Documentation

Input:

• Association data file - upload a space or tab delimited file containing chromosome, position and p-value for each variant. A file header, while not required, will be useful when selecting input columns. Once the file is uploaded the user needs to specify which columns are the respective chromosome, position, and association p-values. Uploaded files will be stored on our secure server for use during LDassoc sessions and will be deleted after 4 hours.
• Select region - choices are Gene, Region, or Variant. Gene requires a RefSeq gene name and base pair window and allows for an optional index variant. Region requires genomic start and end coordinates and allows for an optional index variant. Variant requires an index variant and allows for an optional base pair window (500,000bp is the default). The index variant will be plotted in blue and is used to calculate all pairwise LD statistics. If not required, LDassoc will designate the variant with the lowest p-value as the index variant, unless otherwise specified.
• Reference population(s) - selected from the drop down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.
• LD measure - select if desired output is based on estimated R² or D'.
• Collapse transcripts - choose to combine gene transcripts with the same name in the gene plot.
• RegulomeDB annotation - choose to display RegulomeDB scores in the interactive plot.

Output:

• Interactive plot - interactive plot of index variant and p-values of all bi-allelic variants in the specified plotting region. X axis is the chromosomal coordinates and the Y axis is the -log10 p-value as well as the combined recombination rate. Each point represents a variant and is colored based on D' or R², sized based on minor allele frequency, and labeled based on regulatory potential. Hovering over the point will display detailed information on the index and proxy variants.
• UCSC link - external link to the plotted region in the UCSC Genome Browser. This is useful for exploring nearby genes and regulatory elements in the region.
• Table of Association Results - by default, the ten variants with the lowest p-values and closest distance to the index variant are displayed. External links lead to the variant RS number in dbSNP, coordinates in the UCSC Genome Browser, and regulatory information (if any) in RegulomeDB.
• Download association data for all variants - download a file with information on all variants within the plotting region.

Input:

• List of RS numbers - this can either be entered one per line in the text entry box or uploaded as a file that contains a list of RS numbers in the first column. A maximum of 10 variant RS numbers or chromosomal coordinates (GRCh37) are permitted. All input variants must match a bi-allelic variant. The text entry field is automatically filled if a file of SNPs or genomic coordinates is uploaded.
• Reference population(s) - selected from the drop-down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.
• R²/D' toggle - select if desired output is filtered from a threshold based on estimated R² or D'.
• R²/D' threshold - set threshold for LD filtering. Any variants within -/+ of the specified genomic window and R² or D' less than the threshold will be removed. Value needs to be in the range 0 to 1. Default value is 0.1.
• Tissue(s) - select the GTEx tissue or tissues of interest for searching for eQTLs.
• P-value threshold - define the eQTL significance threshold used for returning query results. Default value is 0.1 which returns all GTEx eQTL associations with P-value less than 0.1. Values can be entered in scientific notation (i.e. "1e-5").
• Window size - set genomic window size for LD calculation. Specify a value greater than or equal to zero and less than or equal to 1,000,000bp. Default value is -/+ 500,000bp.

Output:

• Variants in LD with variants in GTEx QTL - a list of queried variants in LD with a variant reported in the GTEx QTL data. Each variant in the list is a clickable link that brings up a detailed table showing genes with expression associated variants that are in linkage disequilibrium with the input variant(s).
• Details Tables - output table that appears when a variant in the variant list is clicked. Details are provided on SNP rsID, genomic position, R2, D', Gene Symbol of associated gene expression, Gencode ID of the expressed gene, tissue where the association was observed, Effect Size, and P-value. External links lead to the QTL page in the GTEx portal.
• Variants with Warnings - output table that appears when a variant produces a warning in LDexpress. Common reasons for a variant to be on the warning list are if the variant is not found in dbSNP/GTEx or if no variants in LD are found within window of the 1000G reference VCF file. Details are provided on genomic position and why the variant was excluded from the variant list.
• Download GTEx QTL list - clickable link to download a text file in tab-delimited format that lists all query variant RS numbers, respective QTL which are in LD with query variant, and associated gene expression.

