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. 2019 Oct 10;47(22):e146. doi: 10.1093/nar/gkz868

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Examples of novel candidate causal SNPs. (A) Example for autoimmune diseases. Known GWAS SNP rs773125, located on chromosome 12, has the strongest association with RA. However, this SNP was a negative call from our prediction and not located in active regulatory regions in any immune-related tissues. The two positive SNPs (rs773114 and rs1873914) were located in an active regulatory region of CD14+ monocyte and connected to RPS26 according to GM12878 capture Hi-C data (35). (B) Example for psychiatric disorders. rs150721234 has the strongest association strength with SCZ in the LD block located on chromosome 10. However, this SNP was a negative call from our prediction and not located in active regulatory regions in any brain-related tissues. Instead, there was a positive SNP (rs117885390) that showed a lower association strength with SCZ. Dorsolateral prefrontal cortex Hi-C data (38) located this SNP in an enhancer region of ITGB1. This site was an active regulatory region of the dorsolateral prefrontal cortex tissue.