Resources

Dataset

CRISPRi + scRNAseq

README (see README_scCRISPRi_HUDEP_Ilboudo_etal.txt) and count table (see scCRISPRi_HUDEP_Ilboudo_etal.txt) for “CRISPRi + scRNAseq for regulators of fetal hemoglobin in HUDEP-2 (Ilboudo et al.)”

Atrial fibrillation and sinus rhythm

Left atrial appendage bulk RNAseq count tables of atrial fibrillation and sinus rhythm patients from a European dominant cohort (CTSN) and East Asian cohort (Harbin).

CTSN
counts.ctsn.tsv meta.ctsn.tsv
Harbin
counts.harbin.tsv meta.harbin.tsv
LINC01629_KD
counts.LINC01629_KD.tsv meta.LINC01629_KD.tsv

Blood pressure pLoF variants (UKB)

GWAS summary statistics of pLoF variants association with systolic and diastolic blood pressure in UKB reported in this article:

  • Association analyses of predicted loss-of-function variants prioritized 15 genes as blood pressure regulators, Canadian Journal of Cardiology 2023
Systolic blood pressure Diastolic blood pressure
WES pLoF 200k discovery UKB cohort (additive and recessive) file file
WES pLoF 300k replication UKB cohort (additive and recessive) file file
WES pLoF whole 500k UKB cohort (additive and recessive) file file
WES pLoF whole 500k UKB cohort (gene-based test) file file

Blood Cell Consortium (BCX)

Summary association data (see readme_BCX2_meta_analyses.txt), fine-mapping results (see readme_BCX2_CS95_VEP.txt) and g-chromVar enrichment results (see readme_BCX2_gchromVAR_5Sept2019.txt) reported in the following article:

  • Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations, Cell 2020

MR-MEGA GWAMA
Trans-ethnic Trans-ethnic European East-Asian African Hispanics/Latinos
Red blood cells red blood cell count (RBC count) file file file file file file
hemoglobin concentration (HGB) file file file file file file
hematocrit (HCT) file file file file file file
mean corpuscular hemoglobin (MCH) file file file file file file
mean corpuscular volume (MCV) file file file file file file
mean corpuscular hemoglobin concentration (MCHC) file file file file file file
RBC distribution width (RDW) file file file N.A. file file
White blood cells total white blood cell count (WBC count) file file file file file file
neutrophil count (Neutro) file file file file file file
lymphocyte count (Lympho) file file file file file file
monocyte count (Mono) file file file file file file
basophil count (Baso) file file file file file file
eosinophil count (Eosin) file file file file file file
Platelets platelet count (PLT count) file file file file file file
mean platelet volume (MPV) file file file file file file
Fine-mapping results (95% credible sets) BCX2_CR95_VEP.zip
G-chromVar enrichment results CS.trans_all.PP01.strong_atac_overlap.tsv
CS.trans_subancestry.PP01.strong_atac_overlap.tsv

Summary ExomeChip association data (for more information, see readme2.txt) reported in the following article:

  • Rare coding variants pinpoint genes that control human hematological traits, PLoS Genet 2017
Red blood cellsred blood cell count (RBC count)meta_rare_rbc.txt.gz (3.3MB)
hemoglobin concentration (HGB)meta_rare_hgb.txt.gz (3.4MB)
hematocrit (HCT)meta_rare_hct.txt.gz (3.4MB)
mean corpuscular hemoglobin (MCH)meta_rare_mch.txt.gz (3.3MB)
mean corpuscular volume (MCV)meta_rare_mcv.txt.gz (3.3MB)
mean corpuscular hemoglobin concentration (MCHC)meta_rare_mchc.txt.gz (3.3MB)
RBC distribution width (RDW)meta_rare_rdw.txt.gz (3.3MB)
White blood cellstotal white blood cell count (WBC count)meta_rare_wbc.txt.gz (3.4MB)
neutrophil count (Neutro)meta_rare_neutro.txt.gz (3.4MB)
lymphocyte count (Lympho)meta_rare_lympho.txt.gz (3.3MB)
monocyte count (Mono)meta_rare_mono.txt.gz (3.3MB)
basophil count (Baso)meta_rare_bas.txt.gz (3.2MB)
eosinophil count (Eosin)meta_rare_eos.txt.gz (3.2MB)
Plateletsplatelet count (PLT count)meta_rare_plt.txt.gz (3.4MB)
mean platelet volume (MPV)meta_rare_mpv.txt.gz (3.2MB)

Summary ExomeChip association data (for more information, see readme.txt) reported in the following articles:

  • Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits, Am J Hum Genet. 2016
  • Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases, Am J Hum Genet. 2016
  • Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals, Am J Hum Genet. 2016

African ancestryEuropean ancestryAll ancestries
Red blood cellBCX_RBC_AA.tar.gz (56.1MB)BCX_RBC_EA.tar.gz (61.1MB)BCX_RBC_ALL.tar.gz (67.3MB)
White blood cellBCX_WBC_AA.tar.gz (43.4MB)BCX_WBC_EA.tar.gz (48.3MB)BCX_WBC_ALL.tar.gz (56.5MB)
PlateletBCX_PLT_AA.tar.gz (15.8MB)BCX_PLT_EA.tar.gz (17.3MB)BCX_PLT_ALL.tar.gz (19.1MB)

Software

CRISPR Off-Target Tool

This script aims at finding off-targets in CRISPR/Cas9 experiments given a list of single-guide RNAs (sgRNAs).

Supplementary tables for Lessard S, Francioli L, Alfoldi J, Tardif JC, Ellinor PT, MacArthur DG, Lettre G, Orkin SH, and Canver MC. Human genetic variation alters CRISPR/Cas9 on- and off-targeting specificity at therapeutically implicated loci [PNAS 2017]

  • Supplementary data. List of individual aggregate off-target scores for samples from the 1,000 Genomes Project and their local scores. CFD: cutting frequency determination.
  • Supplementary data. List of individual aggregate off-target scores for samples from the French Canadian dataset and their local scores. CFD: cutting frequency determination.

KnockoutQT

This script (knockoutQT.rb) aims to find gene knockouts (KOs) and test their association with a given quantitative phenotype.

[Documentation]  [Ruby script]  [R script]