Input:

• List of RS numbers - this can either be entered one per line in the text entry box or uploaded as a file that contains a list of RS numbers in the first column. A maximum of 30 variant RS numbers are permitted. All input variants must be on the same chromosome and match a bi-allelic variant. The text entry field is automatically filled with the contents of the uploaded file.
• Reference population(s) - selected from the drop down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.

Output:

• Table of observed haplotypes - haplotypes with frequencies greater than 1 percent are displayed vertically and ordered by observed frequency in the selected query sub-population. Variant genotypes are reported in rows and and are sorted by genomic position. Queries should be limited to nearby variants, since haplotype switch rate errors become more common as genomic distance increases. Links are available to dbSNP RS numbers and coordinates in theUCSC Genome Browser.
• Variant file download - download a file listing the order of the queried variants. Variants are ordered by genomic location. This file is used as a key for the order of genotypes in the haplotype file. Only bi-allelic variants with matching dbSNP RS numbers are included. All others are filtered out.
• Haplotype file download - download a file of all observed haplotypes. Haplotype genotypes are in the order of the above variant file.

Input:

• List of RS numbers - this can either be entered one per line in the text entry box or uploaded as a file that contains a list of RS numbers in the first column. A maximum of 300 variant RS numbers are permitted. All input variants must be on the same chromosome and match a bi-allelic variant. The text entry field is automatically filled with the contents of the uploaded file.
• Reference population(s) - selected from the drop down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.
• Genome build - choose to combine gene transcripts with the same name in the gene plot.

Output:

• Interactive heat map - a square plot with dimensions equal to the number of query variants that match a dbSNP RS number. Hovering over the plot with the mouse will display pairwise LD metrics for the respective row and column variants. Variants are ordered by genomic coordinates.
• D prime download - download a file of all pairwise D' statistics.
• R squared download - - download a file of all pairwise R2 statistics.

Input:

• Pair of RS numbers - RS number for query variant 1. RS number must match a bi-allelic variant.
• Reference population(s) - RS number for query variant 2. RS number must match a bi-allelic variant.
• Genome build selected from the drop down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.

Output:

• Two-by-two table - contingency table displaying haplotype counts and allele frequencies for the two query variants. External links are available to dbSNP RS numbers and coordinates in the UCSC Genome Browser.
• Haplotypes - haplotype genotypes, counts, and frequencies.
• Statistics - calculated metrics of linkage disequilibrium including: D prime (D'), R square (R²), and goodness-of-fit (Chi-square and p-value). Goodness-of-fit tests for deviations of expected haplotype frequencies based on allele frequencies.
• Correlated Alleles - alleles that are correlated if linkage disequilibrium is present (R² > 0.1). If linkage equilibrium, no alleles are reported.

Input:

• Variant1 RS number - RS number for query variant 1. RS number must match a bi-allelic variant.
• Variant2 RS number - RS number for query variant 2. RS number must match a bi-allelic variant.
• Reference population(s) selected from the drop down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.
• R²/D' toggle - select if desired output is based on estimated R² or D'.

Output:

• Interactive maps - three interactive maps will be returned as tabbed output. The first tab displays a map with the chosen linkage disequilibrium measure between query variants 1 and 2 for the selected 1000G populations. The second and third tabs will display maps of allele frequency distribution for query variants 1 and 2, respectively, for the selected 1000G populations. Map pins are color coded based on LD/allele frequency and when clicked display additional information for the population.
• Table of populations - a searchable and sortable table is generated showing allele frequency and LD values for the query variants and selected 1000G populations.
• Download table - link to download data in the table of populations.

Input:

• Variant RS number - RS number for query variant. RS number must match a bi-allelic variant.
• Reference population(s) - selected from the drop down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.
• LD measure - select if desired output is based on estimated R² or D'.
• Collapse transcripts - choose to combine gene transcripts with the same name in the gene plot.

