[UI] Variants in Linkage Disequilibrium Table

[engreitz]

New columns + documentation for Variants in Linkage Disequilibrium Table on the Variants Page:

Table title - mouseover help text:

This table lists variants in linkage disequilibrium with the query variant, and summarizes functional evidence about those variants.

Each row reports one variant in one ancestry. LD information is sourced from 1000 Genomes Phase 3 queried from Ensembl.

See Documentation (ADD LINK TO THE DOCUMENTATION)

Table columns and design:

Updated list of Columns: (Column Name (hyperlink if applicable) [API query details, if known]
• rsID - same as existing, no changes
• LD (r^2) - same as existing, no changes
• LD (D') - same as existing, no changes
• Most Severe Consequence - change column ordering
• Cell Types (E-G prediction) - change the name of the column
• Genes (E-G prediction) - change the name of the column
• Cell Types (QTL) - This new column should behave similarly to the Cell Types (E-G prediction) column, but instead report the #unique cell types/biosamples with which this variant is an eQTL based on the newly loaded EBI eQTL Catalogue data, or a sQTL, or a pQTL
• Genes (QTL) - This new column should behave similarly to the Genes (E-G prediction) column, but instead report the #unique genes with which this variant is an QTL based on the newly loaded EBI eQTL Catalogue data, or based on a sQTL or a pQTL
• Cell Types (TF binding) - This new column should be have similarly to above, reporting the #unique biosamples in which ADASTRA Allelic effects on TF binding say that this variant is a "Hit", as in the Allelic effects table on the Variant Page
• Motifs (TF binding) - This new column should behave similarly to above, reporting the #unique motifs in which ADASTRA Allelic effects on TF binding say that this variant is a "Hit"
• Ancestry - same as existing, no changes