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WCMC

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

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Locus annotations

Locus 230

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Factor I cis Discovery rs7439493 4:110,656,730 G/A 0.40 996 0.360 0.041 1.6×10-17 1.040 7.1×10-17 2×10-17
Factor I cis Replication rs7439493 4:110,656,730 G/A 0.39 337 0.209 0.068 0.002 1.030 0.003 0.002

 

Regional association plots

 

Boxplots and histograms for top associations

Complement factor I (Factor I)

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

Complement factor I (Factor I)

Target (abbrv.) Factor I
Target (full name) Complement factor I
Somalogic ID (Sequence ID) SL003328 (2567-5_6)
Entrez Gene Symbol CFI
UniProt ID P05156
UniProt Comment
  • Responsible for cleaving the alpha-chains of C4b and C3b in the presence of the cofactors C4-binding protein and factor H respectively.
Reactome
  • Regulation of Complement cascade
Pathway Studio
  • Alternative Complement Pathway

All locus annotations are based on the sentinel SNP (rs7439493) and 7 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
  • PLA2G12A phospholipase A2, group XIIA
  • CFI complement factor I
Potentially regulated genes
eQTL genes
  • PLA2G12A phospholipase A2, group XIIA
  • CASP6 caspase 6, apoptosis-related cysteine peptidase

 

Results from other genome-wide association studies

Trait P Study Source
cg16243646 (chr4:110651846) 1.9×10-150 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of CASP6 (probeID ILMN_2367113) in cerebellum in Alzheimer's disease cases and controls 3×10-10 22685416 (PMID) GRASP2 eQTL
Gene expression of CCDC109B in peripheral blood monocytes 2.3×10-9 20502693 (PMID) GRASP2 eQTL
Advanced age-related macular degeneration 1.5×10-7 23455636 (PMID) GRASP2 nonQTL
Gene expression of CASP6 (probeID ILMN_2367113) in cerebellum in Alzheimer's disease cases 7.1×10-7 22685416 (PMID) GRASP2 eQTL
Macular degeneration 1.3×10-6 pha002869 (dbGaP) dbGaP via SNiPA
Gene expression of CFI in liver 1.3×10-5 21637794 (PMID) GRASP2 eQTL
Gene expression of CASP6 (probeID ILMN_2367113) in cerebellum in non-Alzheimer's disease samples 6.7×10-5 22685416 (PMID) GRASP2 eQTL
Advanced age-related macular degeneration (choroidal neovascularization) vs. no AMD 1.4×10-4 23455636 (PMID) GRASP2 nonQTL
Total cholesterol 3.3×10-4 20339536 (PMID) GRASP2 nonQTL
Gene expression of CASP6 (probeID ILMN_2367113) in temporal cortex in Alzheimer's disease cases and controls 3.6×10-4 22685416 (PMID) GRASP2 eQTL
Serum concentration of 4-acetaminophen sulfate 4.6×10-4 21886157 (PMID) GRASP2 metabQTL