Summary statistics for "Alternate approach to stroke phenotyping identifies a genetic risk locus for small vessel stroke"

Summary statistics of the GWA studies presented in https://doi.org/10.1101/718221

These are the summary statistics of all imputed SNPs, minus those that showed big differences in allele frequency between different populations (see manuscript for details).

Header description:

"rs_id" = the rs-id for the variant

"chromosome" = the chromosome of the variant

"base_pair_location" = the location in bases, according to human reference genome hg19

"effect_allele" = the allele that is tested for association with the phenotype

"other_allele" = the other allele

"effect_allele_frequency" = the allele frequency of the effect allele (not necessarily the minor allele frequency)

"IMPUTE2_info" = the imputation quality score as computed by IMPUTE2

"beta" = the beta-coefficient from BOLT-LMM

"standard_error" = the standard error of beta

"p-value" = the p-value for association from BOLT-LMM

To convert beta and standard error to odds ratios, you need to know the fraction of cases of the respective GWAS. These can be found in the supplementary material of the manuscript. Use the following formula with the case fraction μ: log OR = β / (μ * (1 - μ)). See the manuscript for more explanation.