Note: GWASs were conducted using dosages in UKBB r2 on all HRC-imputed UKBB markers with minor allele counts >= 20 and information score >= 0.3 on 408,961 samples with White British ancestry. 

The summary statistics are for ALT allele.
For more details about the analysis, please check the manuscript:

Zhou, Wei, Jonas B. Nielsen, Lars G. Fritsche, Rounak Dey, Maiken E. Gabrielsen, Brooke N. Wolford, Jonathon LeFaive et al. "Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies." Nature genetics 50, no. 9 (2018): 1335-1341.

PheWeb to browse results: http://pheweb.sph.umich.edu/SAIGE-UKB/

ICD codes mapped to PheCodes for each phenotype are listed in the file: phecode-icd-map-ukb.txt 

Update log:

November 24, 2017
We have updated the GWAS summary statistics because of the beta column is missing in the previous version
Please use the urls in the table SAIGE_UKBiobank_URL_Nov2017_v3.xlsx to download results

Frbruary 18, 2018
We have removed GWAS summary statistics and plots for 120 sex-specific phenotypes in HRC-SAIGE-sexSpecificTraits.txt, due to mistakes when constructing these phenotypes.

Frbruary 27, 2020
We have re-run SAIGE on the 120 sex specific traits.