Browse Public Results

You can browse FUMA results which are shared in public by users. Registration is not required to browse public results. Please contact the author of the submitted entry for any question regarding the results.
If you want to modify/delete your published results, please login to your account and go to the SNP2GENE job list page. You can modify/delete the information of publicly available results from the corresponding SNP2GENE job.

List of public results
Click a title to browse the results.

ID title author email phenotype publication sumstats sumstats reference notes created date last update
Retrieving data

This is an example page of SNP2GENE job submission. All input options are disabled in this page. Please register to submit your own job.


1. Upload input files

GWAS summary statistics Or : Use example input (Crohn's disease, Franke et al. 2010).
Mandatory
The maximum file size is 600Mb. Please gzip if your file is bigger than 600Mb.
GWAS summary statistics file columns case insensitive
Chromosome:
Position:
rsID:
P-value:
Risk allele:
Other allele:
OR:
Beta:
SE:
Optional. Please fill as much as you can. It is not necessary to fill all column names.
Pre-defined lead SNPs
Optional.
Identify additional independent lead SNPs
Optional.
This is only valid when predefined lead SNPs are provided.
Predefined genomic region
Optional.

2. Parameters for lead SNPs and candidate SNPs identification

Sample size (N) Total sample size (integer): OR
Column name for N per SNP (text):
Mandatory input.
Please provide either total sample size of GWAS study or column name of N in input file.
Maximum P-value of lead SNPs (<)
OK.
r2 threshold to define LD structure of lead SNPs (≥)
OK.
Maximum P-value cutoff (<)
OK.
Population
OK.
Include 1000 genome variant (non-GWAS tagged SNPs in LD)
OK.
Minimum Minor Allele Frequency (≥)
OK.
Maximum distance between LD blocks to merge into a locus (< kb) kb
OK.

3-1. Gene Mapping (positional mapping)

Positional mapping

Perform positional mapping
Optional.
Distance to genes or
functional consequences of SNPs on genes to map 		Maximum distance: kb
OR
Functional consequences of SNPs on genes:
clear
Optional.
Optional SNP filtering by functional annotations for positional mapping
This filtering only applies to SNPs mapped by positional mapping criterion. When eQTL mapping is also performed, this filtering can be specified separately.
All these annotations will be available for all SNPs within LD of identified lead SNPs in the result tables, but this filtering affect gene prioritization.
CADD Perform SNPs filtering based on CADD score.
Optional.
Minimum CADD score (≥)
Optional.
RegulomeDB Perform SNPs filtering based on RegulomeDB score
Maximum RegulomeDB score (categorical)
Optional.
15-core chromatin state Perform SNPs filtering based on chromatin state
Optional.
Tissue/cell types for 15-core chromatin state
Multiple tissue/cell types can be selected. 		clear
Optional.
15-core chromatin state maximum state
Optional.
15-core chromatin state filtering method
Optional.

3-2. Gene Mapping (eQTL mapping)

eQTL mapping

Perform eQTL mapping
Optional.
Tissue types clear
Optional.
eQTL P-value threshold Use only significant snp-gene pairs: (FDR<0.05)
OR
(nominal) P-value cutoff (<):
Optional.
Optional SNP filtering by functional annotation for eQTL mapping
This filtering only applies to SNPs mapped by eQTL mapping criterion.
All these annotations will be available for all SNPs within LD of identified lead SNPs in the result tables, but this filtering affect gene prioritization.
CADD Perform SNPs filtering based on CADD score.
Optional.
Minimum CADD score (≥)
Optional.
RegulomeDB Perform SNPs filtering based on RegulomeDB score
Optional.
Maximum RegulomeDB score (categorical)
Optional.
15-core chromatin state Perform SNPs filtering based on chromatin state
Optional.
Tissue/cell types for 15-core chromatin state
Multiple tissue/cell types can be selected. 		clear
Optional.
15-core chromatin state maximum state
Optional.
15-core chromatin state filtering method
Optional.

3-3. Gene Mapping (3D Chromatin Interaction mapping)

chromatin interaction mapping

Perform chromatin interaction mapping
Optional.
Buildin chromatin interaction data clear
Optional.
Custom chromatin interaction matrices
Optional.
FDR threshold FDR cutoff (<):
Optional.
Promoter region window Please specify both upstream and downstream from TSS. For example, "250-500" means 250bp upstream and 500bp downstream from TSS.
Optional.
Annotate enhancer/promoter regions (Roadmap 111 epigenomes) clear
Optional.
Filter SNPs by enhancers
Optional.
Filter genes by promoters
Optional.
Optional SNP filtering by functional annotation for chromatin interaction mapping
This filtering only applies to SNPs mapped by chromatin interaction mapping criterion.
All these annotations will be available for all SNPs within LD of identified lead SNPs in the result tables, but this filtering affect gene prioritization.
CADD Perform SNPs filtering based on CADD score.
Optional.
Minimum CADD score (≥)
Optional.
RegulomeDB Perform SNPs filtering based on RegulomeDB score
Maximum RegulomeDB score (categorical)
Optional.
15-core chromatin state Perform SNPs filtering based on chromatin state
Optional.
Tissue/cell types for 15-core chromatin state
Multiple tissue/cell types can be selected. 		clear
Optional.
15-core chromatin state maximum state
Optional.
15-core chromatin state filtering method
Optional.

