Table 1. Genome wide significant variants following SCZ meta analysis.
Gene | rsID | CHR | BP (hg18) | Freq | Pval | Direction effect | A1 | A2 | HetPVal | Imputed |
---|---|---|---|---|---|---|---|---|---|---|
SDCCAG8 | rs10927013 | 1 | 241655779 | 0.436 | 8.09 × 10−9 | ++++++++++++++++ | G | T | 0.91 | Y |
rs2039839 | 1 | 241665293 | 0.564 | 1.28 × 10−8 | −−−−−−−−−−−−−−−− | A | G | 0.93 | I | |
rs6703335 | 1 | 241675590 | 0.562 | 3.71 × 10−9 | −−−−−−−−−−−−−−−+ | A | G | 0.91 | I | |
ITIH1 | rs2710323 | 3 | 52790945 | 0.466 | 2.97 × 10−8 | −++−++−+++++++++ | C | T | 0.39 | A |
MHC | rs9379858 | 6 | 26475668 | 0.106 | 1.42 × 10−8 | +++−++−++−++++++ | C | T | 0.35 | A |
rs3799380 | 6 | 26575161 | 0.220 | 2.80 × 10−8 | +++−++−+++++++++ | C | T | 0.82 | I | |
rs6456728 | 6 | 26585758 | 0.779 | 2.36 × 10−8 | −−−+−−+−−−−−−−−− | A | G | 0.82 | I | |
rs7749305 | 6 | 27554545 | 0.100 | 2.57 × 10−8 | +++−++++++++++++ | C | T | 0.29 | Y | |
rs6904596 | 6 | 27599278 | 0.896 | 3.06 × 10−8 | −−−+−−−−−−−−−−−− | A | G | 0.27 | A | |
rs17750424 | 6 | 27809101 | 0.085 | 1.99 × 10−8 | ++++++++++++++++ | C | T | 0.38 | Y | |
rs17693963 | 6 | 27818144 | 0.904 | 1.61 × 10−9 | +++−++++++++++++ | A | C | 0.36 | I A5 | |
rs34706883 | 6 | 27913234 | 0.909 | 3.14 × 10−8 | ++++++++++++++++ | A | C | 0.39 | Y | |
rs13212651 | 6 | 27914964 | 0.909 | 3.34 × 10−8 | ++++++++++++++++ | A | G | 0.39 | Y | |
rs13194781 | 6 | 27923618 | 0.909 | 3.51 × 10−8 | ++++++++++++++++ | A | G | 0.42 | A | |
rs13199772 | 6 | 27942064 | 0.909 | 3.40 × 10−8 | ++++++++++++++++ | A | G | 0.42 | Y | |
MAD1L1 | rs10275045 | 7 | 1887352 | 0.403 | 2.16 × 10−8 | −+−+−−−−−−−+−−−+ | C | T | 0.36 | N |
rs12537914 | 7 | 1914885 | 0.365 | 2.03 × 10−8 | −+−+−−−−−−−+−−−− | C | T | 0.47 | Y | |
rs4721184 | 7 | 1917310 | 0.369 | 2.74 × 10−8 | +−+−+++++++−+++− | C | T | 0.47 | Y | |
rs2056480 | 7 | 1920827 | 0.632 | 1.54 × 10−8 | −−−+−−−−−−−+−−−+ | A | G | 0.56 | I | |
rs4721190 | 7 | 1921258 | 0.596 | 3.83 × 10−8 | −−−+−−−−−−−+−−−+ | A | G | 0.69 | I A5 | |
rs12699477 | 7 | 1935479 | 0.352 | 8.78 × 10−9 | +−+++++++++−++++ | C | T | 0.67 | A | |
rs2280550 | 7 | 1943082 | 0.639 | 3.80 × 10−8 | −+−+−−−−−−−+−−−+ | A | G | 0.49 | Y | |
rs12666575 | 7 | 1970947 | 0.358 | 8.27 × 10−10 | −−−−−−+−−−−+−−−+ | C | T | 0.19 | A | |
rs4721295 | 7 | 2003195 | 0.378 | 6.23 × 10−10 | +−++++−++++−+++− | G | T | 0.07 | I | |
rs1107592 | 7 | 2007958 | 0.62 | 5.64 × 10−9 | +−++++−++++−+++− | A | G | 0.04 | I A5 | |
rs3778969 | 7 | 2106516 | 0.633 | 6.43 × 10−9 | −−−−−−+−−−−+−−−+ | A | G | 0.16 | N | |
rs10224497 | 7 | 2116493 | 0.574 | 1.09 × 10−8 | ++++++−++++−+++− | A | G | 0.13 | I A5 | |
rs10239050 | 7 | 2124916 | 0.615 | 1.11 × 10−8 | +−++++−++++−+++− | A | G | 0.12 | A | |
rs3800913 | 7 | 2129763 | 0.604 | 4.03 × 10−8 | ++++++−++++−+++− | A | G | 0.15 | A | |
rs3800917 | 7 | 2134465 | 0.64 | 2.29 × 10−9 | −+−−−−+−−−−+−−−+ | A | G | 0.22 | I | |
rs3778991 | 7 | 2138981 | 0.656 | 2.21 × 10−9 | −−−−−−+−−−−+−−−− | A | G | 0.20 | A | |
rs3778994 | 7 | 2142381 | 0.616 | 2.53 × 10−9 | −−−−−−+−−−−+−−−− | A | C | 0.21 | A5 | |
rs4721441 | 7 | 2150586 | 0.356 | 9.41 × 10−10 | ++++++−++++−++++ | C | T | 0.29 | Y | |
rs3779003 | 7 | 2151428 | 0.347 | 2.33 × 10−9 | −−−−−−+−−−−+−−−− | C | T | 0.23 | I A5 | |
rs3757440 | 7 | 2239462 | 0.647 | 1.98 × 10−8 | ++++++++++−−+++− | A | G | 0.28 | I A5 | |
rs7787274 | 7 | 2242519 | 0.651 | 1.08 × 10−8 | −−−−−−−−−−−+−−−+ | A | G | 0.21 | Y | |
rs7799006 | 7 | 2244752 | 0.350 | 1.24 × 10−8 | −−−−−−−−−−−+−−−+ | C | T | 0.23 | A | |
CSMD1 | rs6558872 | 8 | 4225547 | 0.571 | 4.75 × 10−8 | −−−−+−−−−+−−−−−+ | A | G | 0.46 | I A5 |
TSNARE1 | rs10098073 | 8 | 143307411 | 0.535 | 9.05 × 10−9 | ++−+++++++++++++ | A | C | 0.93 | I |
rs4129585 | 8 | 143310840 | 0.566 | 2.38 × 10−8 | ++++++++++++++++ | A | C | 0.99 | I |
The final column lists the imputation status of each SNP. Y: imputed in all cohorts; N: not imputed; I: imputed in cohorts genotypes on the Illumina chips; A: imputed in cohorts genotyped on the Affymetrix chips; A5: imputed in cohorts genotyped on the Affymetrix 5.0 and 500 arrays.