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

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Locus annotations

Locus 98

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
C1s trans Discovery rs6695321 1:196,675,861 A/G 0.37 995 -0.529 0.038 9.4×10-40 -1.060 8.6×10-31 3.5×10-17
C1s trans Replication rs6695321 1:196,675,861 A/G 0.35 337 -0.292 0.071 5.1×10-5 -1.040 0.001 0.01
complement factor H-related 5 cis Discovery rs6695321 1:196,675,861 A/G 0.37 995 -0.416 0.044 2.7×10-20 -1.120 2.9×10-20 4.6×10-14
complement factor H-related 5 cis Replication rs6695321 1:196,675,861 A/G 0.35 337 -0.248 0.066 1.9×10-4 -1.080 3.8×10-4 0.003

 

Regional association plots

Complement C1s subcomponent (C1s)

Download the association data used to generate this plot

Complement factor H-related protein 5 (complement factor H-related 5)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Complement C1s subcomponent (C1s)

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

Complement factor H-related protein 5 (complement factor H-related 5)

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

Complement C1s subcomponent (C1s)

Target (abbrv.) C1s
Target (full name) Complement C1s subcomponent
Somalogic ID (Sequence ID) SL000311 (3590-8_3)
Entrez Gene Symbol C1S
UniProt ID P09871
UniProt Comment
  • C1s B chain is a serine protease that combines with C1q and C1r to form C1, the first component of the classical pathway of the complement system. C1r activates C1s so that it can, in turn, activate C2 and C4.
Targeted by drugs (based on IPA annotation)
  • SERPING1
Wiki Pathways
  • Complement Activation, Classical Pathway
  • Complement and Coagulation Cascades
Reactome
  • Classical antibody-mediated complement activation
  • Initial triggering of complement
Pathway Studio
  • Classical Complement Pathway

Complement factor H-related protein 5 (complement factor H-related 5)

Target (abbrv.) complement factor H-related 5
Target (full name) Complement factor H-related protein 5
Somalogic ID (Sequence ID) SL006830 (3666-17_4)
Entrez Gene Symbol CFHR5
UniProt ID Q9BXR6
UniProt Comment
  • Involved in complement regulation. The dimerized forms have avidity for tissue-bound complement fragments and efficiently compete with the physiological complement inhibitor CFH.

All locus annotations are based on the sentinel SNP (rs6695321).
Download the detailed results of SNiPA's block annotation (PDF)

Linked genes


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Genes hit or close-by
  • CFH complement factor H
eQTL genes
  • CFHR3 complement factor H-related 3

 

Results from other genome-wide association studies

Trait P Study Source
Advanced age-related macular degeneration 6.4×10-93 23455636 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration (choroidal neovascularization) vs. no AMD 9.9×10-58 23455636 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration (geographic atrophy) 2.1×10-40 23455636 (PMID) GRASP2 nonQTL
Age-related macular degeneration 1.7×10-13 23577725 (PMID) GRASP2 nonQTL
Age-related macular degeneration (Stage 5 ARMD) 2.5×10-9 23577725 (PMID) GRASP2 nonQTL
Q9BXR6 protein abundance levels 4.1×10-6 22595970 (PMID) GRASP2 pQTL
Age-related macular degeneration in ever smokers 1.8×10-5 23577725 (PMID) GRASP2 nonQTL
Age-related macular degeneration in never smokers 1.2×10-4 23577725 (PMID) GRASP2 nonQTL
Meningococcal disease 2.3×10-4 20694013 (PMID) GRASP2 nonQTL

CFH or CFHR3 may regulate C1S.

This locus harbours a replicated trans-association to Complement C1s subcomponent (C1S). Cis-encoded proteins are CFH and CFHR3.

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.

SOMAscan assay update regarding Complement C1s subcomponent

According to a SOMAscan assay change log issued on 12/22/2016, the SOMAmer reagent 3590-8 (targeting Complement C1s subcomponent) was removed from the SOMAscan panel for the following reason: "Mass spectrometry identifies Complement Factor H as the protein enriched from plasma when the SOMAmer reagent 3590-8 is used for affinity capture."