4. Gene types

Gene type
Multiple gene type can be selected.
OK.

5. MHC region

Exclude MHC region
Optional.
Extended MHC region
e.g. 25000000-33000000
Optional.
Title of job submission:
This is not mandatory, but job title might help you to track your jobs.

After submitting, please wait a couple of seconds until the file is uploaded, and do not move away from the submission page.

Manhattan Plot (GWAS summary statistics)

Manhattan plot of the input GWAS summary statistics.
For plotting, overlapping data points are not drawn (only SNPs with P-value ≤ 1e-5 are kept, see tutorial for details).

Download the plot as


Mahattan Plot (gene-based test)

This is a manhattan plot of the gene-based test as computed by MAGMA based on your input GWAS summary statistics.
The gene-based P-value is downloadable from 'Download' tab from the left side bar.



Download the plot as

Label top genes.


QQ plot (GWAS summary statisics)

This is a Q-Q plot of GWAS summary statistics.
For plotting purposes, overlapping data points are not drawn (Only SNPs with P-value ≤ 1e-5 are kept, see tutorial for details).

Download the plot as

QQ plot (gene-based test)

This is a Q-Q plot of the gene-based test computed by MAGMA.



Download the plot as


MAGMA Gene-Set Analysis

MAGMA gene-set analysis is performed for curated gene sets and GO terms obtained from MsigDB (see here for details).
The table displays either significant gene sets with Pbon < 0.05 or top 10 gene sets when there are less than 10 significant gene sets. Full results are downloadable from "Download" tab.
Note that MAGMA gene-set analyses uses the full distribution of SNP p-values and is different from a pathway enrichment test as implemented in GENE2FUNC that only tests for enrichment of prioritized genes.

Gene SetN genesBetaBeta STDSEPPbon


MAGMA Tissue Expression Analysis

MAGMA gene-property analysis is performed for gene expression of user selected data sets.
Details of gene expression data sets are available at Tutorial. Full results are downloadable from "Download" tab.
Note that MAGMA gene-property analyses uses the full distribution of SNP p-values and is different from a enrichment test of DEG (differentially expressed genes) as implemented in GENE2FUNC that only tests for enrichment of prioritised genes.

Order tissue by :

Summary of SNPs and mapped genes

Functional consequences of SNPs on genes

Statistics are available in "annov.stats.txt". The file is downloadable from the "Download" tab.
Download the plot as

Summary per genomic risk locus

Download the plot as


Result tables


Click row to display a regional plot of GWAS summary statistics.

Genomic LocusuniqIDrsIDchrposP-valuestartendnSNPsnGWASSNPsnIndSigSNPsIndSigSNPsnLeadSNPsLeadSNPs

Click row to display a regional plot of GWAS summary statistics.

NoGenomic LocusuniqIDrsIDchrposP-valuenIndSigSNPsIndSigSNPs

Click row to display a regional plot of GWAS summary statistics.

NoGenomic LocusuniqIDrsIDchrposP-valuenSNPsnGWASSNPs

This table contain all SNPs in LD of identified lead SNPs (functional filtering for gene mapping is not applied in this table).
In this table "alt" is the risk allele if provided in the input GWAS file. See tutorial for details.

This is the result of annotation by ANNOVAR. SNPs can appear multiple times in this table if they are annotated to more than one genes.
uniqIDchrbpGeneSymbolDistanceFunctionExonic functionExon

This table contains prioritized genes based on user defined mapping criteria. Note that these genes do no necessary contain all genes which are locating within genomic loci (depending on mapping paramters).


When signed effect size (beta or OR) is provided in the input GWAS file, risk increasing alleles are aligned to the tested alleles of eQTLs. See tutorial for details.
When P-value or FDR are not available in the original data source, they are replaced with -9.
uniqIDchrpostestedAlleleDBtissueGeneSymbolP-valueFDRsigned_statsRiskincAllelealignedDirection

Chromatin interaction

GenomicLocusregion1region2FDRtypeDBtissue/cellinter/intraSNPsGenes

SNPs and overlapped regulatory elements in region 1

uniqIDrsIDchrposregulatory regiontypetissue/cell

Regulatory elements and genes in regions 2

region2regulatory regiontypetissue/cellgenes

Circos plots of chromatin interactions and eQTLs

Download circos plots (all displayed chromosomes) as


The specific layers and color-coding of the circos plot is described below. See tutorial for details.

