Supporting Information: Finnish LD creates a false shared atrial fibrillation and dementia locus

# Supporting Information: Finnish LD creates a false shared atrial fibrillation and dementia locus This archive accompanies the manuscript *"Finnish LD creates a false shared atrial fibrillationand dementia locus"* (Open Life Sciences). It contains the analysis code and the intermediateresult tables behind every number reported in the paper and its Supplementary Information. ## Contents | File | Size | Entries | Description ||---|---|---|---|| `10_Code_Supporting_Info.zip` | 0.20 MB | 78 | Analysis code. Top level `code/` holds 57 numbered scripts (Python 3.11 and R 4.6, numbered in execution order) plus four utility modules, and `code/sc/` holds the 16 single-cell extraction scripts. `MANIFEST.txt` explains the numbering. || `11_Results_Supporting_Info.zip` | 41.55 MB | 231 | Intermediate result tables, 230 data files plus `MANIFEST.txt`. Directory layout matches what the scripts write: `results/`, `results/ext/`, `results/rev/`, `results/sc/`, `results/eqtl/`. | Unzip both into the same directory so that `code/` and `results/` sit side by side; the scriptsaddress each other by relative path. ## What the result tables contain * `results/coloc_eqtl.csv` - 15,054 eQTL colocalisation tests (GTEx v8 cis-eQTL against FinnGen atrial fibrillation and dementia), the number quoted in the manuscript.* `results/sc/celltype_enrichment.csv` - the 216 single-cell enrichment tests.* `results/coloc_regions.csv` - the 168 colocalisation windows, one per AF locus, with PP.H0-H4 and the top variant in each.* `results/crosstrait_AF_loci.csv` - the 169 AF lead loci with their cross-trait concordance statistics.* `results/rev/` - LD-pruning and colocalisation-prior sensitivity tables, including `ld_1000g_fin.json`, `coloc_p12_sensitivity.json` and `conditional_remeasured.csv`.* `results/ext/` - per-variant windows for the external cohorts (Roselli atrial fibrillation, Bellenguez Alzheimer disease, Nalls Parkinson disease) that drive the 2 x 2 cohort-swap design. Large raw inputs are not redistributed here: the FinnGen release 13 summary statistics,1000 Genomes phase 3 phased genotypes, GTEx v8 cis-eQTL, the GWAS Catalog harmonised summarystatistics and the CELLxGENE atlases are all publicly available from their primary sources, andthe accession numbers are listed in the manuscript's Data Availability statement. ## Reproducing a number 1. Download the public inputs listed in the Data Availability statement.2. Unzip both archives into one working directory.3. Run the numbered scripts in order; each script writes the table it consumes into `results/`. `results/MANIFEST.txt` maps every file to the script that produces it. ## Versions Python 3.11, R 4.6. Package requirements are recorded in the header of each script. ## Licence Code and derived tables: CC BY 4.0 (see `LICENSE.txt`).