2021
DOI: 10.1093/nar/gkab853
|View full text |Cite
|
Sign up to set email alerts
|

VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases

Abstract: Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has fol… Show more

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
1
1
1
1

Citation Types

0
32
0

Year Published

2021
2021
2024
2024

Publication Types

Select...
9

Relationship

0
9

Authors

Journals

citations
Cited by 52 publications
(32 citation statements)
references
References 76 publications
0
32
0
Order By: Relevance
“…The section on ‘ Human genomic variation, diseases and drugs ’ contains papers on two new resources for linking genetic variation to disease. VannoPortal ( 83 ) integrates no fewer than 40 data sources to provide impressively comprehensive linkages between variants and diseases or traits, and boasts a particularly clean and responsive interface. ConVarT ( 84 ) takes the approach of mapping equivalent variants between orthologous protein pairs between human and model organisms such as Caenorhabditis elegans .…”
Section: New and Updated Databasesmentioning
confidence: 99%
“…The section on ‘ Human genomic variation, diseases and drugs ’ contains papers on two new resources for linking genetic variation to disease. VannoPortal ( 83 ) integrates no fewer than 40 data sources to provide impressively comprehensive linkages between variants and diseases or traits, and boasts a particularly clean and responsive interface. ConVarT ( 84 ) takes the approach of mapping equivalent variants between orthologous protein pairs between human and model organisms such as Caenorhabditis elegans .…”
Section: New and Updated Databasesmentioning
confidence: 99%
“…Both SNPs are located within a known ApoE enhancer [65] and were previously described as cis-eQTLs of both genes (in blood or in other tissues), hinting at a potential co-regulation of the expression of both genes [66,67]. Among the 12 trans-pQTLs identified therein, only two co-localized with known eQTLs for the same gene (based on Van-noPortal [43], "Methods"). Last, only one gene located at the trans-pQTL locus was shown to interact with the associated gene (SORT1 and GRN, respectively; physical or regulatory interactions reported in STRING-db, Methods).…”
Section: Contribution Of Human Genetics On Plasma Protein Levelsmentioning
confidence: 98%
“…We assessed the co-localization between the trans-pQTLs identified in this work and previously identified trans-eQTLs associated with the same gene and reported in the GWAS Catalog V1.0.2 [41], in eQTLs from GTEx V8 or in QTLbase v1.2 [42] (http:// mulin lab. org/ qtlba se) through the VannoPortal [43], using a LD threshold of R 2 ≥ 0.8 (computed in Europeans from the 1000 Genome Project) between each pQTL and all SNPs present in a 200-kb window centered on the pQTL.…”
Section: Co-localization Of Trans-pqtls and Trans-eqtlsmentioning
confidence: 99%
“…To estimate the regulatory potential and downstream functional effects of the SNPs, we analyzed the available data of epigenetic effects (HaploReg, RegulomeDB), functional predictions (SNPinfo), and expression and alternative splicing quantitative traits (GTEx consortium atlas) by using the variant annotation database VannoPortal [21]. [+X]-LNA modifications.…”
Section: In Silico Analysis Of Snps Regulatory Potentialmentioning
confidence: 99%