Update 1: Two human pancreatic islet eQTL datasets were added (TIGER and InsPIRE) .

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.

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.

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.

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 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).

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.

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.

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.

Major update 1: Cell type specificity analysis was updated to 3 step workflow. The workflow consists of: 

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.

Minor bugs have been fixed. Bugs include misalignment of alleles in ANNOVAR and miscount of SNPs in LD per independent significant SNPs.

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.

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.

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.

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.

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.

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.

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.

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.

In SNP2GENE, MAGMA tissue expression analysis was added to the "Genome-wide plot". Details are in the SNP2GENE Outputs section of the tutorial.