Background
Methods
Study sample
Preparation of genomic DNA and analysis of genetic polymorphisms
Data analysis
Results
SNP | Position | pHW | MAF | Alleles (major/minor) | Feature |
---|---|---|---|---|---|
rs28947205 | 112,978,286 | 1.0 | 0.021 | C/T | intron |
rs12328178 | 112,978,391 | 1.0 | 0.013 | A/G | intron |
rs28947206 | 112,978,719 | 1.0 | 0.002 | G/T | intron |
rs28947207 | 112,978,748 | 1.0 | 0.011 | C/T | intron |
rs17042686 | 112,979,417 | 0.6071 | 0.066 | G/C | intron |
rs6707930 | 112,980,053 | 1.0 | 0.012 | C/A | missense (Gln34Lys) |
rs13410389 | 112,980,446 | 0.7871 | 0.085 | G/A | intron |
rs34216066 | 112,981,873 | 0.1303 | 0.095 | T/C | intron |
rs28947211 | 112,981,986 | 1.0 | 0.041 | T/C | intron |
rs13392494 | 112,982,098 | 0.175 | 0.464 | C/T | intron |
rs7584409 | 112,985,157 | 0.8851 | 0.31 | A/G | 3’ UTR |
Allelic association analysis
SNP | Reference allele | Control RAF | Plaque psoriasis | Early onset | Late onset | Familial | Sporadic | Spring-summer | Fall-winter | PsA+ | Male | Female | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | |||
rs28947205 | T | 0.021 | 0.042 | 0.0197 | 0.039 | 0.0502 | 0.053 | 0.0086 | 0.036 | 0.112 | 0.047 | 0.0095 | 0.038 | 0.3414 | 0.040 | 0.037 | 0.035 | 0.2001 | 0.050 | 0.0417 | 0.033 | 0.5279 |
rs12328178 | G | 0.013 | 0.036 | 0.0064 | 0.035 | 0.0094 | 0.038 | 0.0124 | 0.034 | 0.0155 | 0.037 | 0.0071 | 0.038 | 0.094 | 0.035 | 0.0081 | 0.040 | 0.0098 | 0.042 | 0.0611 | 0.028 | 0.1299 |
rs28947206 | T | 0.002 | 0.023 |
6.0E-4
| 0.021 |
0.0014
| 0.030 |
1.0E-4
| 0.026 |
4.0E-4
| 0.021 |
0.0013
| 0.024 | 0.0036 | 0.020 |
0.0021
| 0.018 | 0.0069 | 0.026 | 0.0095 | 0.020 | 0.0548 |
rs28947207 | T | 0.011 | 0.045 |
2.0E-4
| 0.043 |
4.0E-4
| 0.053 |
1.0E-4
| 0.039 |
0.0019
| 0.050 |
7.09E-5
| 0.037 | 0.0594 | 0.042 |
5.0E-4
| 0.035 | 0.0137 | 0.049 |
0.0015
| 0.040 | 0.0945 |
rs17042686 | C | 0.066 | 0.076 | 0.4358 | 0.073 | 0.5793 | 0.085 | 0.2965 | 0.066 | 0.9968 | 0.083 | 0.2391 | 0.075 | 0.752 | 0.079 | 0.3278 | 0.101 | 0.0754 | 0.081 | 0.3216 | 0.069 | 0.9764 |
rs6707930 | A | 0.012 | 0.005 | 0.1014 | 0.003 | 0.0424 | 0.010 | 0.8038 | 0.007 | 0.4366 | 0.003 | 0.0577 | 0.000 | 0.3314 | 0.004 | 0.1099 | 0.007 | 0.5659 | 0.007 | 0.6401 | 0.002 | 0.013 |
rs13410389 | A | 0.085 | 0.071 | 0.3241 | 0.074 | 0.4436 | 0.064 | 0.3023 | 0.057 | 0.0852 | 0.084 | 0.9262 | 0.121 | 0.3308 | 0.071 | 0.3225 | 0.075 | 0.6474 | 0.063 | 0.0582 | 0.081 | 0.7473 |
rs34216066 | C | 0.095 | 0.064 | 0.0172 | 0.060 | 0.0104 | 0.075 | 0.3267 | 0.055 | 0.0114 | 0.071 | 0.1139 | 0.013 | 0.0148 | 0.062 | 0.0204 | 0.047 | 0.0171 | 0.080 | 0.238 | 0.044 |
4.0E-4
|
rs28947211 | C | 0.041 | 0.010 |
