Table 2.
Novel Vitamin D Levels Genomic Loci also Associated with Schizophrenia (SCZ) at Conjunctional FDR < 0.05
| Locus | Chr | Lead SNP | A1/A2 | Nearest gene | Functional category | P value Vitamin D | Beta Vitamin D | P value SCZ | Odds Ratio SCZ | conjFDR |
|---|---|---|---|---|---|---|---|---|---|---|
| 3 | 1 | rs2842198 | A/G | HYI-AS1 | intergenic | 2.13E-05 | -8.68E-03 | 1.51E-07 | 0.95 | 8.40E-03 |
| 4 | 1 | rs12567744 | G/A | CDKN2C | intergenic | 3.31E-04 | −7.68E-03 | 1.03E-04 | 1.04 | 4.71E-02 |
| 7 | 1 | rs12743378 | A/G | SDCCAG8 | intronic | 6.55E-06 | 1.28E-02 | 5.10E-07 | 0.94 | 3.91E-03 |
| 10 | 2 | rs999494 | T/C | EMX1 | intronic | 8.85E-05 | −9.90E-03 | 2.61E-07 | 0.95 | 2.10E-02 |
| 11 | 2 | rs13024749 | T/G | LY75:LY75-CD302 | intronic | 3.38E-04 | −7.24E-03 | 3.97E-05 | 1.04 | 4.77E-02 |
| 12 | 2 | rs56393175* | T/G | TM4SF20 | intergenic | 3.18E-05 | −1.12E-02 | 3.04E-06 | 1.05 | 1.09E-02 |
| 13 | 3 | rs61182735 | A/G | AC091493.2 | intergenic | 4.85E-05 | −8.11E-03 | 1.16E-07 | 1.05 | 1.43E-02 |
| 14 | 3 | rs9831428 | A/C | RBMS3 | intronic | 2.02E-04 | 7.52E-03 | 6.77E-05 | 0.97 | 3.70E-02 |
| 17 | 3 | rs2241823 | A/C | ATXN7 | intronic | 1.38E-04 | 8.30E-03 | 1.26E-07 | 1.05 | 2.76E-02 |
| 18 | 3 | rs2088176 | G/A | ROBO2 | intronic | 1.66E-04 | 7.56E-03 | 1.57E-05 | 0.96 | 3.11E-02 |
| 19 | 3 | rs6779146 | C/T | MSL2 | intronic | 1.04E-04 | −9.21E-03 | 1.87E-06 | 1.05 | 2.32E-02 |
| 20 | 3 | rs112936817* | T/G | DGKG | intronic | 3.13E-05 | 1.33E-02 | 1.16E-04 | 0.95 | 4.90E-02 |
| 21 | 4 | rs80279461 | T/G | PCDH7 | intergenic | 1.15E-04 | −1.09E-02 | 1.55E-05 | 0.95 | 2.47E-02 |
| 25 | 5 | rs904612 | A/G | CTB-35F21.1 | ncRNA_intronic | 2.54E-06 | −1.05E-02 | 4.05E-06 | 1.05 | 7.06E-03 |
| 27 | 6 | rs9273493 | T/C | HLA-DQB1:HLA-DQB1-AS1:XXbac-BPG254F23.6 | ncRNA_exonic | 8.21-06 | −9.10E-03 | 2.35E-06 | 1.05 | 4.94E-03 |
| 30 | 7 | rs274632 | A/C | GRM3 | intergenic | 2.24E-04 | −7.43E-03 | 7.98E-05 | 1.04 | 4.03E-02 |
| 32 | 7 | rs568471 | T/C | RNU4-74P | upstream | 1.82E-04 | 1.15E-02 | 6.57E-05 | 0.95 | 3.64E-02 |
| 35 | 8 | rs4734176* | G/A | EMC2 | intronic | 1.98E-04 | −8.13E-03 | 6.63E-05 | 1.04 | 3.66E-02 |
| 37 | 8 | rs10875482 | C/T | TSNARE1 | intronic | 3.05E-04 | −7.40E-03 | 9.96E-12 | 0.94 | 4.49E-02 |
| 39 | 10 | rs11001489* | G/A | C10orf11:RP11-367B6.2 | ncRNA_intronic | 2.24E-04 | 1.20E-02 | 3.41E-05 | 0.94 | 3.73E-02 |
