BrainMeta sQTL & eQTL portal

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, for sQTL mapping 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 for eQTL mapping using the same dataset. See “Tutorial” for the instructions to use this online portal. See “BESD files” for details to download the full sQTL or eQTL summary statistics in SMR binary (BESD) format.

Credits and Acknowledgements

Ting Qi (methods, data analysis and documentation), Hailing Fang (online tool and maintenance), Jian Yang (overseeing, methods, documentation, and maintenance). The online tool was developed based on the source code modified from PheWeb. We thank the Westlake University High Performance Computing Centre for hosting the online tool and the summary data.

Questions and Help Requests

If you have any question, please send an email to Jian Yang at or Ting Qi at


Ting Qi, Yang Wu, Hailing Fang, Futao Zhang, Shouye Liu, Jian Zeng, Jian Yang (2022) Genetic control of RNA splicing and its distinctive role in complex trait variation (under review).

This site was built with PheWeb version 1.3.15.

All positions are on GRCh37.