Supplementary Datasets for Margoliash et al. 2023

This page contains links to the supplementary dataset files for

Margoliash, Jonathan, et al. “Polymorphic short tandem repeats make widespread contributions to blood and serum traits.” bioRxiv (2022): 2022-08.

The supplementary datasets are:

STR association tests, by population and phenotype

The README for these association files is here.
Association statistics referred to in the text 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 association tests.

The URL for each population, phenotype pair is of the form:

https://margoliash-et-al-2023.s3.amazonaws.com/associations/{population}_{phenotype}_str_gwas_results.tab.gz

Populations are:

• white_british
• black
• south_asian
• chinese
• irish
• white_other

Phenotypes are written exactly as listed in Supplementary Table 1.

We filtered STRs with total minor allele dosage less than 20. This amounted to very few STRs for each population, phenotype combination. A list of those STRs (if any) is available at the URL:

https://margoliash-et-al-2023.s3.amazonaws.com/associations/{population}_{phenotype}_str_gwas_results.filtered.tab

SNP and indel association tests, by phenotype

These files were generated using plink2. The columns are described here. The L100 and U100 columns are actually the lower and upper bounds of the 100*(1-5e-8) confidence intervals, but that is rounded to 100 in the column name.

The URL for each phenotype is of the form:

https://margoliash-et-al-2023.s3.amazonaws.com/associations/white_british_{phenotype}_snp_gwas_results.tab.gz

Note that SNP association testing was only performed in the White British population.

Tarballs of fine-mapping outputs by phenotype

Each tarball contains two summary tables: finemapping_first_pass.tab and finemapping_followup.tab, describing the results from standard fine-mapping runs and followup fine-mapping runs under alternate conditions, respectively. Additionally, each tarball contains all the raw fine-mapping outputs for each fine-mapping run for both SuSiE and FINEMAP. Note that fine-mapping was only performed in the White British population.

The README for these files is here.

The URL for each phenotype is of the form:

https://margoliash-et-al-2023.s3.amazonaws.com/finemapping/finemapping_{phenotype}.tgz