Mapping Genetic Variants to Brain Traits

Parameters were set as described above and eQTLs in 10 brain tissues from GTEx. Chromatin interaction mapping was performed using Hi-C data of two brain regions; hippocampus and prefrontal cortex. The extended MHC region (25–34 Mb), Chromosome X and indels were excluded from this analysis. The input GWAS summary statistics are based on the discovery phase and not all reported lead SNPs from the combined results of discovery and replication phases reached genome-wide significance. To include all reported lead SNPs, 111 non-indel lead SNPs were provided to FUMA and additional independent lead SNPs were identified at P < 5e-8 (Supplementary Data 14). Only protein-coding genes were used in mappings and enrichment of DEG in 53 tissue types, Canonical Pathways and GO terms were tested.

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Watanabe K., Taskesen E., van Bochoven A, & Posthuma D. (2017). Functional mapping and annotation of genetic associations with FUMA. Nature Communications, 8, 1826.

Publication 2017

Brain Chromatin Chromosome x Genome Gwas Hippocampus Indel Prefrontal cortex Protein genes Replication Snps Tissue types Tissues

Corresponding Organization :

Other organizations : Vrije Universiteit Amsterdam

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