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. 2010 Nov 2;1:129. doi: 10.3389/fphar.2010.00129
Gene SNP rs Allele/ position nt Effect Type MAF publisheda MAFb HWp Missing values (%) Method Reference
CYP1A2 CHR15; NM_000761
rs2069514 *1C G > A p 0.081 0.007 1 0 Tq-AD Nakajima et al. (1999), Abnet et al. (2007)
rs2069522 C > T p 0 0.037 0.173 0 Maldi Bethke et al. (2007)
rs12720461 *1K C > T p 0 0.003 1 0 Maldi Aklillu et al. (2003)
rs762551f *1F A > C p 0.308 0.32 0.455 0 Maldi Han et al. (2002)
rs72547513 *11 C > A F186L nc No data 0 0 Maldi Murayama et al. (2004), Pucci et al. (2007)
rs56276455 *3 G > A D348N nc No data 0.003 1 0 Maldi Zhou et al. (2009)
rs72547516 *4 A > T I386F nc No data 0 0 Maldi Zhou et al. (2009)
rs56107638 *7 G > A i (0.003) 0 0 Maldi Allorge et al. (2003)
rs28399424 *6 C > T R431W nc No data 0 0 Maldi Zhou et al. (2009)
rs2470890 C > T N516 sc 0.358 0.387 0.492 0 Maldi Gunes and Dahl (2008)
rs4886406 A > C 3′ 0.292 0.323 0.34 4 ILM
CYP1A1 CHR15; NM_000499
rs2470893 G > A 5′ 0.275 0.294 0.029 1.3 ILM
rs2472299f G > A 5′ 0.308 0.319 0.571 0.7 ILM
rs4646421 C > T p 0.075 0.094 0.618 0.7 ILM
rs1048943 *2B/C A > G I462V cn 0.042 0.027 0.143 0.7 Tq-AD Hayashi et al. (1991), Zhang et al. (1996)
AHR (ARYL HYDROCARBON RECEPTOR) CHR7; NM_001621
rs10247158 A > T 5′ 0.152 0.13 1 0 Maldi Bin et al. (2008)
rs10250822 T > C 5′ 0.2 0.217 0.81 0 Maldi Bin et al. (2008)
rs4719497 T > C 5′ 0.1 0.108 1 1.3 ILM
rs2282885 A > G i 0.347 0.413 0.736 0 Maldi Bin et al. (2008)
rs1476080 T > G i 0.325 0.343 0.21 0 Maldi Bin et al. (2008)
rs4236290 T > C i 0.125 0.122 0.697 2 ILM
rs6960165 A > G i 0.196 0.205 1 0.7 Maldi Bin et al. (2008)
rs2158041 C > T i 0.183 0.203 1 1.3 ILM Chen et al. (2009)
rs7811989 G > A i 0.233 0.233 1 0 Maldi Bin et al. (2008)
rs2066853 G > A R554K nc 0.075 0.1 1 0 Maldi Long et al. (2006), Abnet et al. (2007), Wong et al. (2001) Cauchi et al. (2001); Merisalu et al. (2007)
rs4986826 G > A V570I nc 0 0 0.7 Maldi Wong et al. (2001)
AHRR(ARYL HYDROCARBON RECEPTOR REGULATOR); CHR5; NM_020731
rs3756712 T > G i 0.342 0.361 0.723 1.3 ILM
rs4957018 A > G i 0.275 0.322 0.453 0.7 ILM
rs3734145 C > T i 0.25 0.258 0.052 0.7 ILM
rs4957028 T > C i 0.424 0.463 1 1.3 ILM
rs908114 A > G i 0.383 0.329 0.853 2.7 ILM
rs2721020 G > A i 0.225 0.232 1 0.7 ILM
rs7731963 C > A i 0.375 0.411 0.389 6.7 ILM
rs2292596 C > G P189A nc 0.412 0.373 0.296 0 Maldi Watanabe et al. (2001)
rs34453673 G > C D641H nc 0.31 0.403 0.612 0 Maldi Cauchi et al. (2003)
rs10078 A > C 3′u 0.2 0.218 0.81 0.7 ILM
rs2241598 C > T 3′ 0.183 0.211 1 0.7 ILM
ARNT (HIF1β; ARYL HYDROCARBON RECEPTOR NUCLEAR TRANSLOCATOR) CHR1; NM 001668
rs2292166 C > T 5′ 0.217 0.282 0.015 0.7 ILM
rs7412746 C > T 5′ 0.475 0.419 0.737 1.3 ILM
rs11204735 C > T i 0 0.7 Maldi Das et al. (2008)
rs2134688 A > G i 0.142 0.13 0.716 0 Maldi Das et al. (2008)
rs2228099e G > C V189 sc 0.35 0.307 0.255 0 Maldi Kayano et al. (2004)
