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Table 3 List of selected genes, corresponding "risk" haplotype structure, effect estimates and permutation p-values

From: Mapping Haplotype-haplotype Interactions with Adaptive LASSO

SNP ID (allele) Gene (region) "Risk" haplotype a s d s a t d t i aa i ad i da i dd
9508994
(C/T)
PON1
(intron 1)
[TC]M 0 0 0 0 0 -0.45 0 0
20209376
(C/T)
PON1
(intron 5)
[CC]O       p* = 0.001   
659435566
(C/T)
NFKB1
(exon 12)
[CC]M 0 0 0 0 -0.33 0 0 0
659435702
(C/G)
NFKB1
(intron 22)
[TC]O      p* = 0.001    
22767327 (A/T) FLT4
(intron 7)
[AT]M 0 0 0 0 0 -0.30 0 0
22175087 (C/T) FLT4
(intron 8)
[TC]O       p* < 0.001   
1125300 (G/T) SPARC (intron 3) [TT]M 0 -0.38 0 0 0 0 0 0.245
1125290 (G/T) SPARC (intron 5) [TT]O   p* = 0.001       p* < 0.001
634841108 (A/C) TIMP2 (intron 2) [AG]M 0 0 0 0 0 0 0 0.68
634841123 (A/G) TIMP2
(exon 3)
[CG]O         p* < 0.001
634018768 (A/G) HPGD (promoter) [AG]M 0 0 0.44 0 0 0 0 0
636105057 (A/G) HPGD (promoter) [GA]O    p* < 0.001      
17252653 (G/T) MMP9 (intron) [GC]M 0 0 0.53 0 0 0 0 0
17254821 (C/G) MMP9
(exon 10)
[TC]O    p* < 0.001      
  1. M mother's "risk" haplotype information; O offspring's "risk" haplotype information
  2. p* is the permutation p-value.