Date Title Version Description
2024-06-05 14:07:21 - v1.6.1
Update 1: Two human pancreatic islet eQTL datasets were added (TIGER and InsPIRE) .
Update 2: The GENE2FUNC button on the SNP2GENE job page was updated so that SNP2GENE jobs that do not run MAGMA will use GTEx v8 data in the GENE2FUNC tissue expression analyses when the GENE2FUNC button is pressed. Prior to this update, no tissue expression analyses were run and a minor bug prevented the gene table from being displayed.
Update 3: A minor bug with the ANNOVAR enrichment analysis in the SNP2GENE pipeline was fixed. Now if candidate SNPs do not map to a gene but are annotated by ANNOVAR, they will be included in the ANNOVAR enrichment analyses. Previous versions of FUMA excluded variants, which were not mapped to a nearest gene by ANNOVAR in the enrichment analysis.
Update 4: A downloads page was added where some reference data used by FUMA can be downloaded.
Update 5: Variant-gene connections in the eQTL catalogue datasets that had unadjusted P-values >=0.05 were removed. Now only nominally significant variant-gene connections in the eQTL catalogue are available for variant annotation in the SNP2GENE pipeline. 
2024-06-05 14:04:49 - v1.6.0
As of v1.6.0, FUMA SNP2GENE allows input data on build GRCh38 if the input contains chromosome, position, effect allele, and noneffect allele columns. FUMA SNP2GENE previously worked with input data on built GRCh38 if rsIDs were present and chromosome and position columns were not present. This update now allows for input data on build GRCh38 when chromosome, position, effect allele, and noneffect allele columns are present by annotating variants with rsIDs using dbSNP v150 data. To reduce computational time, only variants that are present in any of the FUMA SNP2GENE reference panels will be annotated with rsIDs. Variants that could not be successfully annotated with rsIDs can be downloaded with the rest of the job results.
2024-06-05 14:03:30 - v1.5.6
The MSigDB version was updated to v2023.1.Hs in the SNP2GENE and GENE2FUNC modules. The GWAScatalog version was updated to e110_r2023-07-20 in the SNP2GENE and GENE2FUNC modules. The SNP2GENE geneset file and the GENE2FUNC geneset files from FUMA version 1.3.5d to 1.5.5 are downloadable in the tutorial sections. The new version of these geneset files can also be downloaded in the tutorial sections.
2024-06-05 14:02:54 - v1.5.5 Ensembl v102 and v110 added and Ensembl v92 removed. v92 is no longer available in the BioMart databases.
2024-06-05 14:02:31 - v1.5.4 User roles and permissions added.
2024-06-05 14:02:16 - v1.5.3 Registration vulnerability fixed.
2024-06-05 14:01:52 - v1.5.2 Added an FAQ page.
2024-06-05 14:01:34 - v1.5.1 MAGMA will no longer run by default in the SNP2GENE module. If you would like the MAGMA gene, gene-set, and tissue analysis results or to use the SNP2GENE output as input for the Cell Type module, please select 'Perform MAGMA' (in step 6) on the submission page.
2024-06-05 14:01:15 - v1.5.0 Updated FUMA Cell Type user interphase and added scRNAseq data for human prefrontal cortex from Herring et al. 2022.
2024-06-05 14:00:52 - v1.4.2 Updated the GWAS catalog to e0_r2022-11-29 in the SNP2GENE analysis.
2024-06-05 14:00:28 - v1.4.1 Fixed a bug that caused chromosome 23 variants to be excluded from genomic risk loci when the 1KG EUR reference panel was used. This bug started on February 28 2022 and was fixed on August 30 2022. If, during this period, you have used the 1KG EUR reference panel and your data included chromosome 23, please re-run your analyses.
2024-06-05 14:00:02 - v1.4.0 Major update 1: Ensembl v85 genes have been removed from the job options for SNP2GENE and GENE2FUNC. v85 is no longer available in the BioMart databases.
2024-06-05 13:59:26 - v1.3.9 Fixed a bug where circos plots with more than 10k CI interactions would return an error. Now an arbitrary selection of 10k interactions is visualised. Fixed another bug where sorting genomic positions as strings would result in wrong Risk Loci boundaries in rare occasions.
