We developed a method, THISTLE, which uses individual-level genotype and RNA-seq data or summary-level isoform-eQTL data for splicing QTL (sQTL) mapping (Qi et al. 2022). We applied THISTLE, in combination with a complementary sQTL mapping strategy, to map sQTLs using RNA-seq data of 2,865 brain cortex samples from 2,443 unrelated individuals of European ancestry with genome-wide SNP data. We also applied QTLtools to map eQTLs using the same dataset. See the “Tutorial” for the instructions on how to use this online portal. See the “BESD files” for details on downloading the full sQTL or eQTL summary statistics in SMR binary (BESD) format.
This portal also includes summary statistics and interactive visualizations of cis-eQTLs for long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in the human brain cortex. We mapped cis-eQTLs using linear regression in tensorQTL. Analyses used RNA-seq from 2,865 brain cortex samples from 2,443 unrelated individuals of European ancestry with genome-wide SNP data; for circRNAs, only rRNA-depleted cohorts (CMC, HBCC, BrainGVEx, ROSMAP) were included. See the “BESD files” page to download the full lncRNA and circRNA summary statistics in SMR binary (BESD) format.
• Ting Qi (methods, sQTL and eQTL mapping, documentation)
• Li Chen (ncRNA assembly, ncRNA eQTL mapping, documentation)
• Junren Hou (online tool development & maintenance)
• Hailing Fang (online tool development & maintenance)
• Jian Yang (conceptualization, supervision, methods, documentation)
We thank the Westlake University High-Performance Computing Center for hosting the portal and summary data. The portal adapts source code from PheWeb.
If you have any question, please send an email to Jian Yang at jian.yang@westlake.edu.cn, Ting Qi at qiting@westlake.edu.cn or Li Chen at chenli@westlake.edu.cn.
Chen L, et al. Genetic control of non-coding RNAs in the human brain and their implications for complex traits.. The American Journal of Human Genetics (2025).
Qi T, et al. Genetic control of RNA splicing and its distinct role in complex trait variation. Nature Genetics (2022).
All positions use GRCh37 (hg19). This site was built with PheWeb v1.3.15.