Table 2 The algorithms of psoriasis GWAS
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]) |