The strongest signal on chromosome 13 was from rs75168521, a non-coding intergenic SNP downstream of SLITRK5 (SLIT and NTRK like family member 5); there was no evidence that rs75168521 is an eQTL for SLITRK5 or any other gene. rs75168521 is a perfect LD proxy for rs78886294 which was also genome-wide significant. Both SNPs were also in high D’, but low r2 (D’=1; r2=0.33) with numerous SNPs in the 3’ region of MIR4500HG with the closest SNP being 108 bp from rs75168521. The SNP rs75168521 made chromatin contact with MIR4500HG in bladder, liver and the left ventricle (although the gene is only appreciably expressed in the liver). Several additional distal points of contact were also identified (Supplemental Figure S4). Conditional analyses of the lead variants on chromosomes 3, 5 and 13 indicated that the remaining genome-wide significant SNPs did not represent additional independent loci on each chromosome (Supplemental Figure S5A – S5C). However, additional SNPs in the region did show p-values indicative of potential independent signals that might be clarified with increase in sample size.
