Supplementary datasets for: Polymorphic short tandem repeats make widespread contributions to blood and serum traits

Short tandem repeats (STRs) are genomic regions consisting of repeated sequences of 1-6bp in succession. Single nucleotide polymorphism (SNP) based genome-wide association studies (GWAS) do not fully capture STR effects. To study these effects, we imputed 445,720 STRs into genotype arrays from 408,153 White British UK Biobank participants and tested for association with 44 blood phenotypes. Using two fine-mapping methods, we identify 119 candidate causal STR-trait associations and estimate that STRs account for 5.2–7.6% of causal variants identifiable from GWAS for these traits. These are among the strongest associations for multiple phenotypes, including a coding CTG repeat associated with apolipoprotein B levels, a promoter CGG repeat with platelet traits and an intronic poly-A repeat with mean platelet volume. Our study suggests that STRs make widespread contributions to complex traits, provides stringently selected candidate causal STRs, and demonstrates the need to consider a more ..., Please see the Cell Genomics article or biorXiv preprint for detailed methods.
Alternatively, the relevant portion of the methods from the paper have been pasted below, but lacking references and with some distortions due to the difficulty of copying mathematical formulae. For references to tables, figures, notes and the key resources table, please refer to the paper. 
Selection of UK Biobank participants
We downloaded the fam file and sample file for version 2 of the phased SNP array data (referred to in the UKB documentation as the ‘haplotype’ dataset) using the ukbgene utility (ver Jan 28 2019 14:09:15 - using Glibc2.28(stable)) described in UKB Data Showcase Resource ID 664 (see Key Resources Table). The IDs from the sample file already excluded 968 individuals previously identified as having excessive principal component-adjusted SNP array heterozygosity or excessive SNP array missingness after call-level filtering indicating potential DNA contamination. We further removed withdraw..., , # Supplementary Datasets for “Polymorphic short tandem repeats make widespread contributions to blood and serum traits.”, Margoliash et al. 2023

[https://doi.org/10.5061/dryad.z612jm6jk](https://doi.org/10.5061/dryad.z612jm6jk)

Please see the manuscript for method details of how these datasets were produced. Alternatively, the relevant portion of the methods from the paper have been pasted into the methods section on this page, with some distortions due to the difficulty of copying mathematical formulae.

The two supplementary datasets are:

## STR association tests, by population and phenotype

These files are named `{population}_{phenotype}_str_gwas_results.tab.gz` Association statistics referred to in the paper are from the White British population unless otherwise specified. Association tests in the White British population were performed genome-wide, while STR association tests in the other populations were performed in fine-mapping regions identified by the White British associa...