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Table 2 SCZ-associated variants on chromosome 2-22 and the chromosome X that could meet or do not meet the criterion in the Top 45 genes at the SZGene Database (Updated Dec 23, 2011)

From: Paradox of schizophrenia genetics: is a paradigm shift occurring?

Genes and SNPs Location Allele (min/maj) m A m U OR d
IL1B 2q13      
rs16944   T/C* 0.6289 (N=1,718) 0.6066 (N=2,157) 1.11 0.022
ZNF804A 2q32.1      
rs1344706   G/T* 0.6357 (N=6,487) 0.6032 (N=11,478) 1.14 0.033
CCKAR 4p15.2      
rs1800857   C*/T 0.1666 (N=105) 0.1559 (N=93) 1.32 0.008
GABARB2 5q34      
rs1816072   C/T* 0.6404 (N=1,129) 0.5935 (N=995) 1.22 0.047
rs194072   C/T* 0.8685 (N=1,137) 0.8466 (N=991) 1.20 0.022
rs6556547   T/G* 0.9444 (N=774) 0.9226 (N=620) 1.43 0.022
DTNBP1 6p23      
rs3213207   G/A* 0.8891 (N=8,377) 0.8758 (N=8,886) 1.11 0.013
rs1474605   G/A* 0.8000 (N=3,710) 0.7858 (N=3,588) 1.09 0.014
HIST1H2BJ 6p22.1      
rs6913660   A/C* 0.8927 (N=10,065) 0.8801 (N=34,098) 1.15 0.013
PRSS16 6p22.1      
rs6932590   C/T* 0.7943 (N=7,177) 0.8058 (N=28,270) 1.16 -0.012
rs13219354   C/T* 0.9088 (N=6,478) 0.9020 (N=27,224) 1.20 0.007
PGBD1 6p22.1      
rs13211507   C/T* 0.9518 (N=9,774) 0.9387 (N= 33,694) 1.23 0.013
RPP21 6p21.33      
rs3130375   A/C* 0.9018 (N=2,799) 0.8634 (N=3,082) 1.41 0.038
NOTCH4 6p21.32      
rs3131296   A/G* 0.8912 (N=7,156) 0.8892 (N=28,312) 1.20 0.002
rs2071287   A/G* 0.6858 (N=2,511) 0.6463 (N=2,556) 1.19 0.039
MDGA1 6p21.2      
rs11759115   C/T* 0.8639 (N=1,874) 0.8379 (N=2,582) 1.23 0.026
rs12191311   T*/C 0.3619 (N=1,879) 0.3555 (N=2,605) 1.12 0.006
rs7769372   T*/C 0.2328 (N=1,915) 0.1885 (N=2,576) 1.18 0.044
AH1 6q23.3      
rs2064430   T*/C 0.5672 (N=2,796) 0.5296 (N=13,494) 1.13 0.038
rs11154801   A/C* 0.6633 (N=3,298) 0.6576 (N=14,805) 1.09 0.006
C6orf217 6q23.3      
rs10223338   T/C* 0.7158 (N=2,797) 0.6975 (N=13,522) 1.12 0.018
rs1475069   C*/A 0.7205 (N=3,276) 0.6976 (N=14,639) 1.14 0.023
rs9321521   A/G* 0.6755 (N=2,784) 0.6642 (N=13,311) 1.12 0.011
RELN 7q22.2      
rs7341475   A/G* 0.8327 (N=3,315) 0.8110 (N=8,042) 1.14 0.022
rs262355   A*/T 0.3852 (N=1,128) 0.3563 (N=1,848) 1.14 0.029
PPP3CC 8p21.3      
rs2461491   A*/G 0.4469 (N=6,287) 0.4353 (N=6,200) 1.07 0.015
rs10108011   G*/A 0.3657 (N=4,304) 0.3488 (N=4,465) 1.09 0.0170
SLC18A1 8p21.3      
rs2270641   C*/A 0.3182 (N=759) 0.2802 (N=885) 1.63 0.038
NRG1 8p12      
rs10503929   C/T* 0.8342 (N=3,256) 0.8118 (N=4,181) 1.14 0.022
GWA_10q26.13 10q26.11      
