Table 2 |
||||||||||
|
Genotype and allele counts (and frequencies) in CD patients and in controls |
||||||||||
|
SNP |
Location |
gene |
CASE |
CONTROL |
p |
CASE |
CONTROL |
p |
||
|
|
||||||||||
|
rs182221 |
56, 599, 221 |
MT4 |
G/G |
262 (0.66) |
398 (0.64) |
0.87 |
G |
646 (0.81) |
995 (0.80) |
0.72 |
|
C/G |
122 (0.31) |
199 (0.32) |
C |
154 (0.19) |
247 (0.20) |
|||||
|
C/C |
16 (0.04) |
24 (0.04) |
||||||||
|
rs666636 |
56, 601, 720 |
MT4 |
G/G |
386 (0.95) |
599 (0.95) |
0.70* |
G |
791 (0.98) |
1229 (0.97) |
0.55 |
|
A/G |
19 (0.05) |
31 (0.05) |
A |
19 (0.02) |
35 (0.03) |
|||||
|
A/A |
0 (0.00) |
2 (0.00) |
||||||||
|
rs666647 |
56, 601, 722 |
MT4 |
C/C |
386 (0.95) |
605 (0.95) |
0.73* |
C |
791 (0.98) |
1241 (0.97) |
0.58 |
|
C/T |
19 (0.05) |
31 (0.05) |
T |
19 (0.02) |
35 (0.03) |
|||||
|
T/T |
0 (0.00) |
2 (0.00) |
||||||||
|
rs669293 |
56, 602, 352 |
MT4 |
T/T |
293 (0.73) |
428 (0.67) |
0.16 |
T |
686 (0.85) |
1039 (0.82) |
0.051 |
|
C/T |
100 (0.25) |
283 (0.29) |
C |
120 (0.15) |
231 (0.18) |
|||||
|
C/C |
10 (0.02) |
24 (0.04) |
||||||||
|
rs762604 |
56, 602, 671 |
MT4 |
C/C |
183 (0.45) |
302 (0.48) |
0.18 |
C |
538 (0.67) |
878 (0.70) |
0.15 |
|
C/T |
172 (0.43) |
274 (0.44) |
T |
268 (0.33) |
380 (0.30) |
|||||
|
T/T |
48 (0.12) |
53 (0.08) |
||||||||
|
rs11643815 |
56, 602, 798 |
MT4 |
G/G |
307 (0.76) |
482 (0.76) |
0.53 |
G |
700 (0.86) |
1102 (0.87) |
0.61 |
|
A/G |
86 (0.21) |
138 (0.22) |
A |
110 (0.14) |
162 (0.13) |
|||||
|
A/A |
12 (0.03) |
12 (0.02) |
||||||||
|
rs11644094 |
56, 624, 079 |
MT3 |
A/A |
134 (0.34) |
220 (0.35) |
0.90 |
A |
460 (0.58) |
736 (0.58) |
0.79 |
|
A/G |
192 (0.48) |
295 (0.47) |
G |
338 (0.42) |
527 (0.42) |
|||||
|
G/G |
73 (0.18) |
116 (0.18) |
||||||||
|
rs10636 |
56, 643, 343 |
MT2A |
G/G |
228 (0.57) |
358 (0.57) |
0.66 |
G |
598 (0.74) |
946 (0.75) |
0.67 |
|
C/G |
142 (0.35) |
230 (0.37) |
C |
206 (0.26) |
312 (0.25) |
|||||
|
C/C |
32 (0.08) |
41 (0.07) |
||||||||
|
rs2070836 |
56, 660, 120 |
MT1E |
G/G |
346 (0.85) |
530 (0.84) |
0.56 |
G |
746 (0.92) |
1156 (0.92) |
0.69 |
|
C/G |
54 (0.13) |
96 (0.15) |
C |
64 (0.08) |
106 (0.08) |
|||||
|
C/C |
5 (0.01) |
5 (0.01) |
||||||||
|
rs708274 |
56, 660, 906 |
MT1E |
G/G |
310 (0.78) |
482 (0.77) |
0.22 |
G |
701 (0.88) |
1100 (0.88) |
0.80 |
|
G/T |
81 (0.20) |
136 (0.22) |
T |
95 (0.12) |
144 (0.12) |
|||||
|
T/T |
7 (0.02) |
4 (0.01) |
||||||||
|
rs2270836 |
56, 667, 614 |
MT1M |
C/C |
169 (0.42) |
231 (0.37) |
0.19 |
C |
516 (0.64) |
764 (0.61) |
0.083 |
|
C/T |
178 (0.44) |
302 (0.48) |
T |
286 (0.36) |
