Multiple lines of evidence support this conclusion. First, the SH3BP5-NR2C2 region was the only genome-wide significant (both p<5×10-7 and FDR<0.05) as well as replicable region across whole genome. Second, this region was the only association peak throughout Chromosome 3 at p<0.0001 in meta-analysis (in which the association signals were majorly attributable to the EA sample). It is thus highly likely that the putative causal loci for alcohol and nicotine co-dependence were located within this region. Third, RNA secondary structure may affect RNA stability, RNA 3D structure, intron splicing, exon recognition, transcription level and translation efficiency. Many replicable risk SNPs in SH3BP5-NR2C2 had potentials to slightly (in SH3BP5 and NR2C2) to significantly (in ZFYVE20) alter the RNA secondary structures (Supplemental Table S2), which might further influence the function of proteins and eventually affect the risk for disease, providing additional evidence in support of the hypothesis that SH3BP5-NR2C2 per se contributes to alcohol and nicotine co-dependence. Fourth, all SNPs in this region among those 11 replicable risk markers available for eQTL analysis had nominal cis- and trans-acting regulatory effects on gene expression.
