Table 1 Candidate functional variants in exons or splice sites associated with psoriasis risk
Chr. | Position | Variant | Alleles (P/R) | RAF | Gene | AA | InterPro annotation | Marker (P-value, Study) | r2 |
|---|---|---|---|---|---|---|---|---|---|
Known functional variants | |||||||||
Splice site | |||||||||
6 | 31,380,000 | rs199503730 | G/− | 0.0447 | MICA | 5′ ss | – | rs2395029 (2.00E-26, [19]) | 0.8860 |
Exon | |||||||||
1 | 25,291,010 | rs6672420 | A/T | 0.4791 | RUNX3 | I/N | – | 0.9046 | |
1 | 67,705,958 | rs11209026 | A/G | 0.9384 | IL23R | Q/R | – | rs11209026 (7.00E-07, [24]) | 1.0000 |
rs9988642 (1.00E-26 [25]; 7.00E-14, [29]) | 0.8520 | ||||||||
6 | 31,473,957 | rs3134900 | (C/G)? | NR | MICB | I/M | MHC class I-like antigen recognition-like, MHC classes I/II-like antigen recognition protein | rs3134792 (1.00E-09, [18]) | 0.8008 |
6 | 111,913,262 | rs33980500 | C/T | 0.0855 | TRAF3IP2 | D/N | – | 1.0000 | |
17 | 78,178,893 | rs11652075 | T/C | 0.5099 | CARD14 | W/R | – | rs11652075 (3.00E-08, [25]) | 1.0000 |
19 | 10,463,118 | rs34536443 | C/G | 0.9712 | TYK2 | A/P | Protein kinase domain, Protein kinase-like domain, Serine–threonine/tyrosine–protein kinase, catalytic domain, Tyrosine–protein kinase | rs34536443 (9.00E-31, [25]) | 1.0000 |
19 | 10,469,975 | rs12720356 | C/A | 0.9076 | TYK2 | S/I | Protein kinase domain, Protein kinase-like domain, Serine–threonine/tyrosine–protein kinase, catalytic domain, Tyrosine–protein kinase | rs12720356 (4.00E-11, [25]) | 1.0000 |
19 | 49,206,674 | rs601338 | G/A | 0.4414 | FUT2 | W/* | – | rs492602 (7.00E-13, [30]) | 0.9920 |
19 | 49,206,985 | rs602662 | G/A | 0.4682 | FUT2 | G/S | – | rs492602 (7.00E-13, [30]) | 0.8822 |
22 | 21,982,892 | rs2298428 | C/T | 0.1769 | YDJC | A/T | Glycoside hydrolase/deacetylase, beta/alpha-barrel | rs181359 (2.00E-07, [29]) | 0.8941 |
rs4821124 (4.00E-08, [25]) | 0.9477 | ||||||||
Newly identified functional variants | |||||||||
Splice site | |||||||||
5 | 96,245,518 | rs2549797 | G/A | 0.5199 | ERAP2 | 5′ ss | – | rs2910686 (2.00E-08, [25]) | 0.8051 |
Exon | |||||||||
12 | 5,660,905 | rs60542959 | T/G | 0.9344 | COQ10A | I/M | – | rs2066807 (5.00E-12, [27]) | 0.9523 |
rs2066808 (6.00E-10, [26]) | 0.9388 | ||||||||
rs2066819 (5.00E-17, [25]) | 0.9517 | ||||||||
17 | 73,874,071 | rs4600514 | G/A | 0.1650 | TRIM47 | R/W | B-box-type zinc finger, Zinc finger RING/FYVE/PHD-type | rs55823223 (1.00E-08, [30]) | 0.9075 |