2024-06-05 13:58:58 - v1.3.8 Fixed a bug which caused one annotation to be dropped when filtering variants based on annotations for gene-mapping. Analyses which relied on filtering variants by annotation for gene-mapping should re-submit their jobs.
2024-06-05 13:57:52 - v1.3.7 Added EyeGEx eQTL data.
2024-06-05 13:57:36 - v1.3.6d Updated GWAScatalog to e104_2021-09-15.
2024-06-05 13:57:19 - 1.3.6c Fixed a minor bug to allow for transparent regional plot backgrounds. Fixed a minor bug to allow for analysis of chr23 using UKB 10k reference panel.
2024-06-05 13:56:57 - v1.3.6b Fixed a minor bug in the calculation of annotation enrichment p-values. We re-analyzed results from existing jobs, and the 99th percentile absolute difference between old and new p-values was 0.00000458. However, jobs in which more than 100,000 variants were selected for further analysis may encounter larger differences, and these analyses should be re-run.
2024-06-05 13:56:23 - v1.3.6a Update MAGMA to v1.08. Bug fix for gene2func (DrugBank annotation).
2024-06-05 13:55:58 - v1.3.6 Datasets in the eQTL Catalogue which were not already present in FUMA were added as options for eQTL mapping.
2024-06-05 13:55:32 - v1.3.5d
There was an error during mapping hg38 to hg19 for eQTLs of GTEx v8, which caused some missing significant eQTLs. It has been fixed in the current version. If you have any SNP2GENE jobs with eQTL mapping using GTEx v8, it is strongly recommended to re-do gene-mapping.
2024-06-05 13:54:47 - v1.3.5c
Update 1: GTEx v8 eQTLs and gene expression data were added to SNP2GENE and GENE2FUNC. Due to the limited storage space on the server, GTEx eQTLs for all versions (v6/v7/v8) are now limited to SNP-gene pairs with nominal P-value < 0.05 (before all tested SNP-gene pairs were available). This does not affect your results if you used only significant SNP-gene pairs (with gene Q-value < 0.05).
Update 2: MsigDB was updated to v7.0.
Update 3: GWAS catalog was updated to e96_2019-09-24.
Update 4: Wikipathway was updated to v20191010.
Update 5: DrugBank was updated to v5.1.4.
Update 6: There was a bug in the script to process PsychENCODE eQTL data. This bug caused to filter all PsychENCODE eQTLs during gene mapping. If you used this data, it is strongly advised to re-run gene mapping (you might get more eQTLs but not less).
2024-06-05 13:52:24 - v1.3.5b Minor bugs in the main scripts are fixed.
2024-06-05 13:51:37 - v1.3.5
Major update 1: Reference panels were updated to include as much as variants possible. For 1000 Genome, new reference panel "ALL" was added. UK Biobank reference panel was updated to release 2b (based on genotype data released in May 2018). UK Biobank release 1 and release 2 reference panels are no longer available. Please check Tutorial for more details.
Major update 2: New options for additional SNP annotations (genome based annotations provided as bed files) were added. Annotations can be selected for each mapping separately. Options can be selected to either only annotate SNPs or also filter based on the overlap of selected annotations.
Major update 3: For GENE2FUNC, users can now provide custom gene sets in GMT format.

Minor update 1: A threshold of r2 for the second clumping to define lead SNPs was added as input parameter.
Minor update 2: Additional data sets were added to eQTLs and chromatin interaction mappings.
Minor update 3: Additional data sets were added to cell type analyses.
Minor update 4: Enrichments of functional consequence of candidate SNPs are now tested against SNPs in the user selected reference panel.
Minor update 5: GWAS catalog was updated to e96 2019-05-03.
Minor update 6: Gene window size for MAGMA gene analysis can be specified for up- and downstream separately.
2024-06-05 13:46:55 - v1.3.4d Script for cell type specificity analysis has been optimised and minor bugs are fixed.
