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Connecting genetic risk to disease endpoints through the human blood plasma proteome

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Locus annotations

Locus 93

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Collectin Kidney 1 cis Discovery rs7588285 2:3,648,186 G/C 0.21 996 0.699 0.050 1.1×10-40 1.290 1.9×10-41 1.6×10-44
Collectin Kidney 1 cis Replication rs3820897 2:3,642,361 G/A 0.35 337 0.570 0.065 1.4×10-16 1.350 6.7×10-17 1.1×10-12
IL-19 trans Discovery rs7588285 2:3,648,186 G/C 0.21 996 0.679 0.051 2.7×10-37 1.140 3.2×10-36 6.1×10-37
IL-19 trans Replication rs3820897 2:3,642,361 G/A 0.35 337 0.585 0.060 8.7×10-20 1.150 1.3×10-18 1.4×10-17
IL-1b trans Discovery rs7588285 2:3,648,186 G/C 0.21 996 0.332 0.055 2.5×10-9 1.080 5.2×10-6 0.067
IL-1b trans Replication rs3820897 2:3,642,361 G/A 0.35 337 0.297 0.080 2.4×10-4 1.100 0.003 0.165

 

Regional association plots

 

Boxplots and histograms for top associations

Collectin-11 (Collectin Kidney 1)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Interleukin-19 (IL-19)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Interleukin-1 beta (IL-1b)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Collectin-11 (Collectin Kidney 1)

Target (abbrv.) Collectin Kidney 1
Target (full name) Collectin-11
Somalogic ID (Sequence ID) SL006713 (4430-44_3)
Entrez Gene Symbol COLEC11
UniProt ID Q9BWP8
UniProt Comment
  • Lectin that binds to various sugars including fucose and mannose. Has a higher affinity for fucose compared to mannose. Does not bind to glucose, N-acetylglucosamine and N-acetylgalactosamine. Also binds lipopolysaccharides (LPS). Involved in fundamental development serving as a guidance cue for neural crest cell migration (By similarity).
Reactome
  • Scavenging by Class A Receptors

Interleukin-19 (IL-19)

Target (abbrv.) IL-19
Target (full name) Interleukin-19
Somalogic ID (Sequence ID) SL004354 (3035-80_2)
Entrez Gene Symbol IL19
UniProt ID Q9UHD0
UniProt Comment
  • May play some important roles in inflammatory responses. Up-regulates IL-6 and TNF-alpha and induces apoptosis (By similarity).
Pathway Interaction Database
  • IL23-mediated signaling events

Interleukin-1 beta (IL-1b)

Target (abbrv.) IL-1b
Target (full name) Interleukin-1 beta
Somalogic ID (Sequence ID) SL001795 (3037-62_1)
Entrez Gene Symbol IL1B
UniProt ID P01584
UniProt Comment
  • Potent proinflammatory cytokine. Initially discovered as the major endogenous pyrogen, induces prostaglandin synthesis, neutrophil influx and activation, T-cell activation and cytokine production, B-cell activation and antibody production, and fibroblast proliferation and collagen production. Promotes Th17 differentiation of T-cells.
Targeted by drugs (based on IPA annotation)
  • canakinumab
  • gevokizumab
  • canakinumab/INS
  • gallium nitrate
Biomarker applications (based on IPA annotation)
  • diagnosis
  • efficacy
  • prognosis
Wiki Pathways
  • Alzheimers Disease
  • Cytokines and Inflammatory Response
  • Folate Metabolism
  • IL-1 signaling pathway
  • Leptin signaling pathway
  • MAPK signaling pathway
  • Monoamine Transport
  • Myometrial Relaxation and Contraction Pathways
  • NOD pathway
  • Regulation of toll-like receptor signaling pathway
  • Selenium Pathway
  • Senescence and Autophagy
  • Serotonin Transporter Activity
  • TCR Signaling Pathway
  • Toll-like receptor signaling pathway
  • Type II interferon signaling (IFNG)
  • Vitamin B12 Metabolism
Pathway Interaction Database
  • Cellular roles of Anthrax toxin
  • IFN-gamma pathway
  • IL1-mediated signaling events
  • IL12-mediated signaling events
  • IL23-mediated signaling events
  • IL27-mediated signaling events
Reactome
  • CLEC7A/inflammasome pathway
  • Interleukin-1 processing
  • Interleukin-1 signaling
Pathway Studio
  • CNR1/2 → IL1B/2/4/6/10 production
  • Dectin-1 (CLEC7A) Signaling
  • IL1R → NF-kB signaling
  • IL1R → STAT3 signaling
  • NOD-like Receptors in Pathogen Recognition
  • Nociception-related IL1B expression targets
  • Summarized nociception-related expression targets
  • TLR4 Signaling in Leukocytes
  • Th17 Cell Differentiation
  • Toll-like Receptors Act through MYD88-TIRAP Signaling

All locus annotations are based on the sentinel SNP (rs7588285) and 6 proxy variant(s) that is/are in linkage disequilibrium r2 ≥ 0.8. Linkage disequilibrium is based on data from the 1000 Genomes Project, phase 3 version 5, European population and was retrieved using SNiPA's Block Annotation feature.
Download the detailed results of SNiPA's block annotation (PDF)

Linked genes

Genes hit or close-by