Fig. 4

An intragenic transcript of NRGN is influenced by a schizophrenia GWAS eQTL. a NRGN region overview with all the TSSs identified by CAGEseq. Here we identified 11 CAGE-clusters for the NRGN locus, nine sense and two antisense. Underlined in red is the NRGN_tss4 influenced by rs12807809, the highest associated SNP from the schizophrenia GWAS study Stefansson et al. [83]. b Zooming in on the actual transcription start site of NRGN_tss4 shows CAGEseq expression signal. Primers were designed based on the CAGEseq expression and on the first exon this resulted in part of a novel transcript in this NRGN locus. c Two boxplots showing the association of GWAS hit SNP rs12807809 and the SNP with the highest p value rs35306015 with the expression (log(tpm + 1)) of NRGN_tss4, respectively. For the GWAS hit rs12807809, the heterozygous carriers are clearly separated in two groups with 19 individuals showing the same expression pattern as the homozygotes AA while the remaining 13 carriers show the expression pattern of the homozygotes BB suggesting an underlying effect. This effect is not present for the rs35306015 variant. The minor allele frequency (MAF) for rs35306015 in our cohort (MAF = 0.076) is similar to the European frequency in 1000 Genomes. d Haplotypes drawn with Haploview using genotypes from all the 119 included individuals in this study. Note the specific haplotype with 8 % frequency for the 17 individuals presenting highest expression for NRGN_tss4, highlighted with a red bar. Of the 17 haplotype carriers, 16 are heterozygous and one homozygous. Black asterisks represent variants unique to this haplotype and in perfect linkage disequilibrium in our dataset