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snp2hla website  

SNP2HLA is a tool to impute amino acid polymorphisms and single nucleotide polymorphisms in human luekocyte antigenes (HLA) within the major histocompatibility complex (MHC) region in chromosome 6.

Environment Modules

Run module spider snp2hla to find out what environment modules are available for this application.

System Variables

  • HPC_SNP2HLA_DIR - installation directory
  • HPC_SNP2HLA_BIN - executable directory


If you publish research that uses snp2hla you have to cite it as follows:

Xiaoming Jia*, Buhm Han*, Suna Onengut-Gumuscu, Wei-Min Chen, Patrick J. Concannon, Stephen S. Rich, Soumya Raychaudhuri, Paul I.W. de Bakker. "Imputing Amino Acid Polymorphisms in Human Leukocyte Antigenes." PLoS One. 8(6):e64683. 2013.

If you use the Pan-Asian reference panel, please cite the following papers:

1. Pillai NE et al. "Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations." Hum Mol Genet, [epub ahead of print doi:10.1093/hmg/ddu149. 2014.]

2. Okada Y et al. (2014) Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations. Hum Mol Genet, In press.