VIPRS

Variational Inference of Polygenic Risk Scores

Estimate genetic variant effect sizes from GWAS summary statistics and an LD reference, directly in your browser.

A Manhattan plot has clustered association peaks across 22 chromosomes, with hits at P below five times ten to the minus eight highlighted in coral. A six-variant LD matrix shows squared correlations. An arrow leads from these inputs to a bell-shaped distribution of polygenic scores with an illustrative upper-tail threshold. Scoring additionally requires individual genotypes; this application exports effect weights. All plotted data and the threshold are illustrative. GWAS summary statistics LD reference 04812 −log₁₀(P) 16121822 Chromosome P < 5 × 10⁻⁸ 112233445566 Variant 01 LD (r²) Polygenic score Downstream scoring with individual genotypes Threshold Standardized PRS
Summary statistics + LD → effect weights → PRS Illustrative data and threshold

02 · Reference data

LD reference

Local + cloud
UK Biobank LD referenceHapMap3

Choose the ancestry matching your GWAS. The hosted pattern selects all chromosomes.

hf://datasets/shz9/ukb-ld/EUR/chr_*.zip

Hosted archives are streamed on demand while fitting; they are not downloaded in full first. To select fewer chromosomes, use custom URLs or globs.

Dataset details

LD between HapMap3 variants from imputed UK Biobank genotypes, with approximately independent LD blocks. View dataset ↗

01 · GWAS data

Summary statistics

Enter a GCST accession. GRCh37/hg19 summary statistics are downloaded from the GWAS Catalog FTP server ↗ using parallel byte ranges when the server supports them.

Choose summary statistics independently of your LD source. Variants are matched to the reference before fitting.

Model

A point mass at zero and one Gaussian component for nonzero effects.

Optimization settings
Model previewGenetic architecture
1 spike + 1 slab

Illustrative distribution of effect sizes under the selected prior.

A point mass at zero and one centered Gaussian slab for nonzero genetic effects.
Spike · exactly zeroSlab · nonzero effects