Output:

• Interactive plot - interactive plot of query variant and all bi-allelic dbSNP variants plus or minus 500 kilobases(Kb) of the query variant. X axis is the chromosomal coordinates and the Y axis is the pairwise R2 value with the query variant as well as the combined recombination rate. Each point represents a proxy variant and is colored based on function, sized based on minor allele frequency, and labeled based on regulatory potential. Hovering over the point will display detailed information on the query and proxy variants.
• UCSC link - external link to the plotted region (query variant -/+ 500 Kb) in the UCSC Genome Browser. This is useful for exploring nearby genes and regulatory elements in the region.
• Table of proxy variants - by default, the ten variants with the highest R2 values and closest distance to the query variant are displayed. External links lead to the variant RS number in dbSNP, coordinates in the UCSC Genome Browser, and regulatory information (if any) in RegulomeDB.
• Download all proxy variants - download a file with information on all variants -/+ 500 Kb of the query variant with a pairwise R² value greater than 0.01.

Input:

• List of RS numbers - this can either be entered one per line in the text entry box or uploaded as a file that contains a list of RS numbers in the first column. A maximum of 50 variant RS numbers or chromosomal coordinates (GRCh37) are permitted. All input variants must match a bi-allelic variant. The text entry field is automatically filled with the contents of the uploaded file.
• Reference population(s) selected from the drop-down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.
• R²/D' toggle - select if desired output is filtered from a threshold based on estimated R² or D'.
• R²/D' threshold - set threshold for LD filtering. Any variants within -/+ of the specified genomic window and R² or D' less than the threshold will be removed. Value needs to be in the range 0 to 1. Default value is 0.1.
• Window size - set genomic window size for LD calculation. Specify a value greater than or equal to zero and less than or equal to 1,000,000bp. Default value is -/+ 500,000bp.

Output:

• Variants in LD with GWAS Catalog - a list of queried variants in LD with a variant reported in the GWAS Catalog. Each variant in the list is a clickable link that brings up a detailed table showing disease-associated variants that are in linkage disequilibrium with the variant.
• Details Tables - output table that appears when a variant in the variant list is clicked. Details are provided on GWAS trait, genomic position, alleles, R2, D', Effect Size (95% CI), Beta or OR, and P-value. External links lead to the result variant in the GWAS Catalog.
• Variants with Warnings - - output table that appears when a variant produces a warning in LDtrait. Common reasons for a variant to be on the warning list are if the variant is not found in dbSNP or if no variants in LD are found within window of the GWAS Catalog. Details are provided on genomic position and why the variant was excluded from the variant list.
• Download GWAS Catalog annotated variant list - clickable link to download a text file in tab-delimited format that lists all query variant RS numbers and their respective GWAS Catalog results.

Input:

• For LD score calculation - genotype information as .bim/.bed/.fam files, as well as window in centiMorgan (cM) or kilobasepairs (kb) selected from the drop-down menu.
• For heritability analysis GWAS summary statistics (format: tab-separated files with columns accepted by https://github.com/bulik/ldsc/blob/master/munge_sumstats.py, e.g. with effect size, p-value, SNP identifiers, and allelic information, note header naming format is important). For example: SNP (Variant ID e.g., rs number), A1 (Allele 1, interpreted as reference allele for signed sumstat), A2 (Allele 2, interpreted as non-reference allele for signed sumstat), Frq (Allele frequency), BETA or [linear/logistic] regression coefficient (0 --> no effect; above 0 --> A1 is trait/risk increasing), P (p-Value), N (Sample size). In addition, a reference population needs to be selected from the drop down menu.
• For genetic correlation - GWAS summary statistics (format: tab-separated files with columns accepted by https://github.com/bulik/ldsc/blob/master/munge_sumstats.py, e.g. with effect size, p-value, SNP identifiers, and allelic information, note header naming format is important). For example: SNP (Variant ID e.g., rs number), A1 (Allele 1, interpreted as reference allele for signed sumstat), A2 (Allele 2, interpreted as non-reference allele for signed sumstat), Frq (Allele frequency), BETA or [linear/logistic] regression coefficient (0 --> no effect; above 0 --> A1 is trait/risk increasing), P (p-Value), N (Sample size). In addition, a reference population needs to be selected from the drop down menu.
• Reference population - One 1000 Genomes Project/Genome Aggregation Database (gnomAD) sub-population is required for heritability analysis or genetic correlation.

