Online Resource 2: supplementary result tables

The 26 numbered CSV files contain the supplementary results. INDEX.csv gives the number of data rows, a description and the original project source of each table. Source paths record provenance; they are not links within this ZIP. Study metadata are in ARTICLE_INFORMATION.txt.

01–03: primary screen, forward sensitivity and reverse MR.
04–05: colocalization priors and variant posteriors.
06–09: multivariable MR, conditional strength and LD.
10–12: related CD3 gates and shared instruments.
13–14: CD247 expression MR and observational expression comparisons.
15–16: Steiger prevalence and reliability sensitivity.
17–18: external outcomes using available and common instruments.
19–20: leave-one-out results and harmonization quality control.
21–24: archived secondary MR estimators and diagnostic results.
25–26: phenotype selection and the earlier positional-pruning MVMR sensitivity.

The primary screen uses the same 73-trait Benjamini–Hochberg family under both IVW variance conventions. For CD3 on CD39-positive resting CD4 regulatory T cells, the original FDR is 0.042 and the variance-floor FDR is 0.084; these estimates use the same data. Follow-up P values are exploratory. Reverse-MR coefficients describe continuous immune traits, whereas forward odds ratios describe ALS susceptibility. Expression results include within-study and across-study corrections.

Files 21–24 preserve the original diagnostic outputs; they are not additional reruns of the final analysis. Methods and figure legends are in Online Resource 1. Reproduction scripts and their supported inputs are in Online Resource 3.