| 41 | 11 | rs2582894 | G/T | RP11-22P4.1 | intergenic | 1.18E-04 | −1.03E-02 | 1.78E-05 | 0.95 | 2.51E-02 |
| 42 | 11 | rs6591434 | G/A | RP11-734C14.2 | intergenic | 2.76E-04 | −7.78E-03 | 8.61E-08 | 1.05 | 4.24E-02 |
| 43 | 11 | rs484201 | T/C | MACROD1 | intronic | 2.53E-04 | −7.41E-03 | 4.44E-06 | 1.04 | 4.02E-02 |
| 45 | 11 | rs7948931 | C/T | DLG2 | intronic | 6.60E-05 | 8.08E-03 | 1.44E-05 | 1.04 | 1.74E-02 |
| 46 | 11 | rs61123830 | A/G | GRAMD1B | intergenic | 4.25E-05 | 8.90E-03 | 7.09E-05 | 0.96 | 3.80E-02 |
| 48 | 12 | rs10860964 | C/T | RP11-328J6.1 | intergenic | 2.82E-05 | 8.59E-03 | 6.39E-09 | 0.95 | 1.01E-02 |
| 49 | 12 | rs7313797 | C/T | KCTD10 | UTR5 | 1.55E-04 | −7.58E-03 | 9.48E-05 | 0.97 | 4.42E-02 |
| 50 | 12 | rs2464196 | A/G | HNF1A | exonic | 2.40E-04 | 8.05E-03 | 7.43E-05 | 1.04 | 3.89E-02 |
| 51 | 12 | rs79478560 | A/G | DNAH10 | intronic | 4.63E-06 | −9.53E-03 | 3.89E-07 | 1.05 | 3.11E-03 |
| 53 | 14 | rs17522122 | T/G | AKAP6 | intergenic | 2.59E-04 | −7.34E-03 | 1.08E-10 | 1.06 | 4.08E-02 |
| 56 | 15 | rs8035957 | C/T | RASGRP1 | intronic | 1.63E-05 | −9.85E-03 | 8.35E-06 | 1.04 | 1.12E-02 |
| 57 | 15 | rs12905223 | C/T | UBE2Q2P1:LINC00933 | ncRNA_exonic | 1.01E-04 | −8.68E-03 | 1.69E-09 | 0.94 | 2.28E-02 |
| 60 | 16 | rs116001925 | T/C | RP11-439I14.3 | intergenic | 1.05E-05 | 1.88E-02 | 5.17E-05 | 0.92 | 3.21E-02 |
| 61 | 16 | rs61733486 | T/C | PRMT7 | exonic | 2.40E-04 | −1.58E-02 | 2.87E-06 | 1.09 | 3.89E-02 |
| 62 | 16 | rs78004870 | T/G | FANCA | exonic | 1.40E-06 | 1.05E-02 | 3.27E-06 | 0.96 | 6.13E-03 |
| 63 | 17 | rs6502219 | C/T | ARHGAP44 | intronic | 1.44E-05 | 9.38E-03 | 6.60E-06 | 1.04 | 9.66E-03 |
| 64 | 17 | rs11263770 | A/G | MYO19 | intergenic | 5.99E-05 | −8.03E-03 | 4.83E-06 | 0.96 | 1.64E-02 |
| 65 | 17 | rs6504584 | T/G | CALCOCO2 | UTR3 | 6.16E-05 | 8.42E-03 | 3.31E-05 | 0.96 | 2.51E-02 |
| 67 | 19 | rs8103241 | G/A | NFIX | intronic | 2.36E-05 | 8.43E-03 | 5.07E-05 | 0.97 | 3.17E-02 |
| 70 | 20 | rs6020924* | T/G | KCNG1 | intergenic | 5.90E-06 | 1.30E-02 | 5.97E-05 | 0.95 | 3.46E-02 |
Note: The most strongly associated SNPs in independent genomic loci shared between SCZ and vitD at conjFDR < 0.05. Chromosomal position (Chr), nearest gene, and functional category, as well as P values and effect sizes (Odds ratio and Beta for SCZ and Vitamin D, respectively) from original summary statistics. The effect allele is A1. Novel for SCZ marked with *.