Output:

• For LD Score calculation - A summary of LD Scores, the MAF/LD Score Correlation Matrix, full LD Scores file, as well as the option to download input data, in addition to a code prompt output summary.
• For heritability analysis - Total Observed scale heritability, Lambda GC, Mean Chi^2, Intercept and LDSC Ratio, as well as a code prompt output summary.
• For genetic correlation - tables with heritability of phenotype 1, heritability of phenotype 2, Genetic Covariance, Genetic Correlation and a Summary of Genetic Correlation Results, as well as a code prompt output summary.

Input:

• List of RS numbers - this can either be entered one per line in the text entry box or uploaded as a file that contains a list of RS numbers in the first column. A maximum of 5,000 variant RS numbers are permitted. All input variants do not need to be on the same chromosome. The text entry field is automatically filled with the contents of the uploaded file.
• Genotyping Arrays - selected commercial genotyping arrays from the drop down list. At least one array must be selected, but more than one may be selected as input.

Output:

• Array Table - output table of variant rows and array columns. The presence of an "X" designates the variant is present on the respective commercial genotyping array. Variants are ordered by genomic location. External links lead to the variant RS number in dbSNP and coordinates in the UCSC Genome Browser
• Download Chip Details - download a file with information on all variants and commercial genotyping array membership.

Input:

• List of RS numbers - this can either be entered one per line in the text entry box or uploaded as a file that contains a list of RS numbers in the first column. A maximum of 5,000 variant RS numbers are permitted. All input variants must be on the same chromosome and match a bi-allelic variant. The text entry field is automatically filled with the contents of the uploaded file.
• Reference population(s) - selected from the drop down menu. At least one 1000 Genomes Project sub-population is required, but more than one may be selected.
• R² threshold - set R² threshold for LD pruning. One of each pair of variants with a R² greater than the threshold is removed. Value needs to be in the range 0 to 1. Default value is 0.1.
• MAF threshold - set MAF threshold for LD pruning. Variants with a MAF less than or equal to the threshold are removed. Value needs to be in the range 0 to 1. Default value is 0.01.

Output:

• LD Thinned Variant List - a list of LD pruned variants based on the specified SNPclip parameters. Each variant in the list is a clickable link that brings up a detailed table showing other variants that are in linkage disequilibirum with the variant. Variants are ordered by input order, so to force a variant to be in the LD thinned list it should be at the top of the input list.
• Details Tables - output table that appears when a variant in the thinned variant list is clicked. Details are provided on genomic position, alleles, and why the variant was included or excluded from the thinned variant list. External links lead to the variant RS number in dbSNP and coordinates in the UCSC Genome Browser
• Variants with Warnings - output table that appears when a variant produces a warning in SNPclip. Common reasons for a variant to be on the warning list include a variant with an MAF below the MAF threshold, a query that is not a RS number, and a RS number not found in the 1000G reference VCF file. Details are provided on genomic position, alleles, and why the variant was included or excluded from the thinned variant list. External links lead to the variant RS number in dbSNP and coordinates in the UCSC Genome Browser
• Download Thinned Variant List - download a text file that lists all thinned variant RS numbers, one per line.
• Download Thinned Variant List with Details - download a text file that lists all query variant RS numbers, genomic locations, alleles and details of whether the variant was kept or removed.