1.75E-5
| 0.008 |
1.58E-5
| 0.017 | 0.058 | 0.007 |
3.0E-4
| 0.013 |
0.0018
| 0.000 | 0.0627 | 0.010 |
6.83E-5
| 0.008 | 0.0095 | 0.012 | 0.0635 | 0.009 |
4.0E-4
|
rs13392494 | T | 0.464 | 0.515 | 0.0822 | 0.522 | 0.0568 | 0.492 | 0.4916 | 0.526 | 0.0668 | 0.507 | 0.1855 | 0.407 | 0.4282 | 0.511 | 0.1284 | 0.442 | 0.5997 | 0.540 | 0.1847 | 0.482 | 0.9231 |
rs7584409 | G | 0.310 | 0.328 | 0.4439 | 0.330 | 0.4223 | 0.323 | 0.7017 | 0.329 | 0.502 | 0.329 | 0.4687 | 0.300 | 0.8522 | 0.326 | 0.5148 | 0.324 | 0.6925 | 0.331 | 0.8454 | 0.326 | 0.6515 |
SNP | Reference allele | Control RAF | BSA ≤ 10 | BSA 11–30 | BSA ≥ 31 | PASI ≤10 | PASI 11–20 | PASI ≥21 | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | RAF | P value | |||
rs28947205 | T | 0.021 | 0.041 | 0.0799 | 0.045 | 0.0243 | 0.041 | 0.0504 | 0.036 | 0.1314 | 0.034 | 0.1804 | 0.054 |
0.0032
|
rs12328178 | G | 0.013 | 0.033 | 0.0344 | 0.033 | 0.0246 | 0.039 |
0.0053
| 0.031 | 0.045 | 0.022 | 0.2429 | 0.051 |
3.0E-4
|
rs28947206 | T | 0.002 | 0.021 |
0.0023
| 0.028 |
2.0E-4
| 0.021 |
0.0018
| 0.021 |
0.0018
| 0.017 | 0.0075 | 0.031 |
7.38E-5
|
rs28947207 | T | 0.011 | 0.039 |
0.0038
| 0.047 |
3.0E-4
| 0.048 |
2.0E-4
| 0.038 |
0.0039
| 0.036 | 0.0060 | 0.060 |
8.64E-6
|
rs17042686 | C | 0.066 | 0.098 | 0.0834 | 0.062 | 0.8463 | 0.073 | 0.6552 | 0.095 | 0.0982 | 0.071 | 0.7567 | 0.061 | 0.7902 |
rs6707930 | A | 0.012 | 0.000 | 0.0539 | 0.005 | 0.2288 | 0.008 | 0.5211 | 0.002 | 0.1131 | 0.002 | 0.1145 | 0.009 | 0.6308 |
rs13410389 | A | 0.085 | 0.056 | 0.1455 | 0.096 | 0.5856 | 0.058 | 0.1116 | 0.071 | 0.4649 | 0.083 | 0.9044 | 0.060 | 0.1548 |
rs34216066 | C | 0.095 | 0.059 | 0.0642 | 0.073 | 0.2135 | 0.059 | 0.0262 | 0.054 | 0.0175 | 0.084 | 0.5635 | 0.056 | 0.0193 |
rs28947211 | C | 0.041 | 0.003 |
0.0011
| 0.013 | 0.0093 | 0.012 |
0.0047
| 0.008 |
0.0017
| 0.010 |
0.0047
| 0.013 | 0.0087 |
rs13392494 | T | 0.464 | 0.508 | 0.2753 | 0.500 | 0.3266 | 0.534 | 0.0452 | 0.519 | 0.1425 | 0.471 | 0.8657 | 0.549 | 0.0159 |
rs7584409 | G | 0.310 | 0.308 | 0.9415 | 0.317 | 0.8073 | 0.348 | 0.1793 | 0.295 | 0.6002 | 0.303 | 0.8179 | 0.377 | 0.0239 |
Haplotype analysis
Haplotype | Frequency | Controls | Patients | Chi Square | P value |
---|---|---|---|---|---|
Block 1 | |||||
CAGC | 0.957 | 0.976 | 0.948 | 7.9 |
0.0049
|
TGTT | 0.020 | 0.004 | 0.028 | 12.198 |
5.0E-4
|
TGGT | 0.016 | 0.018 | 0.016 | 0.076 | 0.7831 |
Block 2 | |||||
CGTTC | 0.493 | 0.509 | 0.486 | 0.88 | 0.3482 |
CGTTT | 0.359 | 0.327 | 0.374 | 3.745 | 0.053 |
CATTT | 0.080 | 0.083 | 0.078 | 0.109 | 0.7409 |
CGCTT | 0.039 | 0.034 | 0.041 | 0.519 | 0.4714 |
CGCCT | 0.015 | 0.011 | 0.024 | 4.493 | 0.034 |