Welcome to Brain xQTLServe

This resource provides summary statistics on the impact of genetic variation on multiple types of molecular traits derived from the human brain cortex. The resource includes quantitative trait loci (QTLs) for gene expression (eQTLs), DNA methylation (mQTLs), and H3K27 histone acetylation (haQTLs). Data underlying this project were generated from the ROS and MAP studies (available through Synapse) and the CommonMind Consortium (CMC).

xQTL pipeline


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.

*co-senior authors


xQTL Analyses

Updated xQTL Statistics (June 2021)
Statistics for all tested xQTLs as well as xQTLs declared significant after Bonferroni correction can be downloaded by chromosome here. Updates include employing HRC to impute genotype data, increasing the number of subjects, applying a wider window (5Kb to 50Kb) for mQTL estimation, and using linear regression for xQTL estimation:
Original xQTL Statistics (Oct 2017)
GxE Analyses

Explore associations between SNPs and molecular traits in your browser!

You can query our data in two ways: by providing a (i) SNP rsID, or a (ii) gene symbol.

SNP Query

Query xQTL associations for a specific SNP.

SNP query »

Gene Query

Query SNPs associated with expression levels of a specific gene.

gene query »