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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.PositionVariantAlleles (P/R)RAFGeneAAInterPro annotationMarker (P-value, Study)r2
Known functional variants
 Splice site
  631,380,000rs199503730G/−0.0447MICA5′ ssrs2395029 (2.00E-26, [19])0.8860
 Exon
  125,291,010rs6672420A/T0.4791RUNX3I/Nrs7536201 (2.00E-12, [25]; 2.00E-08, [29])0.9046
  167,705,958rs11209026A/G0.9384IL23RQ/Rrs11209026 (7.00E-07, [24])1.0000
        rs9988642 (1.00E-26 [25]; 7.00E-14, [29])0.8520
  631,473,957rs3134900(C/G)?NRMICBI/MMHC class I-like antigen recognition-like, MHC classes I/II-like antigen recognition proteinrs3134792 (1.00E-09, [18])0.8008
  6111,913,262rs33980500C/T0.0855TRAF3IP2D/Nrs33980500 (1.00E-16, [23]; 4.00E-45, [25]; 1.00E-23, [29])1.0000
  1778,178,893rs11652075T/C0.5099CARD14W/Rrs11652075 (3.00E-08, [25])1.0000
  1910,463,118rs34536443C/G0.9712TYK2A/PProtein kinase domain, Protein kinase-like domain, Serine–threonine/tyrosine–protein kinase, catalytic domain, Tyrosine–protein kinasers34536443 (9.00E-31, [25])1.0000
  1910,469,975rs12720356C/A0.9076TYK2S/IProtein kinase domain, Protein kinase-like domain, Serine–threonine/tyrosine–protein kinase, catalytic domain, Tyrosine–protein kinasers12720356 (4.00E-11, [25])1.0000
  1949,206,674rs601338G/A0.4414FUT2W/*rs492602 (7.00E-13, [30])0.9920
  1949,206,985rs602662G/A0.4682FUT2G/Srs492602 (7.00E-13, [30])0.8822
  2221,982,892rs2298428C/T0.1769YDJCA/TGlycoside hydrolase/deacetylase, beta/alpha-barrelrs181359 (2.00E-07, [29])0.8941
        rs4821124 (4.00E-08, [25])0.9477
Newly identified functional variants
 Splice site
  596,245,518rs2549797G/A0.5199ERAP25′ ssrs2910686 (2.00E-08, [25])0.8051
 Exon
  125,660,905rs60542959T/G0.9344COQ10AI/Mrs2066807 (5.00E-12, [27])0.9523
        rs2066808 (6.00E-10, [26])0.9388
        rs2066819 (5.00E-17, [25])0.9517
  1773,874,071rs4600514G/A0.1650TRIM47R/WB-box-type zinc finger, Zinc finger RING/FYVE/PHD-typers55823223 (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