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| 1 | +# Supplementary Tables |
| 2 | + |
| 3 | +- **Table S1**: ColocBoost xQTL-only colocalization and AD-xQTL colocalization results. |
| 4 | + - *TableS1_ROSMAP_xQTL_only_colocboost_export.bed*: colocalization results for 17 xQTL-only in ROSMAP corhorts |
| 5 | + - *TableS1_ROSMAP_eQTL_only_colocboost_export.bed*: colocalization results for 10 eQTL-only in ROSMAP corhorts |
| 6 | + - *TableS1_ROSMAP_bulk_only_colocboost_export.bed*: colocalization results for 3 bulk-only in ROSMAP corhorts |
| 7 | + - *TableS1_ROSMAP_pseudo_bulk_only_colocboost_export.bed*: colocalization results for 6 pseudo-bulk-only in ROSMAP corhorts |
| 8 | + - *TableS1_GTEx_brain_eQTL_only_colocboost_export.bed*: colocalization results for 13 brain eQTL-only GTEx cohorts |
| 9 | + - *TableS1_AD_Bellenguez_ROSMAP_xQTL_colocboost_export.bed*: colocalization results for AD Bellenguez GWAS with 17 xQTL in ROSMAP corhorts |
| 10 | +- **Table S2**: Significantly enriched pathways for genes underlying neuron- and microglia-specific colocalizations. |
| 11 | +- **Table S3**: GTEx eQTL from 13 bulk brain tissues. |
| 12 | +- **Table S4**: ColocBoost 95% CoS-gene links validated by two CRISPRi data. |
| 13 | +- **Table S5**: List of annotations used in S-LDSC. |
| 14 | +- **Table S6**: 57 complex diseases used in disease heritability enrichment analysis. |
| 15 | +- **Table S7**: 129 variants with MaxVCP>0.5 enriched in variants confidently fine‐mapped (PIP>0.95) in 94 UK Biobank traits and 930 Million Veteran Program (MVP) GWAS traits. |
| 16 | +- **Table S8**: Heritability enrichment analysis for AD GWAS in Bellenguez 2022 conditional on 97 baseline-LD annotations. |
| 17 | +- **Table S9**: Feature comparison of multi-trait colocalization methods (green: feature supported/allowed). |
| 18 | +- **Table S10**: Realistic cross-trait sharing patterns from genome-wide fine-mapping results from 62 FunGen-xQTL contexts by calculating how often signals overlapped among those contexts and then sampled from these observed overlap frequencies to define what subset of traits each simulated causal variant share. |
| 19 | + |
| 20 | +### Column Descriptions for Table S1. |
| 21 | + |
| 22 | +| Column Name | Type | Description | |
| 23 | +|-----------------------|-----------|-----------------------------------------------------------------------------| |
| 24 | +| `chr` | integer | Chromosome number | |
| 25 | +| `start` | integer | Genomic start coordinate (0-based) | |
| 26 | +| `end` | integer | Genomic end coordinate (1-based) | |
| 27 | +| `a1` | character | Effect allele | |
| 28 | +| `a2` | character | Reference allele | |
| 29 | +| `variant_ID` | character | Unique variant ID in format `chr:pos:ref:alt` for ROSMAP and `chr_pos_ref_alt_b38` for GTEx | |
| 30 | +| `gene_ID` | character | Ensembl gene ID | |
| 31 | +| `event_ID` | character | Trait combination that colocalizes within the same 95% colocalization confidence set (CoS). | |
| 32 | +| `cos_ID` | character | Unique identifier for each 95% colocalization confidence set (CoS). | |
| 33 | +| `vcp` | double | Variant Colocalization Probability—estimated probability that a variant is shared among colocalized traits. | |
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