Home Advanced search Download Tutorial


The SNPxGE2 database contains the computationally predicted human SNP-coexpression associations, that is, the differential co-expression between 2 genes is associated with the genotype of an SNP. This data was generated from a large scale association study that was based on the HapMap data, which covered 269 individuals from 4 human populations, 556,873 SNPs and 15,000 gene expression profiles. In order to reduce the computational cost, the SNP-coexpression associations were assessed using gap/substitution scores instead of logistic regression models. The implementation was carried out using 128 Linux cluster nodes in ~30 days and assessed a total of ~1013 SNP-expression-expression combinations. The database can be queried via either gene symbols or reference SNP IDs. For each association, a detailed information page is provided.

Citation: Wang Y et al. (2012) SNPxGE2: a database for human SNP-coexpression associations. Bioinformatics, 28 (3): 403-410..


Yupeng wang. E-mail: wyp1125@gmail.com.

Search for SNP-coexpression associations by gene symbol(s) or ref SNP ID(s): example



Population # of SNPs # of expression profiles # of SNP-coexpression associations
CEU 407,733 15,000 9,522
CHB 360,109 15,000 1,427
JPT 347,415 15,000 474
YRI 481,321 15,000 33,346
Pooled 556,873 15,000 50,792