a specific exon representing transcript variant 4 (NM_020211, encoding RGMa isoform 3). Similarly, exon ENSE00001304160, specifically represents transcript variant 2 (NM_001166286, encoding RGMa isoform 2). Only ENSE00001532613, representing transcript variant 4, was variably expressed among the 11 tissues studied, and cerebellum was the only brain tissue with both the lowest expression and with the lowest gene-exon residual regression score for RGMA (Figure 3A and 3B). Further correlation analysis between rs12442183 genotype and the gene-exon expression residual scores of the four exons revealed that only ENSE00001532613 (representative of transcript variant 4) was differentially expressed (P=2×10-3) among rs12442183*T risk allele carriers in frontal cortex (Figure 3C). Among the other nine brain tissues, there were no significant correlations between rs12442183 genotype and gene-exon residual scores (data not shown). We also tested whether rs12442183 was an eQTL in LCLs across 6 global populations, including CEU, YRI, LWK, MEX, CHB and JPT, but found no significant associations (all linear model P-values >0.05), indicating that rs12442183 may be a specific eQTL for RGMA transcript variant 4 (encoding RGMa isoform 3) in frontal cortex.
