This is a resource for assessing the impact of genetic variation on multiple types of molecular traits derived from the human brain cortex:
Data underlying this project were generated from the ROS and MAP studies (available through Synapse) and the CommonMind Consortium (CMC).
Gene expression quantitative trait loci (eQTLs) are based on 494 individuals from ROSMAP, and 13484 expressed genes.
DNA methylation quantitative trait loci (mQTLs) are based on 468 individuals from ROSMAP, and 420103 methylation sites.
Histone acetylation quantitative trait loci (haQTLs) are based on 433 individuals from ROSMAP, and 26384 acetylation domains.
Context-specific eQTLs based on 502 individuals from ROSMAP and 598 individuals from CMC, and 10961 expressed genes.
Ng B, White CC, Klein H, Siebert SK, McCabe C, Patrick E, Xu J, Yu L, Gaiteri C, Bennett D, Mostafavi S*, De Jager PL*. “An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome.” Nature Neuroscience. 2017.
The combined results for our xQTL analyses, as well as matlab code for our xQTL-weighted GWAS, are below:
SNP information (minor allele, position) is available here, and SNP MAF is available here.
eQTL associations, passing Bonferroni threshold, data can be dowloaded here and genome-wide association statistics are here.
mQTL associations, passing Bonferroni threshold, can be downloaded here and genome-wide associations statistics are here.
haQTL associations, passing Bonferroni threshold, can be downloaded here and genome-wide association statistics are here.
Cell-specificity p-values for all eQTLs are available here.
Pathway annotations for latent variables derived from ROSMAP and CMC expression are available here.
Correlations between ROSMAP-CMC latent variables and ROSMAP phenotype variables are available here.
GxE eQTLs from a meta-analysis of ROSMAP and CMC samples are available here.
Interaction effect p-values between GxE SNPs and transcription factor expression are available here.