Table 2 Summary of the SMR analyses across the 13 brain regions.

From: Mendelian randomization integrating GWAS and eQTL data revealed genes pleiotropically associated with major depressive disorder

Regions Number of genes Top probe Tope gene CHR Top SNP PSMR Q_value
Amygdala 5 ENSG00000186470.9 BTN3A2 6 rs9393703 3.08 × 10−7 2.40 × 104
Anterior cingulate cortex 5 ENSG00000186470.9 BTN3A2 6 rs28551159 2.46 × 107 3.40 × 104
Caudate 7 ENSG00000186470.9 BTN3A2 6 rs9379853 7.76 × 108 1.62 × 104
Cerebellar hemisphere 21 ENSG00000227207.2 RPL31P12 1 rs1460943 7.53 × 1011 1.97 × 107
Cerebellum 30 ENSG00000227207.2 RPL31P12 1 rs1460943 1.34 × 1012 5.03 × 109
Cortex 7 ENSG00000219392.1 RP1-265C24.5 6 rs2295594 6.13 × 108 1.42 × 104
Frontal cortex 4 ENSG00000186470.9 BTN3A2 6 rs9379853 2.20 × 107 3.78 × 104
Hippocampus 3 ENSG00000186470.9 BTN3A2 6 rs9393703 5.32 × 107 5.90 × 104
Hypothalamus 3 ENSG00000186470.9 BTN3A2 6 rs72841536 5.34 × 107 6.25 × 104
Nucleus accumbens 3 ENSG00000219392.1 RP1-265C24.5 6 rs4713135 1.63 × 108 2.91 × 105
Putamen 2 ENSG00000186470.9 BTN3A2 6 rs9379853 3.41 × 107 4.95 × 104
Spinal cord 2 ENSG00000186470.9 BTN3A2 6 rs71557332 1.72 × 107 1.58 × 104
Substantia nigra 1 ENSG00000186470.9 BTN3A2 6 rs28551159 4.42 × 106 2.92 × 103
  1. Number of genes means the number of statistically significant genes in each region after correction for multiple testing using false discovery rate (Q value < 0.05); top probe and gene is the probe and the corresponding gene having the smallest PSMR in the region; top SNP is the top associated cis-eQTL for the corresponding probe in the eQTL analysis; PSMR is the P-value for SMR analysis.
  2. CHR chromosome, SNP single-nucleotide polymorphism, SMR summary data-based Mendelian randomization, QTL quantitative trait loci.