Table 1.
p values for SNP-schizophrenia and SNP-mRNA expression associations
| “CACNA1C SNP - Schizophrenia” associations. | “SNP - CACNA1C mRNA” associations | Effect | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Europeans | Africans | Europeans | Europeans | direction | |||||||||||||
| Sample #1 | #2 | #3 | #4 | BRAINEAC | GTEx | of risk | |||||||||||
| Genomic | Risk | Case=1351 | 1044 | 621 (offspring) | Risk | 1195 | Effect | CRBL | FCTX | OCTX | TCTX | Effect | AMYL | ACC | or effect | ||
| Class | SNP | position (b36) | allele | Control=1378 | 2052 | 1205 (parents) | allele | 954 | allele | 138 | 138 | 138 | 138 | allele | 210 | 210 | alleles |
| #1 | rs2238096 | 2620174 | a | - | >0.05 | 0.021 | A | 0.047 | a | >0.05 | 1.6×10−3 | 0.022 | 0.050 | - | - | - | ↑↑- |
| #2 | rs10848680 | 2635439 | G | 0.005 | - | 0.020 | - | G | 0.020 | >0.05 | >0.05 | >0.05 | A | 0.050 | >0.05 | ↑↑↓ | |
| #2 | rs216047 | 2636121 | T | 1.8×10−4 | - | 0.013 | - | T | 0.024 | >0.05 | >0.05 | >0.05 | C | 0.035 | >0.05 | ↑↑↓ | |
| #2 | rs1894979 | 2637260 | G | 2.3×10−4 | - | 0.004 | - | G | 0.023 | >0.05 | >0.05 | >0.05 | A | 0.050 | >0.05 | ↑↑↓ | |
| #2 | rs3794291 | 2639926 | C | 0.048 | - | 0.007 | - | C | 0.026 | >0.05 | >0.05 | >0.05 | T | 0.035 | >0.05 | ↑↑↓ | |
| #2 | rs10161181 | 2640991 | A | - | >0.05 | 0.001 | a | 0.011 | A | 0.025 | >0.05 | >0.05 | >0.05 | - | - | - | ↑↑- |
| #2 | rs10161275 | 2641279 | T | 0.046 | >0.05 | 0.009 | - | T | 0.026 | >0.05 | >0.05 | >0.05 | - | - | - | ↑↑- | |
| #2 | rs11062298 | 2641970 | A | 0.039 | - | 0.001 | a | 0.015 | A | 0.029 | >0.05 | >0.05 | >0.05 | C | 0.050 | >0.05 | ↑↑↓ |
| #2 | rs11062299 | 2641999 | T | >0.05 | 0.011 | 0.002 | >0.05 | T | 0.029 | >0.05 | >0.05 | >0.05 | C | 0.050 | >0.05 | ↑↑↓ | |
| #2 | rs10848682 | 2642017 | C | >0.05 | 0.011 | 0.002 | - | C | 0.029 | >0.05 | >0.05 | >0.05 | G | 0.050 | >0.05 | ↑↑↓ | |
| #2 | rs10774052 | 2642432 | C | 0.039 | - | 0.002 | >0.05 | C | 0.036 | >0.05 | >0.05 | >0.05 | - | - | - | ↑↑- | |
| #2 | rs7315556 | 2644116 | G | >0.05 | 0.009 | 0.002 | - | G | 0.037 | >0.05 | >0.05 | >0.05 | A | 0.037 | >0.05 | ↑↑↓ | |
| #2 | rs7310079 | 2645738 | T | >0.05 | 0.027 | 0.044 | - | T | 0.034 | >0.05 | >0.05 | >0.05 | - | - | - | ↑↑- | |
| #3 | rs7306298 | 2647572 | A | - | 0.030 | 0.011 | - | - | - | - | - | - | A | >0.05 | 0.042 | ↑-↑ | |
| #3 | rs10744567 | 2651077 | G | >0.05 | 0.034 | 0.015 | - | - | - | - | - | - | G | >0.05 | 0.020 | ↑-↑ | |
| #3 | rs7136355 | 2653737 | C | - | 0.019 | 0.004 | - | - | - | - | - | - | C | >0.05 | 0.020 | ↑-↑ | |
| #3 | rs2302729 | 2654233 | C | - | 0.028 | 0.020 | >0.05 | - | - | - | - | - | C | >0.05 | 0.012 | ↑-↑ | |
Abbreviations: cerebellar cortex (CRBL), frontal cortex (FCTX), occipital cortex (OCTX), temporal cortex (TCTX), amygdale (AMYL), and anterior cingulate cortex (ACC). The italic bold lowercase risk allele is a major allele (f>0.5). #1, #2 and #3 are classified based on R2>0.85 within each class. ↑ and ↓, increase or decrease risk for disease, or mRNA expression level, referencing to the disease-risk alleles; “-”, missing.