rs1889740e G > A i No data 0.307 0.255 0 Maldi Das et al. (2008)
rs10305724 C > T i 0.125 0.057 0.383 0.7 ILM
CAR (NR1I3; CONSTITUTIVE ANDROSTANE RECEPTOR) CHR1; NM_00177469
rs6686001 C > A i 0.13 0.143 0.739 0 Maldi
rs3003596 T > C i 0.49 0.363 0.289 0 Maldi
C > T i 0.242 0.19 0.063 0 Maldi Oliver et al. (2010)
398T > G T > G V133G nc No data 0 Maldi Ikeda et al. (2005)
rs2307424 C > T P180 sc 0.471 0.311 0.252 1.3 ILM Oliver et al. (2010)
rs2307418 A > C i 0.183 0.153 0.529 4 ILM
rs4073054 G > T i 0.408 0.476 0.247 2 ILM Oliver et al. (2010)
HNF1α (TCF1; HEPATOCYTE NUCLEAR FACTOR 1 HOMEOBOX A) CHR12; NM_000545
-58 A > C p No data 0 0.7 Maldi Gragnoli et al. (1997)
rs1169288 A > G I27L nc 0.283 0.393 0.864 0 Maldi Holmkvist et al. (2006), Cauchi et al. (2008), Ryffel (2001)
rs1800574 C > T A98V nc 0.029 0.023 1 0 Maldi Giuffrida et al. (2009)
rs1169300 G > A i 0.292 0.315 0.851 0.7 ILM Ridker et al. (2008)
rs2071190 T > A i 0.22 0.19 1.0 0 Maldi Weedon et al. (2005)
rs1169302 T > G i 0.45 0.433 0.318 0.7 ILM Ridker et al. (2008)
rs2464196 G > A S487N nc 0.292 0.317 1 0 Maldi Ridker et al. (2008)
rs1169306 C > T i 0.375 0.377 1 0 Maldi
rs1169307 T > C i 0.392 0.426 0.319 0.7 ILM
rs735396 A > G i 0.383 0.382 0.727 1.3 ILM Reiner et al. (2008), Ridker et al. (2008)
HNF4α (NR2A1; HEPATOCYTE NUCLEAR FACTOR 4 ALPHA) CHR20; NM_000448
rs4810424 G > C p 0.164 0.157 0.364 0 Maldi Bagwell et al. (2005)
Sookoian et al. (2010)
rs2144908 G > A p 0.183 0.16 0.539 0 Maldi Lamba et al. (2008), Muller et al. (2005), Holmkvist et al. (2008), Black et al. (2008)
rs2868094 T > C p 0.317 0.28 0.316 0 Maldi
rs6031544 C > T p 0.283 0.289 0.842 0.7 ILM SNP@promoter
rs3212183 T > C i 0.413 0.45 0.0029 0 Maldi Muller et al. (2005)
rs6073432 A > C i 0.309 0.307 0.057 0 Maldi
rs13041396 C > G i 0.24 0.207 0.133 0 Maldi
c.379 C > T R127W nc No data 0 Maldi Lausen et al. (2000)
rs1800961 C > T T139I nc No data 0.02 0.05 0 ILM Sookoian et al. (2010), Lu et al. (2008)
c.460 C > T R154X nc No data 0 Maldi Lausen et al. (2000)
rs6103731 G > A i 0.484 0.423 0.404 0 Maldi
rs3818247 G > T i 0.39 0.367 0.86 0 Maldi Love-Gregory et al. (2004)
IL1β (INTERLEUKIN 1 BETA) CHR2; NM 000576
rs1143627 C > T p 0.367 0.293 0.238 0 Maldi Liu et al. (2010)
rs1143634 C > T F105 cs 0.223 0.22 0.811 0 Maldi
IL1RN (INTERLEUKIN 1 RECEPTOR ANTAGONIST) CHR2; NM_000577
rs2637988 G > A i 0.392 0.399 0.733 0.7 ILM
rs3213448 G > A i 0.117 0.128 0.469 0.7 ILM
rs419598 T > C A57 Cs 0.275 0.287 0.84 4.7 ILM
rs315952 T > C S133 cs 0.258 0.295 0.555 0.7 ILM
rs397211 T > C 3′ 0.314 0.342 0.856 0.7 ILM
NFKB1 (NUCLEAR FACTOR NF-KAPPA-B P105 SUBUNIT) CHR4; NM_003998
rs28362491 del >  ATT G 5′ 0.34 0.361 0.019 2 Maldi Karban et al. (2004)
rs3774937 T > C p/i 0.367 0.326 0.853 0.7 ILM
rs230530 T > C i 0.364 0.446 0.403 2 ILM
rs4647992 C > T i 0.067 0.047 0.344 0.7 ILM
rs230526 C > T i 0.467 0.396 0.230 0.7 ILM Liu-Mares et al. (2007)
rs4648022 C > T i 0.067 0.077 1 0.7 ILM Cerhan et al. (2008)
