GTEx MCP Server

analyze_ld_structure

Analyze linkage disequilibrium patterns around eQTL variants to understand genetic associations and co-inheritance in specific genomic regions.

Instructions

Analyze linkage disequilibrium structure around eQTL variants

Input Schema

Name	Required	Description	Default
`chr`	Yes	Chromosome (e.g., chr1, chr2, chrX)
`population`	No	Population for LD analysis (default: EUR)	EUR
`position`	Yes	Genomic position (1-based)
`windowSize`	No	Window size around position (default: 100000)

Input Schema (JSON Schema)

{
  "properties": {
    "chr": {
      "description": "Chromosome (e.g., chr1, chr2, chrX)",
      "type": "string"
    },
    "population": {
      "default": "EUR",
      "description": "Population for LD analysis (default: EUR)",
      "enum": [
        "EUR",
        "AFR",
        "AMR",
        "EAS",
        "SAS"
      ],
      "type": "string"
    },
    "position": {
      "description": "Genomic position (1-based)",
      "type": "integer"
    },
    "windowSize": {
      "default": 100000,
      "description": "Window size around position (default: 100000)",
      "type": "integer"
    }
  },
  "required": [
    "chr",
    "position"
  ],
  "type": "object"
}

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