LinDA

LinDA (LINkage Disequilibrium-based Annotation) browser.

LinDA is a tool that, for a given variant, determines all variants in Linkage Disequilibrium and whether they intersect with other association studies. A large manually curated collection of QTL and association studies can be easily interrogated and results displayed with interactive plots and tables. LinDA also offers additional tools, such as computing variant frequency and pair-wise phasing, thus facilitating interpretation of results.

Tools

Variant LD Browser

Search by genetic variant to obtain the annotations (e/sQTLs, GWAS..) for the query variant and for the variants in LD with the query.

Variant AF Browser

Visualize the Allele Frequencies of a genetic variant among the human populations.

Pairwise Variants Browser

Compute pairwise statistics between genetic variants (Phase of the alleles, LD, Frequency).

eGene Browser

Given a Gene name as query, it returns whether the gene has eQTLs whether they LD overlaps with complex traits and diseases GWAS variants.

Genome Browser

Visualize eQTLs and genes among the human genome.

Overview

The LD browser is the main tool implemented in LinDA. For a given variant, it determines all the variants in Linkage Disequilibrium and whether they intersect with other association studies (QTLs and GWAS). The user can specify range of LD and the specific population in which the LD has to be retrieved. There are 32 populations of the 1000 Genomes project than can be queried for LD.

The output of the LD browser is a sequence of table each reporting the intersection with the other association studies (e.g. our eQTL Catalog). In each table are reported details about the statistical association, the gene annotation and the experiment metadata.

The eQTLs catalog

The expression Qualitative Traits Loci (eQTLs) are genetic polymorphisms associated with changes in gene expression levels and they have been successfully used to interpret the molecular role of Genome Wide Association Studies (GWAS) variants. Up to date few eQTLs databases exist but they collect only a small portion of the available datasets.

We collected several studies and here is the description of the most important features.

Feature	Counts
Projects	56
Human populations	15
Body districts	35
Datasets	282
eGenes	38,255
eQTLs	673,410

The molecular QTLs catalogs

We are continuously collecting the results of QTLs and disease association studies. A brief summary about the traits collected and the number of associations found is reported in the table on the right.

Type of Catalog	Type of trait	Associated trait	Associated variants
eQTLs	Whole gene RNA level	38,255 (1)	748,308
sQTLs	Transcript level	24,009 (1)	188,577
aseQTL	Allele-specific expression	523	689
polyAQTL	Alternative polyA	2,414	3,820
repeatQTL	Repeats expression level	6,069	4,811
pQTLs	protein expression level	1,561	879
dhsQTLs	DnaseI hyupersensitive sites	6,069	6,069
hQTLs	Histone modifications	58,197	60,121
mQTLs	DNA methylation	219,508	316,376

(1) Results are collapsed at gene-level