498 (0.39) |
|||||
|
T/T |
54 (0.13) |
98 (0.16) |
||||||||
|
rs9936741 |
56, 667, 785 |
MT1M |
T/T |
387 (0.96) |
610 (0.95) |
0.94* |
T |
792 (0.98) |
1249 (0.98) |
0.94 |
|
C/T |
18 (0.04) |
29 (0.05) |
C |
18 (0.02) |
29 (0.02) |
|||||
|
C/C |
0 (0.00) |
0 (0.00) |
||||||||
|
rs7190725 |
56, 673, 290 |
MT1A |
G/G |
308 (0.76) |
483 (0.76) |
0.99 |
G |
706 (0.87) |
1109 (0.87) |
0.94 |
|
G/T |
90 (0.22) |
143 (0.22) |
T |
104 (0.13) |
165 (0.13) |
|||||
|
T/T |
7 (0.02) |
11 (0.02) |
||||||||
|
rs964372 |
56, 686, 030 |
MT1B |
G/G |
317 (0.78) |
514 (0.81) |
0.65 |
G |
714 (0.88) |
1142 (0.89) |
0.34 |
|
C/G |
80 (0.20) |
114 (0.18) |
C |
96 (0.12) |
134 (0.11) |
|||||
|
C/C |
8 (0.02) |
10 (0.02) |
||||||||
|
rs2070839 |
56, 686, 242 |
MT1B |
C/C |
152 (0.38) |
256 (0.40) |
0.17 |
C |
503 (0.63) |
792 (0.62) |
0.89 |
|
C/T |
199 (0.50) |
280 (0.44) |
T |
301 (0.37) |
480 (0.38) |
|||||
|
T/T |
51 (0.13) |
100 (0.16) |
||||||||
|
rs2291956 |
56, 692, 218 |
MT1F |
C/C |
308 (0.76) |
481 (0.76) |
0.97 |
C |
705(0.87) |
1104 (0.87) |
0.97 |
|
C/T |
89 (0.22) |
142 (0.22) |
T |
103 (0.13) |
162 (0.13) |
|||||
|
T/T |
7 (0.02) |
10 (0.02) |
||||||||
|
rs2298847 |
56, 701, 294 |
MT1G |
T/T |
310 (0.77) |
495 (0.79) |
0.28 |
T |
709 (0.88) |
1107 (0.89) |
0.58 |
|
A/T |
89 (0.22) |
117 (0.19) |
A |
99 (0.12) |
143 (0.11) |
|||||
|
A/A |
5 (0.01) |
13 (0.02) |
||||||||
|
rs4784708 |
56, 703, 914 |
MT1H |
G/G |
376 (0.94) |
565 (0.89) |
0.0197* |
G |
778 (0.97) |
1196 (0.94) |
0.016 |
|
C/G |
26 (0.06) |
66 (0.10) |
C |
26 (0.03) |
70 (0.06) |
|||||
|
C/C |
0 (0.00) |
2 (0.00) |
||||||||
|
rs2062545 |
56, 704, 125 |
MT1H |
A/A |
364 (0.90) |
580 (0.91) |
0.43* |
A |
768 (0.95) |
1214 (0.96) |
0.42 |
|
A/G |
40 (0.10) |
54 (0.09) |
G |
42 (0.05) |
56 (0.04) |
|||||
|
G/G |
1 (0.00) |
1 (0.00) |
||||||||
|
rs2062546 |
56, 704, 217 |
MT1H |
T/T |
353 (0.87) |
566 (0.89) |
0.35* |
T |
757 (0.94) |
1200 (0.95) |
0.36 |
|
A/T |
51 (0.13) |
68 (0.11) |
A |
51 (0.06) |
68 (0.05) |
|||||
|
A/A |
0 (0.00) |
0 (0.00) |
||||||||
|
rs2301234 |
56, 716, 982 |
MT1X |
G/G |
173 (0.43) |
248 (0.39) |
0.41 |
G |
517 (0.64) |
791 (0.62) |
0.35 |
|
G/T |
171 (0.43) |
395 (0.46) |
T |
287 (0.36) |
479 (0.38) |
|||||
|
T/T |
58 (0.14) |
92 (0.14) |
||||||||
|
|
||||||||||
|
*p value calculated from comparing rare homozygote + heterozygote group against common homozygote group |
||||||||||
|
Morgan et al. Journal of Negative Results in BioMedicine 2012 11:8 doi:10.1186/1477-5751-11-8 |
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