| Variant List | Description | Labs | Files |
|---|---|---|---|
| Stanford FCC | Variants in enhancers in cardiovascular disease GWAS loci (coronary artery disease, congenital heart disease, pulmonary hypertension, etc.) that act in smooth muscle cells, endothelial cells, cardiomyocytes, or macrophages. Our variant-editing assays are focused on deep editing / mutagenesis of a small set of enhancers that contain high-confidence GWAS variants. | Thomas Quertermous, Stanford & Jesse Engreitz, Stanford | |
| Liver GWAS variants | For selected traits relevant to liver identify lead GWAS variants and their ancestry-relevant LD proxies (r2>.8) for MPRA. | Hyejung Won, UNC | |
| GWAS variants associated with LDL-C, HDL-C, CAD, BP, neutrophil counts, red blood cell traits | Variants are selected from largest available trans-ancestry meta-analyses. For each sentinel variants, we retrieve variants in strong LD (r2>0.8) using the 4 ancestral populations from TOPMed. We also had additional variants based on fine-mapping (PIP>0.1). Depending on locus, we subset variants based on functional annotations. | Luca Pinello, MGH | IGVFFI0132XPDE |
| GWAS variants associated with coronary artery disease in smooth muscle cell | CAD GWAS lead SNPs were LD-expanded and genes within +/- 500kb were interscted with gene expresssion and HiC data sets for smooth muscle cell type | Thomas Quertermous, Stanford & Jesse Engreitz, Stanford | |
| Allele Specific Binding/RegulomeDB | Allele-specific TF binding (ASB) SNVs Called with AlleleDB | Alan Boyle, UMich | |
| iPSC/Fibroblast eQTLs | eQTLs selected from scRNA studies in fibroblasts and iPSCs | Chongyuan Luo, UCLA | |
| Variants relevant to lipid levels | Comprehensive set of ~2500 variants in GWAS loci associated with lipid levels and that affect lipid handling in hepatocytes/HepG2 | Richard Sherwood, Brigham and Women's Hospital and Luca Pinello, MGH | |
| Functional variants in GM12878 | A set of 100 variants within 5 genomic regions in GM12878 that are predicted to be functional | Jie Liu, UMich | |
| Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution | Dense readout of variant effects of multiple disease related loci. | Martin Kircher, BIH | |
| Proximal promoter variants | Over 170K variants in 60K different promoter regions (excluding core promoter) across the genome. Variants where selcted via in-silico mutagenesis o a sequence based model (positive/negative and neutral prediction). Library will be tested in multile cell-lines. | Martin Kircher, BIH | |
| gnomAD variantions in CREs of neuro/heart disease associated genes (+ actionable genes) | Comprehensive annotation of all GnomAD variants in the designed regions. On rare variants we made a pre-seclection using Enformer to reduce the number. | Martin Kircher, BIH | |
| Coronary Artery Disease related variants | Coronary artery disease related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Diastolic Blood Pressure related variants | Diastolic blood pressure related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Hematocrit related variants | Hematocrit related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| HDL Cholesterol related variants | High density lipoprotein related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Hemoglobin related variants | Hemoglobin concentration related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| LDL Cholesterol related variants | Low density lipoprotein related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Mean corpuscular hemoglobin concentration related variants | Mean corpuscular hemoglobin concentration related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Mean corpuscular hemoglobin concentration related variants | Mean corpuscular hemoglobin related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Mean corpuscular volume related variants | Mean corpuscular volume related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Neutrophil numeration related variants | Neutrophil numeration related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Neutrophil percentage related variants | Neutrophil percentage related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Pulse pressure related variants | Pulse pressure related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Red Blood Cell count related variants | Red blood cell count related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Red cell distribution width related variants | Red cell distribution width related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Reticulocyte count related variants | Reticulocytes count related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Reticulocyte percentage related variants | Reticulocytes percentage related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Systolic Blood Pressure related variants | Systolic blood pressure related variants, either in LD with GWAS associated variants (r2>=0.8TOPMed, in white, black, east Asians or south east Asians) or finemapped. | Guillaume Lettre, MHI | |
| Lupus clinvar variants | Lupus variants submitted to clinvar | Anshul Kundaje, Stanford | |
| Lupus gwas variants | Multi-ancestry lupus variants identified through GWAS in EUR and EAS populations | Anshul Kundaje, Stanford | |
| Coronary Artery Disease gwas variants | Discovery and systematic characterization of risk variants and genes for coronary artery disease in over a million participants. Million vet data (MVP) and CARDIoGRAM+C4D (Aragam et al 2022) | Thomas Quertermous, Stanford & Jesse Engreitz, Stanford | |
| VarChamp variants phase 1 | Broad sample of ~16,000 variants from ClinVar encompassing all annotation classes and a range of diseases used in variant painting and yeast to hypbrid | CCSB, DFCI | |
| Psoriasis related variants | A list of 700 selected psoriasis GWAS variants | Maureen Sartor, UMich | |
| CAVA variants phase 1 | List of SNVs for genes identified for VAMP-seq and SGE MAVEs | Doug Fowler & Lea Starita, UW | |
| VAMP-seq and MULTI-step studies | A set of variants related explored using VAMP-seq and MULTI-step | Doug Fowler, UW | IGVFFI0740EUMM,IGVFFI4384NHDN |
| Chromosome X RBC IGVFDS2176XIDA | A set of variants explored with MAGeCK CRISPR in Red Blood Cells | Daniel Bauer, HSCI | IGVFFI7806CLOH |
This list is the proposed variant lists for IGVF. Submitted variant lists can be searched on the portal.