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.