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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


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Genes hit or close-by
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
cg21205320 (chr2:3648304) 3.6×10-86 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg15955046 (chr2:3643706) 7.2×10-67 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of COLEC11 in liver 8.6×10-15 18462017 (PMID) GRASP2 eQTL
Gene expression of ALLC in liver 1.7×10-14 18462017 (PMID) GRASP2 eQTL
"Gene expression of COLEC11 [transcript NM_024027, probe A_23_P120125] in liver" 1.7×10-11 21637794 (PMID) GRASP2 eQTL
cg10945539 (chr2:3642471) 6.9×10-11 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg19867917 (chr2:3642605) 4.4×10-8 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg05408590 (chr2:3648504) 1.8×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of hCT1650054.2 in liver 2×10-6 18462017 (PMID) GRASP2 eQTL
cg17872886 (chr2:3642708) 7.3×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg00835279 (chr2:3642686) 8.9×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs

Variation in COLEC11 may induce variation in IL19.

This locus harbours a replicated trans-pQTLs with Interleukin-19 (IL19) and a replicated cis-pQTL with Collectin-11 (COLEC11). There is also a trans-pQTL with Interleukin-1 beta (IL1B) at this locus, which displays nominal association in QMDiab (p=2.4×10-4).

The information gathered here is a result of an attempt to keep track of all interesting information that we encountered while investigating these loci. Please bear in mind that the annotation given here is neither complete nor free of errors, and that all information provided here should be confirmed by additional literature research before being used as a basis for firm conclusions or further experiments.