rs1598859 T > C i 0.343 0.379 1 3.3 ILM Liu-Mares et al. (2007)
rs4648072 A > G M507V nc 0.075 0.013 0.049 0.7 Maldi SIFT-score 0.44
rs1609798 C > T i 0.331 0.329 1 0.7 ILM
rs997476 C > A 3′ 0.1 0.057 0.068 1.3 ILM
rs10489113 A > G 3′ 0.225 0.182 1 1.3 ILM
PGC1α (PPARGC1α; PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR GAMMA COACTIVATOR 1-ALPHA) CHR4; NM_013261
rs4361373 C > T i 0.192 0.141 1 0.7 ILM
rs4550905 A > G i 0.325 0.27 0.676 1.3 ILM
rs6448226 A > G i 0.375 0.34 0.465 2 ILM
rs2970853 G > A i 0.308 0.211 0.218 2 ILM Juang et al. (2010)
rs2932976 G > A i 0.271 0.314 0.334 3.3 ILM
rs2970847 C > T T394 sc 0.208 0.153 1 0 Maldi Bhat et al. (2007), Juang et al. (2010)
rs8192678 G > A G482S nc 0.367 0.322 0.708 2.7 Maldi Deeb and Brunzell (2009), Wang et al. (2007)
rs2932965 G > A i 0.25 0.171 0.771 0.7 ILM
rs12650562 G > A i 0.435 0.426 0.74 0.7 ILM
PXR (NR1I2; PREGNANE X RECEPTOR) CHR3; NM_003889
rs1523130 G > A 5′ 0.407 0.423 0.403 0 Maldi Lamba et al. (2008)
rs3814055i C > T 5′ 0.4 0.417 0.4 0 Maldi* Zhang et al. (2001)
rs1523127 A > C 5′ 0.408 0.42 0.314 0 Maldi* Zhang et al. (2001), King et al. (2007)
rs2276706i G > A i 0.39 0.417 0.4 0 Maldi Zhang et al. (2001)
rs4234666 C > G i 0.318 0.233 1 0 Maldi
rs1403527 T > G i 0.11 0.226 1 2.7 ILM
rs1403526 A > G i 0.242 0.341 0.068 1.3 ILM
rs55764158 C > A i 0.293 0.29 0.078 0 Maldi Lamba et al. (2008)
rs16830505 A > G i 0.15 0.117 0.694 0.7 ILM
rs2472677 C > T i 0.5 0.427 0.096 0 Maldi Lamba et al. (2008)
rs4440154 C > T i 0.35 0.384 0.119 2 ILM
rs2461823 T > C i 0.35 0.379 0.164 0.7 ILM
rs13059232 T > C i 0.358 0.379 0.217 3.3 Maldi Lamba et al. (2008)
69245C > T C > T i No data 0.077 1 Maldi Lamba et al. (2008)
rs7643645 A > G i 0.43 0.363 0.598 0 Maldi Lamba et al. (2008)
rs12721613 *2 C > T P27S nc 0 0 0.7 Maldi Hustert et al. (2001)
rs12721607 *3 G > A G36R nc 0.03 0.027 1 0 Maldi Hustert et al. (2001)
rs72551372 *10 G > A nc No data 0 0.7 Maldi Hustert et al. (2001)
rs72551374 A > G i No data 0 0.7 Maldi Hustert et al. (2001), Lim and Huang (2007)
rs3732357 G > A i 0.225 0.336 0.009 0.7 ILM
rs6785049 A > G i 0.302 0.413 0.018 0 Maldi* Zhang et al. (2001)
rs2276707 C > T i 0.058 0.22 0.641 0 Maldi* Zhang et al. (2001)
rs3732359 G > A 3′u 0.075 0.277 0.091 6 Maldi Oleson et al. (2010)
rs1054191 G > A 3′u 0.233 0.14 0.079 0 Maldi Zhang et al. (2001)
rs3814057 T > C 3′u 0.188 0.218 0.81 0.7 Maldi Zhang et al. (2001)
RARα (NR1B1; RETINOIC ACID RECEPTOR ALPHA) CHR17; NM_001033603
rs13706g G > A V441Id 5′d 0.142 0.094 0.618 0.7 ILM
rs2715553 T > C i No data 0.483 0.87 1.3 ILM
rs9303286g G > C i 0.06 0.093 0.617 0 Maldi
rs482284 G > A i 0.283 0.267 1 0 Maldi
rs4890109 G > T i 0.058 0.027 0.0016 2 ILM
RXRα (NR2B1; RETINOID X RECEPTOR ALPHA) CHR9; NM_002957
rs3818740 T > C i 0.225 0.294 0.423 4.7 ILM
rs3132297 C > T i 0.222 0.157 1 0 Maldi
rs3118529 T > C i 0.227 0.29 0.557 0 Maldi
rs4240705 A > G i 0.4 0.369 0.597 0.7 ILM
