Supplementary Tables

Supplementary Tables#

  • Table S1: ColocBoost xQTL-only colocalization and AD-xQTL colocalization results.

    • TableS1_ROSMAP_xQTL_only_colocboost_export.bed: colocalization results for 17 xQTL-only in ROSMAP corhorts

    • TableS1_ROSMAP_eQTL_only_colocboost_export.bed: colocalization results for 10 eQTL-only in ROSMAP corhorts

    • TableS1_ROSMAP_bulk_only_colocboost_export.bed: colocalization results for 3 bulk-only in ROSMAP corhorts

    • TableS1_ROSMAP_pseudo_bulk_only_colocboost_export.bed: colocalization results for 6 pseudo-bulk-only in ROSMAP corhorts

    • TableS1_GTEx_brain_eQTL_only_colocboost_export.bed: colocalization results for 13 brain eQTL-only GTEx cohorts

    • TableS1_AD_Bellenguez_ROSMAP_xQTL_colocboost_export.bed: colocalization results for AD Bellenguez GWAS with 17 xQTL in ROSMAP corhorts

  • Table S2: Significantly enriched pathways for genes underlying neuron- and microglia-specific colocalizations.

  • Table S3: GTEx eQTL from 13 bulk brain tissues.

  • Table S4: ColocBoost 95% CoS-gene links validated by two CRISPRi data.

  • Table S5: List of annotations used in S-LDSC.

  • Table S6: 57 complex diseases used in disease heritability enrichment analysis.

  • 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.

  • Table S8: Heritability enrichment analysis for AD GWAS in Bellenguez 2022 conditional on 97 baseline-LD annotations.

  • Table S9: Feature comparison of multi-trait colocalization methods (green: feature supported/allowed).

  • 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.

  • annotations_maxVCP: Folder includes 5 maxVCP-based annotation in disease heritability enrichment analysis.

Column Descriptions for Table S1.#

Column Name

Type

Description

chr

integer

Chromosome number

start

integer

Genomic start coordinate (0-based)

end

integer

Genomic end coordinate (1-based)

a1

character

Effect allele

a2

character

Reference allele

variant_ID

character

Unique variant ID in format chr:pos:ref:alt for ROSMAP and chr_pos_ref_alt_b38 for GTEx

gene_ID

character

Ensembl gene ID

event_ID

character

Trait combination that colocalizes within the same 95% colocalization confidence set (CoS).

cos_ID

character

Unique identifier for each 95% colocalization confidence set (CoS).

vcp

double

Variant Colocalization Probability—estimated probability that a variant is shared among colocalized traits.
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