rs17101921   A*/G 0.06667 (N=7,447) 0.04318 (N=13,039) 1.28 0.023
DRD4 11p15.5      
rs4646984   S/L* 0.7750 (N=1,558) 0.7292 (N=1,499) 1.27 0.046
rs1800955   C*/T 0.4235 (N=2,450) 0.4018 (N=2,506) 1.12 0.022
TPH1 11p15.1      
rs1800532   A*/C 0.4752 (N=2,416) 0.4299 (N=3,623) 1.16 0.045
rs1799913   A*/C 0.4546 (N=1,323) 0.4171 (N=2,201) 1.14 0.038
GWA_11p14.1 11p14.1      
rs1602565   C*/T 0.1346 (N=5,475) 0.1152 (N=10,845) 1.19 0.019
DRD 2 11q23.1      
rs6277   C*/T 0.4968 (N=3,156) 0.4527 (N=3,960) 1.40 0.044
rs6275   T*/C 0.3106 (N=2,436) 0.2927 (N=2,918) 1.15 0.018
rs1801028   G*/C 0.0245 (N=4,304) 0.0207 (N=5,920) 1.33 0.004
NRGN 11q24.2      
rs12807809   C/T* 0.8403 (N=7,213) 0.8190 (N=28,490) 1.15 0.021
OPCML 11q25      
rs3016384   T/C* 0.5374 (N=5,491) 0.5141 (N=10,900) 1.10 0.023
GRIN2B 12p13.1      
rs1019385   T/G* 0.5604 (N=687) 0.4885 (N=650) 1.33 0.072
DAO 12q24.11      
rs4623951   C/T* 0.7038 (N=1,509) 0.6788 (N=1,521) 1.14 0.025
HTR2A 13p14.13      
rs6311   A*/G 0.4441 (N=2,594) 0.4115 (N=2,869) 1.21 0.033
DAOA 13q33.3      
rs778293   G*/A 0.3149 (N=2,899) 0.2770 (N=3,218) 1.18 0.038
rs3916971   T/C* 0.5622 (N=844) 0.5211 (N=922) 1.19 0.041
AKT1 14q32.33      
rs3803300   A*/G 0.1068 (N=1,301) 0.1039 (N=1,424) 1.36 0.003
GWA_16p13.12 16p13.12      
rs7192086   T*/A 0.2701 (N=7,179) 0.2456 (N=12,623) 1.12 0.025
RPGRIP1L 16q12.2      
rs9922369   A*/G 0.0403 (N=6,494) 0.0336 (N=11,449) 1.32 0.007
HP 16q22.3      
Hp_1/2   1/2* 0.6208 (N=1,300) 0.5911 (N=1,976) 1.14 0.030
SRR 17p13.3      
rs408067   G*/A 0.3166 (N=1,145) 0.2779 (N=1,146) 1.22 0.039
TCF4 18q21.2      
rs9960767   C*/A 0.0514 (N=9,755) 0.0467 (N=33,648) 1.23 0.005
APOE 19q13.32      
e4-allele   E2/3/4* 0.1391 (N=1,596) 0.1139 (N=3,038) 1.16 0.025
COMT 22q11.21      
rs737865   C/T* 0.6916 (N=7,397) 0.6803 (N=10,411) 1.06 0.011
rs4818   G*/C 0.3503 (N=177) 0.3081 (N=99) 1.05 0.042
  1. On chromosomes 2-22 and the chromosome X, 17 variants at 15 loci (CCKAR, DTNBP1, HIST1H2BJ, PRSS16, PGBD1, NOTCH4, MDGA1, AH1, C6orf217, PPP3CC, DRD 2, AKT1, RPGRIP1L, TCF4, COMT) could meet the criterion under the assumption that the mutation rates at those loci are near the upper limit in the autosomes and the X chromosome. 15 protective genes (IL1B, ZNF804A, GABARB2, RELN, GWA_10q26.13, DRD4, TPH1, GWA_11p14.1, GRIN2B, DAO, HTR2A, DAOA, GWA_16p13.12, SRR, APOE) are located on 2q, 5q, 7q, 10q, 11p, 12p, 12q, 13p, 13q, 16p, 17p, and 19q, where no SCZ-associated variants that could meet the criterion are located
  2. *alleles associated with SCZ.