The UK Biobank resource with deep phenotyping and genomic data.

Summary of the UK Biobank resource and genotyping array content.Summary of the major components of the UK Biobank resource. See Extended Data Table 1 for more details. The figure also shows a schematic representation of the different categories of content on the UK Biobank Axiom genotype array. Numbers indicate the approximate count of markers within each category, ignoring any overlap. A more detailed description of the array content is available in the UK Biobank Axiom Array Content Summary2.

Summary of genotype data quality and content.All plots show properties of the UK Biobank genotype data after applying quality control. a, MAF distribution based on all samples (805,426 markers). The inset shows rare markers only (MAF < 0.01). b, The distribution of the number of batch-level quality control (QC) tests that a marker fails (see Methods). For each of four MAF ranges, we show the fraction of markers that fail the specified number of batches. c, Comparison of MAF in UK Biobank with the frequency of the same allele in ExAC, among the European-ancestry participants within each study (Supplementary Information). This analysis used 91,298 overlapping markers. Each hexagonal bin is coloured according to the number of markers falling in that bin (log10 scale). The dashed red line shows x = y. The markers with very different allele frequencies seen on the top, bottom and left-hand sides of the plot comprise approximately 300 markers. This is 0.3% of all markers in the comparison (see Supplementary Information for discussion). d, Mean log2 ratios (L2R) on X and Y chromosomes for each sample, indicating probable sex chromosome aneuploidy (see Methods). There are 652 samples with a probable sex chromosome aneuploidy (indicated by crosses). Locations of clusters of individuals with different putative karyotypes are indicated by Greek symbols: λ = X0 (or mosaic XX/X0), θ = XXX, α = XXY, and π = XYY. Counts of individuals in these regions are given in Supplementary Table 2. The colours indicate different combinations of self-reported sex, and sex inferred by Affymetrix (from the genetic data). For almost all samples (99.9%), the self-reported and the inferred sex are the same, but for a small number of samples (378) they do not match (see Supplementary Information for discussion).

Ancestral diversity and familial relatedness.a, Each point represents a UK Biobank participant (n = 488,377 samples) and is placed according to their principal component (PC) scores in each of the top four principal components. Colours and shapes indicate the self-reported ethnic background of each individual. See Extended Data Table 3 for proportions in each category. b, Distribution of the number of relatives that participants have in the UK Biobank cohort. The height of each bar shows the count of participants (log10 scale) with the stated number of relatives. The colours indicate the proportions of each relatedness class within a bar. c, Examples of family groups within the UK Biobank cohort. Points represent participants, and coloured lines between points indicate their inferred relationship (for example, blue lines join full siblings). The integers show the total number of family networks in the cohort (if more than one) with that same configuration, ignoring third-degree pairs.

Association statistics for human height.Results (P values) of association tests between human height and genotypes using three different sets of data for chromosome 2. In a–c, P values are shown on the −log10 scale, capped at 50 for visual clarity and uncorrected for multiple comparisons. Markers with −log10(P) > 50 are plotted at 50 on the y axis and shown as triangles rather than dots. Horizontal red lines denote P = 5 × 10−8. a, Results for published meta-analysis by GIANT32 (n = 253,288), with NCBI GWAS catalogue markers superimposed in red (plotted at the reported P values). b, Association statistics (from linear mixed model, see Methods) for UK Biobank markers in the genotype data (n = 343,321). c, Association statistics (from linear mixed model, see Methods) for UK Biobank markers in the imputed data (n = 343,321). Points coloured pink indicate genotyped markers that were used in pre-phasing and imputation. This means that most of the data at each of these markers comes from the genotyping assay. Black points (the vast majority, ~8 million) indicate fully imputed markers. d, Venn diagram of the results of counting the number of 1-Mb windows with at least one locus with P < 5 × 10−8 in the GIANT, UK Biobank genotyped and UK Biobank imputed datasets (see Methods). Percentages in brackets are the proportion of the union of such windows across all three data sources (1,215). There were only three windows contained in UK Biobank genotyped data and not the imputed data. e, Comparison of Z-scores in UK Biobank (y axis) and GIANT (x axis). Z-scores were calculated as effect size divided by standard error, but only for markers with P < 5 × 10−8 in GIANT, for a set of 575 associated regions, which we also used for the credible set analysis (see Methods). The marker with the smallest P value (in GIANT) within each region is highlighted with blue circles. The black dotted line shows x = y, and the red solid line shows the linear regression line estimated on these data. The standard error of the regression coefficient is shown in brackets. Pearson’s correlation was used to calculate the r2 value.