rs3118570 A > C i 0.18 0.153 1 0 Maldi Cauchi et al. (2003), Kölsch et al. (2009)
rs1536475 G > A i 0.17 0.163 1 0 Maldi Kölsch et al. (2009)
rs3132293 G > A i 0.22 0.209 0.451 2.7 Maldi Cauchi et al. (2003), Kölsch et al. (2009)
rs1805348 G > A A457 sc 0.025 0.023 1 0 Maldi
SRC-1 (NCOA1; NUCLEAR RECEPTOR COACTIVATOR 1) CHR2; NM_003734
rs995647 A > G i 0.1 0.111 0.082 0.7 ILM
rs11677500 G > A i 0.433 0.469 1 3.3 ILM
rs2119115 A > C i 0.267 0.299 0.439 2 ILM
rs12468225 A > C i 0.136 0.137 0.481 0 Maldi
rs4578807 A > G i 0.133 0.145 0.512 1.3 ILM
rs4665716 A > G i 0.075 0.055 0.007 2.7 ILM
rs11682130 T > G i 0.433 0.473 0.514 1.3 ILM
rs6743362 A > C i 0.058 0.034 0.205 0.7 ILM
rs12617941 G > A i 0.075 0.047 0.274 0.7 ILM
rs6724282 A > G 3′ 0.075 0.062 0.014 2.7 ILM
rs9309308 T > C 3′ 0.225 0.297 0.242 1.3 ILM
USF1 (UPSTREAM STIMULATORY FACTOR 1) CHR1; NM_009053
rs3813609 C > G 5′c 0.3 0.373 0.601 0 Maldi Holzapfel et al. (2008)
rs2774279 G > A R873 (ARHG AP30) 5′c 0.38 0.26 0.286 0 Maldi Auro et al. (2008)
rs1556259 T > C i 0.083 0.127 0.47 0 Maldi Holzapfel et al. (2008)
rs2774276 C > G i 0.21 0.247 0.269 0 Maldi
rs2073658h G > A i 0.283 0.363 0.48 0 Maldi OMIM, Meex et al. (2008)
rs3737787h C > T 3′u 0.309 0.363 0.48 0 Maldi Holzapfel et al. (2008), Collings et al. (2008), Meex et al. (2008), Naukkarinen et al. (2005)
VDR (NR1I1; VITAMIN D RECEPTOR) CHR12; NM_000376
rs4516035 T > C 5′ 0.458 0.493 1 1.3 ILM
rs3890733 C > T i 0.35 0.382 0.605 1.3 ILM
rs4760648 C > T i 0.457 0.433 0.183 0.7 ILM
rs2853564 T > C i 0.452 0.419 0.502 1.3 ILM
rs10735810(has merged to rs2228570) T > A M1T nc 0.442 0.34 0.71 4 Maldi Guo et al. (2006),
rs11574090 C > G L230V nc No data 0 0.7 Maldi
rs2239186 T > C i 0.203 0.229 0.638 2.7 ILM
rs2189480 C > A i 0.398 0.413 0.731 4 ILM
rs2239179 A > G i 0.408 0.405 0.497 1.3 ILM
rs1540339 G > A i 0.398 0.391 0.165 2 ILM
rs7962898 T > C i 0.425 0.497 0.87 0 Maldi
rs1544410 G > A i 0.442 0.4 0.609 0 Maldi Purdue et al. (2007)
rs7975232 A > C i 0.422 0.493 1 0 Maldi Purdue et al. (2007)
rs731236 T > C I352 sc 0.44 0.372 1 8.7 Maldi Purdue et al. (2007)

i, Intronic; nc, non-synonymous coding; sc, synonymous coding; 3′u, 3′ untranslated region; 5′ upstream of mRNA; p, promoter; 3′, downstream of mRNA; Maldi, MALDI-TOF MS (mass assisted light desorption time of flight mass spectrometry) multiplexed genotyping assay; ILM, Illumina 300k Bead Chip; Tq-AD, TaqMan allelic discrimination genotyping assay (Applied Biosystems); calculation of MAF, minor allele frequency; HWp, Hardy–Weinberg p-value and missing values see Materials and Methods section.

aHapMapCEU or alternative population of Caucasian origin (dbSNP-homepage; Build 131).

bMinor allele frequency found in this study.

cOverlap to ARHGAP30 coding region.

dLocated in CDC6 (cn).

e,f,g,h,iSNPs linked pairwise 100% within the one gene.

*MALDI-TOF genotype data provided by E. Schaeffeler, IKP, Stuttgart