2024-06-05 13:46:36 - v1.3.4c
Minor bug update on GENE2FUNC gene set enrichment test. It has been testing P(X>x), but now it tests P(X&ge;x). This change will affect the results of "Tissue specificity" and "Gene sets" in GENE2FUNC process. If you wish to update the existing job, please contact the developer.
2024-06-05 13:45:44 - v1.3.4b
MAGMA reference panels were modified. There were mil-filtering of some SNPs in the pre-process (only for UK biobank references). This might cause different results of MAGMA gene, gene-set and gene-property analyses.
2024-06-05 13:44:46 - v1.3.4
Major update 1: Cell type specificity analysis was updated to 3 step workflow. The workflow consists of: 
  1. per dataset cell type analysis,
  2. within dataset conditional analysis and,
  3. across datasets conditional analysis.
Additional datasets were curated in addition to the ones available from v1.3.3. Please check Tutorial for details.

Minor update 1: MAGMA was updated to v1.07 to facilitate conditional analyses in cell type specificity analysis. This does not affect the results of SNP2GENE MAGMA analyses, however, the extension of gene-set/gene-property analysis has been changed to XXX.gsa.out.
Minor update 2: GWAS catalog was updated to e93 2019-01-11.
Minor update 3: MsigDB was updated to v6.2.
Minor update 4: WikiPathways was updated to v20190110.
Minor update 5: Additional HiC datasets (adult and fetal cortex samples) were added to the chromatin interaction mapping.
2024-04-30 16:43:56 - v1.3.3d
Minor bugs have been fixed. Bugs include misalignment of alleles in ANNOVAR and miscount of SNPs in LD per independent significant SNPs.
2024-04-30 16:43:19 - v1.3.3c
Cis- and trans-eQTLs from eQTLGen are now available for eQTL mapping. The eQTLGen is a meta-analysis of 37 datasets with in total of 31,684 individuals. To annotate new eQTLs for your existing SNP2GENE jobs, you can use the "re-do gene mapping" option.
2024-04-30 16:42:45 - v1.3.3b
As requested, additional options for the window size of MAGMA gene analysis have been added. In the new version, 0, 1, 5, 10, 15, 20, 25, 30, 40, and 50kb (both sides) are available.
2024-04-30 16:42:08 - v1.3.3
The Cell type specificity analysis based on scRNA-seq datasets using MAGMA is now available. This is currently a beta version, further improvement of plots and additional info will be available soon.
2024-04-30 16:41:35 - v1.3.2 Some scripts have been optimized. Chromatin interaction mapping with large number of SNPs is now much faster than before.
2024-04-30 16:41:15 - v1.3.1b
A minor bug in chromatin interaction mapping has been fixed. This missed some promoter annotations in region 2 which might have caused over-filtering of chromatin interactions. This affects the mapped genes only when you activate the filtering based on the promoter in chromatin interaction mapping.
2024-04-30 16:40:09 - v1.3.1
  • Major update 1: The UK Biobank reference panel has been added. There are three types of reference panels available for UKB; release 1 white British, release 2 white British, and release 2 European. Each reference panel consists of randomly selected 10,000 subjects. MAGMA reference was created for each of these populations by further randomly selecting 1,000 subjects since the run time is very long by using 10K subjects. Please check Tutorial for details.
  • Major update 2: You can now publish your FUMA results to the public allowing other users to browse your results. The browse page does not require users to login which makes it possible to share your results to a larger population in an easy way!! Please check Tutorial for details.

  • Minor update 1: Emsemble v92 genes are now available for both SNP2GENE and GENE2FUNC. Ensembl v85 can be selected from the option, but the default is updated to v92.
  • Minor update 2: MsigDB is updated to v6.1 and WikiPathways is updated to 20180410.
  • Minor update 3: An info tab is added to the header. You can check the current version of FUMA and how many jobs are currently running/queued.
2024-04-30 16:31:09 - v1.3.0
  • Major update 1: The following 4 eQTL data sets are added, GTEx v7, MuTHER, CommonMind Consortium, and xQTLServer. Each data set has a different description for the tested allele, P-value, and FDR. Please check Tutorial for details before start using these new data sets. To be able to replicate previous results, GTEx v6 eQTLs are also kept as options. Because of this, when "all" is selected for eQTL mapping, both GTEx v6 and GTEx v7 are going to be used. To avoid this, please manually check data sets.
