4H_rs17025079 Log homocysteine 0.0006 0.0709 0.0001 3.41 1.16
PCSK9_rs10888896 Log homocysteine 0.0239 0.0567 0.0009 2.33 1.13
IL22RA1_rs3795299 CHD 0.0859 0.0138 0.0009 2.41 0.70
SERPINE1_rs2227672 Body mass index 0.0113 0.0219 0.0003 2.69 0.54
SNP-SNP Interactions (20 of 173) SNP1 SNP2 Subset 1 p-value Subset 2 p-value Full Sample p-value R2 × 100 CV R2 × 100
RHAG_rs11759060 GLS_rs1921913 0.0032 0.0225 8.0 E-06 5.49 2.61
F8 _rs7053448 MPO_rs34704261 0.0354 0.0279 0.0001 4.10 2.58
RHAG_rs11759060 GLS_rs3771316 0.0032 0.0225 8.0 E-06 5.49 2.55
MPO_rs34704261 F8_rs1800291 0.0362 0.0279 0.0001 4.10 2.44
SLC20A1_rs10758 IL22RA1_rs12093987 0.0439 0.0085 4.0 E-05 5.44 2.35
SLC20A1_rs3827758 IL22RA1_rs12093987 0.0315 0.0915 0.0004 3.88 2.27
KITLG_rs995029 TLR4_rs1927911 0.0035 0.0586 5.0 E-05 5.58 2.27
SLC20A1_rs1053652 IL22RA1_rs12093987 0.0237 0.0045 5.0 E-05 5.07 2.22
MPO_rs34704261 F8_rs4898399 0.0433 0.0315 0.0002 4.18 2.11
RHAG_rs2518100 GLS_rs1921913 0.0029 0.0534 0.0001 4.50 2.11
MMP2_rs243834 IL28RA_rs4330872 0.0136 0.0856 0.0002 4.46 2.09
RHAG_rs2518100 GLS_rs3771316 0.0029 0.0534 0.0001 4.50 1.95
MPO_rs8077532 F8_rs1800291 0.0417 0.0802 0.0003 3.93 1.93
NMUR1_rs10933376 GPR55_rs2969126 0.0945 0.0022 4.3 E-05 5.03 1.90
ACCN4_rs3770234 TNFSF10_rs3136596 0.0246 0.0007 0.0001 4.65 1.84
PRKAR2B_rs257376 PKRAR2B_rs3729877 0.0085 0.0027 4.8 E-05 3.55 1.84
CX3CR1_rs2853712 F2_rs3136435 0.0153 0.0480 0.0010 3.31 1.82
KITLG_rs1492347 TLR4_rs10116253 0.0049 0.0577 0.0001 5.44 1.81
F8_rs7053448 MPO_rs8077532 0.0417 0.0802 0.0003 3.93 1.81
MPO_rs8077532 F8_rs4898399 0.0515 0.0822 0.0006 4.04 1.81

For all associations, the outcome was leukoaraiosis volume transformed using the natural logarithm and adjusted for age, sex, and total brain volume.

P-value refers to the model p-value (SNP main effects) or the partial F-test p-value of the interaction terms (SNP-Covariate interactions and SNP-SNP interactions).

For SNP-Covariate and SNP-SNP interaction models, CV R2 × 100 refers to the difference in CV R2 × 100 between the full model (including interaction terms) and the reduced model (including main effects only).

ACCN4 amiloride-sensitive cation channel neuronal 4;CAPN10 calpain 10 (cysteine protease); CX3CR1 chemokine, CX3C motif, receptor 1; F2 coagulation factor 2; F3 coagulation factor 3; F8 coagulation factor 8; GLS glutaminase, phosphate activated; GPR55 G protein-coupled receptor 55;IL22RA1 interleukin 22 receptor, alpha-1;IL28RA interleukin 28 receptor; ITGB3 integrin, beta-3; KITLG KIT tyrosine kinase receptor ligand; LTA4H leukotriene A4 hydroxylase; MMP2 matrix metalloproteinase 2 (72 kDa type IV collagenase); MPO myeloperoxidase; NMUR1 neuromedin U receptor 1 (G protein-coupled receptor 66);PCSK9 proprotein convertase, subtilisin/kexin-type, 9;PRKAR2B protein kinase, cAMP-dependent, regulatory, type II, beta; RHAG rhesus blood group-associated glycoprotein; SERPINE1 plasminogen activator inhibitor 1; SLC20A1 solute carrier family 20 (phosphate transporters), member 1; TGFB3 transforming growth factor, beta 3; TLR4 toll-like receptor 4; TNFSF10 tumor necrosis factor ligand superfamily, member 10