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).
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.
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:
- eQTLs are based on 534 individuals from ROSMAP and 16918 expressed genes
- mQTLs are based on 543 individuals from ROSMAP and 420103 CpG sites
- haQTLs are based on 561 individuals from ROSMAP and 26384 acetylation domains
Original xQTL Statistics (Oct 2017)
- SNP information (minor allele, position) is available here, and SNP MAF is available here.
- eQTLs declared significant after Bonferroni correction, and computed on 494 individuals from ROSMAP, can be dowloaded here and statistics for all tested eQTLs are here.
- mQTLs declared significant after Bonferroni correction, and computed on 468 individuals from ROSMAP and 420103 CpG sites, can be downloaded here and statistics for all tested mQTLs are here.
- haQTLs declared significant after Bonferroni correctiond, and computed on 433 individuals from ROSMAP and 26384 acetylation domains, can be downloaded here and statistics for all tested haQTLs are here.
- MATLAB code for our xQTL-weighted GWAS is here.
- Cell-specificity p-values for all eQTLs are based on 494 individuals from ROSMAP and 13484 expressed genes 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, based on 502 individuals from ROSMAP, 598 individuals from CMC, and 10961 expressed genes, are available here.
- Interaction effect p-values between GxE SNPs and transcription factor expression are available here.