This document lists a number of genotyped autosomal SNPs (65) which have been found to show significantly different allele frequencies between the UK BiLEVE array and the UK Biobank array. These SNPs are in the interim data release but should be excluded from analyses.

A number (27) of these SNPs were used in phasing and imputation. UKB strongly recommends conditioning on array in association tests to ameliorate the effect of these SNPs. There could still be a subtle bias in the neighbourhood of these SNPs after conditioning, but this will depend upon the phenotype being tested for association. UKB recommends looking carefully at any results with imputed SNPs in the regions of the affected SNPs, including confirming any GWAS hits with the genotyped-only data and looking at cluster plots of the genotype data.

Additionally, there are a number of SNPs (46) on chromosome X which show a significant allele frequency difference between males and females or show differences between arrays. UKB recommends that these SNPs be excluded from all analyses.

These SNPs were identified as those with a p-value less than 1E-40 in a Fisher exact test on genotype counts.

This resource is not suitable for displaying within a web-browser.
It can be downloaded or viewed using the link: UKBioBiLallfreqSNPexclude.dat

If you have wget available (typically on linux systems), then you can also obtain a copy using the command

 wget  -nd  biobank.ndph.ox.ac.uk/ukb/ukb/docs/UKBioBiLallfreqSNPexclude.dat