Date Title Version Description
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.