Ensembl Ld Tools

Configuration File: ensembl_ld_tools.json Tool Type: Local Tools Count: 3

This page contains all tools defined in the ensembl_ld_tools.json configuration file.

Available Tools

EnsemblLD_get_ld_pairwise (Type: EnsemblLDTool)

Get pairwise linkage disequilibrium (LD) statistics between two specific variants from the Ensemb…

EnsemblLD_get_ld_pairwise tool specification

Tool Information:

  • Name: EnsemblLD_get_ld_pairwise

  • Type: EnsemblLDTool

  • Description: Get pairwise linkage disequilibrium (LD) statistics between two specific variants from the Ensembl REST API. Returns r-squared and D’ across ALL 1000 Genomes populations, allowing comparison of LD patterns across ancestries. Useful for assessing whether two GWAS signals are correlated or independent. Example: rs6792369 vs rs1042779 shows r2=1.0 in East Asian populations but r2=0.84 in African populations.

Parameters:

  • variant1 (string) (required) rs ID of the first variant. Examples: ‘rs6792369’, ‘rs429358’.

  • variant2 (string) (required) rs ID of the second variant. Examples: ‘rs1042779’, ‘rs7412’.

Example Usage:

query = {
    "name": "EnsemblLD_get_ld_pairwise",
    "arguments": {
        "variant1": "example_value",
        "variant2": "example_value"
    }
}
result = tu.run(query)

EnsemblLD_get_ld_region (Type: EnsemblLDTool)

Get region-wide pairwise linkage disequilibrium (LD) from the Ensembl REST API: every r-squared a…

EnsemblLD_get_ld_region tool specification

Tool Information:

  • Name: EnsemblLD_get_ld_region

  • Type: EnsemblLDTool

  • Description: Get region-wide pairwise linkage disequilibrium (LD) from the Ensembl REST API: every r-squared and D’ pair among ALL variants inside a chromosomal window for one 1000 Genomes Phase 3 population. This is the LD matrix used as input to statistical fine-mapping (e.g. SuSiE, FINEMAP) and LD-aware clumping at a GWAS locus. The window must be <= 1 Mb (Ensembl limit). Region format: ‘chr:start..end’. Example: region ‘6:25837556..25840000’ in CEU returns 4 LD pairs, e.g. rs62394274/rs62394275 with r2=1.0 and d_prime=1.0.

Parameters:

  • region (string) (required) Chromosomal window as ‘chr:start..end’ (1-based, GRCh38), max 1 Mb. Example: ‘6:25837556..25840000’.

  • population (string) (required) 1000 Genomes population. Format: ‘1000GENOMES:phase_3:<POP>’. Common populations: ‘CEU’ (CEPH Utah), ‘YRI’ (Yoruba), ‘CHB’ (Han Chinese Beijing), ‘GBR’ (British), ‘JPT’ (Japanese Tokyo), ‘KHV’ (Kinh Vietnamese). Example: ‘1000GENOMES:phase_3:CEU’.

  • r2_threshold ([‘number’, ‘null’]) (optional) Minimum r-squared threshold to report. Set higher (e.g., 0.8) for strong LD only.

  • d_prime_threshold ([‘number’, ‘null’]) (optional) Minimum D’ threshold to report. Set e.g., 0.8 for high D’ only.

Example Usage:

query = {
    "name": "EnsemblLD_get_ld_region",
    "arguments": {
        "region": "example_value",
        "population": "example_value"
    }
}
result = tu.run(query)

EnsemblLD_get_ld_variants (Type: EnsemblLDTool)

Get linkage disequilibrium (LD) data for a variant from the Ensembl REST API. Returns all variant…

EnsemblLD_get_ld_variants tool specification

Tool Information:

  • Name: EnsemblLD_get_ld_variants

  • Type: EnsemblLDTool

  • Description: Get linkage disequilibrium (LD) data for a variant from the Ensembl REST API. Returns all variants in LD with the query variant in a specified 1000 Genomes population, with r-squared and D’ statistics. LD measures the non-random association of alleles at different loci, critical for GWAS interpretation and fine-mapping. Example: rs1042779 in KHV population returns 708 LD partners with r2 and D’ values.

Parameters:

  • variant_id (string) (required) rs ID of the variant. Examples: ‘rs1042779’, ‘rs429358’, ‘rs7903146’, ‘rs6792369’.

  • population (string) (required) 1000 Genomes population. Format: ‘1000GENOMES:phase_3:<POP>’. Common populations: ‘KHV’ (Kinh Vietnamese), ‘CEU’ (CEPH Utah), ‘YRI’ (Yoruba), ‘CHB’ (Han Chinese Beijing), ‘GBR’ (British), ‘JPT’ (Japanese Tokyo), ‘ASW’ (African SW US). Example: ‘1000GENOMES:phase_3:CEU’.

  • r2_threshold ([‘number’, ‘null’]) (optional) Minimum r-squared threshold to report. Default: 0.05. Set higher (e.g., 0.8) for strong LD only.

  • d_prime_threshold ([‘number’, ‘null’]) (optional) Minimum D’ threshold. Default: none. Set e.g., 0.8 for high D’ only.

Example Usage:

query = {
    "name": "EnsemblLD_get_ld_variants",
    "arguments": {
        "variant_id": "example_value",
        "population": "example_value"
    }
}
result = tu.run(query)