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Table 2 The algorithms of psoriasis GWAS

From: The immunological and genetic aspects in psoriasis

Chromosomal Reported gene(s) SNP Algorithms Ref.
1q21.3 LCE3B, LCE3D rs6677595 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
LCE3D, LCE3A rs4085613 Plink 1.02, PCA, Cochran-Armtiage trend test, Cochran-Mantel-Hanezel stratification analysis (Zhang et al. [2009])
LCE3D rs4112788 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
1p36.23 SLC45A1, TNFRSF9 rs11121129 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
1p36.11 RUNX3 rs7536201
IL28RA rs7552167
rs4649203 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
PCA, PLINK 1.07, R, EIGENSTRAT, Cochran-Armitage trend test (Cheng et al. [2013])
1p31.3 IL23R rs2201841 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
rs9988642 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
rs11209026 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
2q24.3 IFIH1 rs17716942 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
2p16.1 FLJ16341, REL rs62149416 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
REL rs702873 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
NR rs842636 MACH version 1.0, Meta-analysis (Stuart et al. [2010])
2p15 B3GNT2 rs10865331 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
5q33.3 PTTG1 rs2431697 R, PCA, Cochran-Armitage trend test, Heterogeneity tests (Sun et al. [2010])
IL12B rs12188300 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
rs2546890 MACH v.1.0.16, MACH2DAT, gPLINK v2.049, CopyCaller v1.0, METAL (Ellinghaus et al. [2010])
rs3213094 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
rs2082412 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
rs3213094 Plink 1.02, PCA, Cochran-Armtiage trend test, Cochran-Mantel-Hanezel stratification analysis (Zhang et al. [2009])
5q33.1 TNIP1/ANXA6 rs3762999 R, PCA, Cochran-Armitage trend test, Heterogeneity tests (Sun et al. [2010])
rs999556
TNIP1 rs17728338 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
rs2233278 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
IL13, IL4 rs1295685 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
IL13 rs20541 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
5q15 ERAP1 rs27432 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
rs27524 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
rs151823 R, PCA, Cochran-Armitage trend test, Heterogeneity tests (Sun et al. [2010])
5q15 LNPEP rs2303138 PCA, PLINK 1.07, R, EIGENSTRAT, Cochran-Armitage trend (Cheng et al. [2013])
6q25.4 EXOC2, IRF4 rs9504361 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
6q25.3 TAGAP rs2451258
6q23.3 TNFAIP3 rs582757 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
   rs610604 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
6q21 TRAF3IP2 rs33980500 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
rs458017 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
rs13196377 birdseed-v2 algorithm, MACH1, Χ2 test, Cochran-Mantel-Haenszel tests, PHASE (Huffmeier et al. [2010])
rs13190932
rs13210247
rs33980500 MACH v.1.0.16, MACH2DAT, gPLINK v2.049, CopyCaller v1.0, METAL (Ellinghaus et al. [2010])
rs240993 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
6p21.33 HLA-C rs1265181 Plink 1.02, PCA, Cochran-Armtiage trend test, Cochran-Mantel-Hanezel stratification analysis (Zhang et al. [2009])
rs13191343 birdseed-v2 algorithm, MACH1, Chi-Square test, Cochran-Mantel-Haenszel tests, PHASE (Huffmeier et al. [2010])
rs12191877 MACH v.1.0.16, MACH2DAT, gPLINK v2.049, CopyCaller v1.0, METAL (Ellinghaus et al. [2010])
rs10484554 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
rs12191877 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
rs10484554 STRUCTURE, EIGENSTRAT, Cochran-Armitage Test, R, Haploview 3.2 (Liu et al. [2008])
rs3134792 Haploview software, Fisher's exact test, PLINK, I2 statistic (Capon et al. [2008])
HLA-B, HLA-C rs4406273 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
HCP5 rs2395029 STRUCTURE, EIGENSTRAT, Cochran-Armitage Test, R, Haploview 3.2 (Liu et al. [2008])
7p14.1 ELMO1 rs2700987 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
8p23.2 CSMD1 rs7007032 R, PCA, Cochran-Armitage trend test, Heterogeneity tests (Sun et al. [2010])
rs10088247
9q34.13 TSC1 rs1076160 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
9q31.2 KLF4 rs10979182 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
9p21.1 DDX58 rs11795343
10q22.3 ZMIZ1 rs1250546
11q24.3 ETS1 rs3802826
ZC3H12C rs4561177
11q13.1 RPS6KA4, PRDX5 rs645078
12q13.3 STAT2, IL23A rs2066819 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
IL23A, STAT2 rs2066808 Χ2 statistic, logistic regression , MACH (Nair et al. [2009])
SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
12q13.2 RPS26 rs12580100 Imputation(MACH software version 1.0), Meta-analysis (Stuart et al. [2010])
13q14.11 COG6 rs7993214 STRUCTURE, EIGENSTRAT, Cochran-Armitage Test, R, Haploview 3.2 (Liu et al. [2008])
GJB2 rs3751385 R, PCA, Cochran-Armitage trend test, Heterogeneity tests (Sun et al. [2010])
14q13.2 NFKBIA, PSMA6 rs12586317 Imputation(MACH software version 1.0), Meta-analysis (Stuart et al. [2010])
NFKBIA rs8016947 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
Cochran–Armitage trend test, Cochran–Mantel–Haenszel stratification analysis, PLINK 1.07, R 15.1 (Li et al. [2013])
16p13.13 PRM3, SOCS1 rs367569 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
16p11.2 PRSS53, FBXL19 rs12445568
FBXL19,POL3S rs10782001 Imputation(MACH software version 1.0), Meta-analysis (Stuart et al. [2010])
17q25.3 CARD14 rs11652075 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
17q21.2 PTRF, STAT3, STAT5A/B rs963986
17q11.2 NOS2 rs28998802
rs4795067 Imputation(MACH software version 1.0), Meta-analysis (Stuart et al. [2010])
NR rs1975974
18q22.1 SERPINB8 rs514315 R, PCA, Cochran-Armitage trend test, Heterogeneity tests (Sun et al. [2010])
18q21.2 POL1, STARD6, MBD2 rs545979 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
19q13.41 ZNF816A rs9304742 R, PCA, Cochran-Armitage trend test, Heterogeneity tests (Sun et al. [2010])
19p13.2 ILF3,CARM1 rs892085 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
TYK2 rs34536443
rs12720356 SNPTEST, R, IMPUTE2, PHASE, logistic regression (Strange et al. [2010])
rs280519
20q13.13 ZNF313 rs2235617
RNF114 rs1056198 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
ZNF313 rs495337 Haploview software, Fisher's exact test, PLINK, I2 statistic (Capon et al. [2008])
20q13.12 SDC4 rs1008953 Imputation(MACH software version 1.0), Meta-analysis (Stuart et al. [2010])
22q11.21 UBE2L3 rs4821124 PLINK, minimac, IMPUTE2, PCA (Tsoi et al. [2012])
  1. PCA, principal-component analysis.