  • Manhattan plot: The most outer layer. Only SNPs with P < 0.05 are displayed. SNPs in genomic risk loci are color-coded as a function of their maximum r2 to the one of the independent significant SNPs in the locus, as follows: red (r2 > 0.8), orange (r2 > 0.6), green (r2 > 0.4) and blue (r2 > 0.2). SNPs that are not in LD with any of the independent significat SNPs (with r2 ≤ 0.2) are grey.
    The rsID of the top SNPs in each risk locus are displayed in the most outer layer. Y-axis are raned between 0 to the maximum -log10(P-value) of the SNPs.
  • Chromosome ring: The second layer. Genomic risk loci are highlighted in blue.
  • Mapped genes by chromatin interactions or eQTLs: Only mapped genes by either chroamtin interaction and/or eQTLs (conditional on user defined parameters) are displayed. If the gene is mapped only by chromatin interactions or only by eQTLs, it is colored orange or green, respectively. When the gene is mapped by both, it is colored red.
  • Chromosome ring: The third layer. This is the same as second layer but without coordinates to make it easy to align position of genes with genomic coordinate.
  • Chromatin interaction links: Links colored orange are chromatin interactions. Since v1.2.7, only the interactions used for mapping based on user defined parameters are displayed.
  • eQTL lilnks: Links colored green are eQTLs. Since v1.2.7, only the eQTLs used for mapping based on user defined parameters are displayed.
Since creating a circos plot might take long time with a large number of points and links, the maximum number of points and links are limited to 50,000 and 10,000 per plot (chromosome), respectively, in the default plot. Therefore, if there are more than 50,000 SNPs with P-value < 0.05 in a chromosome, top 50,000 SNPs (sorted by P-value) are displayed in the plot. This is same for eQTLs and chromatin interactions, e.g. if there are more than 10,000 eQTLs in a chromosome, top 10,000 eQTLs (sorted by P-value for eQTLs, FDR for chromatin interactions) are displayed in the plot. These can be optimized by downloading config file and re-creating input text files for SNPs and links. Please refer github repository FUMA circos plot for details.




This table only shows subset of information from GWAS catalog.
Please download a output file (gwascatalog.txt) from "Download" tab to get full information

Genomic LocusIndSigSNPchrbprsIDPMIDTraitFirstAuthDateP-value

Regional Plot (GWAS association)

Please click one of the row of 'Genomic risk loci', 'lead SNPs' or 'ind. sig. SNPs' tables to display a regional plot.
You can zoom in/out by mouse scroll.
Each SNP is color-coded based on the highest r2 to one of the ind. sig. SNPs, if that is greater or equal to the user defined threshold. Other SNPs (i.e. below the user-defined r2) are colored in grey. The top lead SNPs in genomic risk loci, lead SNPs and ind. sig. SNPs are circled in black and colored in dark-purple, purple and red, respectively.

Regional plot with annotation

Select annotation(s) to plot:
GWAS association statistics
CADD score
RegulomeDB score
Chromatine 15 state
Please select at least one tissue type.
Tissue/Cell types: clear


eQTL
Chromatin interaction

Download files

Parameter settings
Genomic risk loci table
lead SNP table (independent lead SNPs at r2 0.1)
Independent Significant SNPs table (independent at user defined r2)
SNP table (Candidate SNPs with chr, bp, P-value, CADD, RDB, nearest gene, genomic risk loci and lead SNPs)
ANNOVAR results (uniqID, annotation, gene and distance, SNP-gene pair per line) and enrichment statistics.
Annotations (CADD, RDB and Chromatin state of 127 tissue/cell types)
Gene table (mapped genes)
eQTL table (eQTL of selected tissue types)
Chromatin interaction tables (chromatin interactions overlap with candidate SNPs and regulatory elements)
SNPs in GWAS catalog (full features)
MAGMA (full) results
Variants dropped during rsID annotation from GRCh38 input
Select All Clear

Summary of input genes


Download files

Parameter settings
Summary of input genes
IDs of input genes (including Ensembl ID, entrez ID and gene symbol)
Data for expression heatmap of user selected gene expression data sets
Tissue specificity restuls (enrichment test results of DEG sets for user selected expression data sets)
Gene set analysis results (only include significnat gene sets)
Gene table with multiple externam IDs
Select All Clear

Parameters

Gene expression heatmap

Data set:

Expression Value:
Order genes by: Order tissues by:

Download the plot as

Differrentially expressed genes

Significantly enriched DEG sets (Pbon < 0.05) are highlighted in red.


Order tissue by :

Enrichment of input genes in Gene Sets

Plots and tables only display gene sets with adjusted P-value < 0.05. When adjusted P-value threshold is set to > 0.05, all results passed threshold are included in the GS.txt field downloadable from "Summary" tab.
If there is no significant gene sets (adjusted P-value < 0.05) in user provided custom gene sets, they are not displayed in this page, but all results passed threshold are included in the GS.txt field downloadable from "Summary" tab.

Links to external databases

ENSGentrezIDsymbolOMIMUniProtIDDrugBankGeneCards