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Table 1 Candidate functional variants in exons or splice sites associated with psoriasis risk

From: An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer

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 – rs7536201 (2.00E-12, [25]; 2.00E-08, [29]) 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 – rs33980500 (1.00E-16, [23]; 4.00E-45, [25]; 1.00E-23, [29]) 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
  1. An asterisk in “AA” column indicates a stop codon. As for rs3134792 and its functional variants, the direction of effects is unknown
  2. P/R protective/risk, RAF risk allele frequency, NR not reported, AA amino acids, 5′ ss 5 prime splice site, r2 r-squared value between functional variants and GWAS variants
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BMC Medical Genomics

ISSN: 1755-8794

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