Reference Panels

Our server offers imputation from the following reference panels:

HRC (Version r1.1 2016)

The HRC panel consists of 64,940 haplotypes of predominantly European ancestry.

Number of Samples 32,470
Sites (chr1-22) 39,635,008
Chromosomes 1-22, X
Website; HRC r1.1 Release Note

1000 Genomes Phase 3 (Version 5)

Phase 3 of the 1000 Genomes Project consists of 5,008 haplotypes from 26 populations across the world.

Number of Samples 2,504
Sites (chr1-22) 49,143,605
Chromosomes 1-22, X

Genome Asia Pilot - GAsP

Number of Samples 1,654
Sites (chr1-22) 21,494,814
Chromosomes 1-22

Genome Asia v2 - GAsP

Number of Samples 6,461
Sites (chr1-22) -
Chromosomes 1-22

Four-digit Multi-ethnic HLA v1 (2021)

The multi-ethnic HLA panel consists of 36,586 haplotypes of five global populations. We have released the panel at both two-field (four-digit) and G-group resolution.

Number of Samples 18,293
Sites (chr6) 56,310 (1,781 HLA alleles; 4,513 HLA amino acids; 10,924 SNPs within HLA; 39,092 scaffold SNPs)
Chromosomes 6:28,000,000-34,000,000

Please cite this manuscript if you would like to include imputed results from the panel in your work:

Luo, Y., Kanai, M., Choi, W., Li, X., Yamamoto, K., Ogawa, K., Gutierrez-Arcelus, M., Gregersen, P. K., Stuart, P. E., Elder, J. T., Fellay, J., Carrington, M., Haas, D. W., Guo, X., Palmer, N. D., Chen, Y.-D. I., Rotter, J. I., Taylor, K. D., Rich, S., … Raychaudhuri, S. (2020). A high-resolution HLA reference panel capturing global population diversity enables multi-ethnic fine-mapping in HIV host response.

Four-digit Multi-ethnic HLA v2 (2022)

Number of Samples 20,349
Sites (chr6) 22,733 (570 HLA alleles; 3,449 HLA amino acids; 4,023 SNPs within HLA; 14,691 scaffold SNPs)
Chromosomes 6:27,970,031-33,965,553

Multi-ethnic HLA v2 Details


  • We added Japanese samples with HLA alleles called with deep target sequencing (n = 723; Hirata et al. Nat Genet. 2019).
  • Add Estonian biobank samples with IRB approval (n = 2,233; Mitt et al. Eur J Hum Genet. 2017).

HLA alleles:

  • We used gold-standard HLA allele calls (instead of inferred calls from whole genome sequencing) when possible.
  • We updated and recalled HLA alleles using HLA-LA (Dilthey et al. Bioinformatics. 2019) in Jackson Heart Study (n = 3,026).
  • We updated and recalled HLA alleles using HLA-LA in Estonian Biobank (n = 2,233).

Scaffold variants:

  • We added population-specific SNP variants which are common in one population but rare in the other populations when they are in 1KG and pass QC, by cross-cohort SNP imputation within the reference panel.
  • We removed all SNP variants that are not included in the commonly-used genotyping arrays.

Minimac4 options:

  • We optimized --probThreshold, --diffThreshold, --topThreshold parameters in minimac4. Optimized parameters are now used for all HLA panels.

Imputation results:

  • We output 2-digit and 4-digit-resolution HLA alleles. We do not output higher resolution HLA alleles in this version.

CAAPA - African American Panel

Whole genome sequences were available on 883 individuals from 19 case-control studies of asthma included in the Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) and were used to summarize the genomic contributions to individuals of African ancestry.

Number of Samples 883
Sites (chr1-22) 31,163,897
Chromosomes 1-22
Website Further details can also be found here

HRC (Version r1 2015)

This HRC panel consists of 64,976 haplotypes of predominantly European ancestry.

Number of Samples 32,488
Sites (chr1-22) 39,741,659
Chromosomes 1-22, X
Website; HRC r1 Release Note

1000 Genomes Phase 1 (Version 3)

Number of Samples 1,092
Sites (chr1-22) 28,975,367
Chromosomes 1-22, X

HapMap 2

Number of Samples 60
Sites (chr1-22) 2,542,916
Chromosomes 1-22