  • Major update 2: Indels are now included in the 1000 genome reference. Note that only bi-allelic SNPs and indels are available in FUMA.
  • Major update 3: GTEx v7 and BrainSpan gene expression data sets were added to MAGMA gene expression analysis in SNP2GENE and DEG enrichment analysis in GENE2FUNC.
  • Major update 4: For existing SNP2GENE jobs, it is possible to re-perform gene mapping with different parameters from v1.3.0. Please check the tutorial for details.

  • Minor update 1: For the SNP2GENE job submission, the previous parameter setting can be loaded by selecting job ID.
  • Minor update 2: A summary page is added to the GENE2FUNC results page.
  • Minor update 3: The GWAS catalog is updated to version e91_2018-02-06.
2024-04-30 16:25:49 - v1.2.8
Positional mapping based on distance between SNPs and genes has been improved. It was purely based on the distance annotated by ANNOVAR until v1.2.7, however, ANNOVAR only annotates intergenic SNPs to two closet genes. From v1.2.8, the distance between SNPs and genes is checked independently from ANNOVAR. This change is more likely to affect your results when positional mapping is performed, with a distance much larger than 10kb. There must be no effect if positional mapping is performed based on the functional consequence of SNPs annotated by ANNOVAR.
2024-04-30 16:23:22 - v1.2.7
Filtering chromatin interactions in circos plot has been updated. Only chromatin interactions (orange links) and eQTLs (green links) used for mapping are displayed in circos plot from this version on. If you wish to update the circos plot of an existing SNP2GENE job, please contact the developer providing the jobID.
2024-04-30 16:20:47 - v1.2.4
  • Minor bug in chromatin interaction mapping fixed.
  • Chromatin interaction mapping has missed some overlapping interactions with risk loci. If you have any SNP2GENE job with chromatin interaction mapping submitted before the 1st of September 2017, it's strongly recommended to re-submit jobs or please contact the developers to update the results.
2024-04-30 16:18:07 - v1.2.3
GWAScatalog has been updated to release e89 2017-08-15. Please be aware that jobs submitted to SNP2GENE before 22th of August 2017 used the previous version (e85 2016-09-27). If you wish to update GWAScatalog results for your SNP2GENE jobs, please contact the developers providing the jobID.
2024-04-30 16:02:21 - v1.2.0
  • Major update 1: Chromatin interaction mapping is newly added to the SNP2GENE process which utilizes 3D genome data such as Hi-C, ChIA-PET, and so on. Built-in Hi-C data is obtained from GSE87112 and the user can also provide custom chromatin interaction data. See tutorial for details.
  • Major update 2: Browse Public Results page is newly added and does not require registration/login. On that page, pre-computed results can be browsed with full features (e.g. interactive plots and download).
  • Minor updates: 
    1. SNP2GENE process has been improved. 
    2. eQTLs are aligned with the risk increasing alleles in the input GWAS file (see Tutorial for details). To avoid confusion, allele names in the SNPs table were updated to non_efefct_allele/effect_allele from ref/alt.
2024-04-30 15:54:46 pLI and ncRVIS v1.1.2 Two gene scores (pLI and ncRVIS) are added to the gene table. See links, for detailed information for each score.
2024-04-30 15:53:03 - v1.1.2 The speed of SNP2GENE process is improved.
2024-04-30 15:52:33 SNPs filtering with functional annotation v1.1.1
SNPs filtering with functional annotation for gene mapping is now reflected in the regional plot with annotations. Details are described at the bottom of the page of regional plot with annotations.
2024-04-30 15:50:38 Tissue expression analyses v1.1.0
In SNP2GENE, MAGMA tissue expression analysis was added to the "Genome-wide plot". Details are in the SNP2GENE Outputs section of the tutorial.
2024-04-30 15:47:26 First version v1.0.0 The first version was freezed.