Molecular Vision: Chen, Mol Vis 2009; 15:2349-2357. Table 3

Table 3. Allele and genotype association analysis for the three SNPs of LOXL1.

SNP	XFS/XFG (n=50) Count (proportion)	Control (n=125) Count (proportion)	x²	p value	OR (95%CI)
rs1048661
Allele
T	89 (0.89)	129 (0.52)	42.53	6.95×10^-11	7.59 (3.87-14.89)
G	11 (0.11)	121 (0.48)
Genotype
TT	43 (0.86)	27 (0.22)	67.72	<0.001	8.69 (4.15-18.20)**
GT	3 (0.06)	75 (0.60)
GG	4 (0.08)	23 (0.18)
Total	43/3/4 (TT/GT/GG)	27/75/23 (TT/GT/GG)	61.72	3.97×10^-15	NA
rs3825942
Allele
G	100 (1.00)	224 (0.90)	11.24	8.00×10^-4	NA*
A	0 (0.00)	26 (0.10)
Genotype
GG	50 (1.00)	101 (0.80)	11.13	3.84×10^-3	NA*
GA	0 (0.00)	22 (0.18)
AA	0 (0.00)	2 (0.02)
Total	50/0/0 (GG/GA/AA)	101/22/2 (GG/GA/AA)	17.63	3.84×10^-3	NA
rs2165241
Allele
C	98 (0.98)	225 (0.90)	6.42	0.01	5.44 (1.27-23.43)
T	2 (0.02)	25 (0.10)
Genotype
CC	48 (0.96)	100 (0.80)	7.01	8.00×10^-3	6.0 (1.37-26.37)**
CT	2 (0.04)	25 (0.20)
TT	0 (0.00)	0 (0.00)
Total	48/2/0 (CC/CT/TT)	100/25/0 (CC/CT/TT)	7.01	8.00×10^-3	NA

There were significant differences for the allelic proportion between case and control groups for all the three SNPs. T allele of rs1048661, G of rs3825942, and C of rs2165241 were risk alleles for the disorder. The genotypes TT for rs1048661, GG for rs3825942, and CC for rs2165241 were “risk” genotypes for the disease. Total indicate the general test of association in the 2-by-3 table of disease-by-genotype. NA: not available. The single asterisks indicate that all patients had G allele and genotype of GG for rs3825942, so the OR values couldn’t be calculated. The double asterisks indicate the OR values and p values derived from comparision of the specific genotype with all the others, i.e., TT versus GT+GG at rs1048661, CC versus CT+TT at rs2165241.