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WCMC

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

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Locus annotations

Locus 200

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Factor B cis Discovery rs550513 6:31,920,687 C/T 0.08 996 0.702 0.076 1.3×10-19 1.100 4.4×10-19 3.4×10-20
Factor B cis Replication rs541862 6:31,916,951 A/G 0.12 337 0.612 0.107 2.1×10-8 1.110 3.8×10-8 2.4×10-8

 

Regional association plots

 

Boxplots and histograms for top associations

Complement factor B (Factor B)

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

Complement factor B (Factor B)

Target (abbrv.) Factor B
Target (full name) Complement factor B
Somalogic ID (Sequence ID) SL000414 (4129-72_1)
Entrez Gene Symbol CFB
UniProt ID P00751
UniProt Comment
  • Factor B which is part of the alternate pathway of the complement system is cleaved by factor D into 2 fragments: Ba and Bb. Bb, a serine protease, then combines with complement factor 3b to generate the C3 or C5 convertase. It has also been implicated in proliferation and differentiation of preactivated B-lymphocytes, rapid spreading of peripheral blood monocytes, stimulation of lymphocyte blastogenesis and lysis of erythrocytes. Ba inhibits the proliferation of preactivated B-lymphocytes.
Reactome
  • Activation of C3 and C5
  • Alternative complement activation
  • Regulation of Complement cascade
Pathway Studio
  • Alternative Complement Pathway

All locus annotations are based on the sentinel SNP (rs550513) and 18 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
  • C2 complement component 2
  • C2-AS1 C2 antisense RNA 1
  • XXbac-BPG116M5.17
  • CFB complement factor B
  • NELFE negative elongation factor complex member E
  • MIR1236 microRNA 1236
  • SKIV2L superkiller viralicidic activity 2-like (S. cerevisiae)
Potentially regulated genes
eQTL genes
  • SKIV2L superkiller viralicidic activity 2-like (S. cerevisiae)
  • NELFE negative elongation factor complex member E
  • PRRT1 proline-rich transmembrane protein 1
  • NEU1 sialidase 1 (lysosomal sialidase)

 

Results from other genome-wide association studies

Trait P Study Source
Advanced age-related macular degeneration 9.5×10-45 23455636 (PMID) GRASP2 nonQTL
Rheumatoid arthritis 6×10-41 20453842 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration (choroidal neovascularization) vs. no AMD 1.4×10-32 23455636 (PMID) GRASP2 nonQTL
Gene expression of SKIV2L///DOM3Z in blood 3×10-29 21829388 (PMID) GRASP2 eQTL
Macular degeneration 2.9×10-19 pha002869 (dbGaP) dbGaP via SNiPA
Age-related macular degeneration 8.8×10-17 22694956 (PMID) GRASP2 nonQTL
Advanced age-related macular degeneration (geographic atrophy) 1.5×10-15 23455636 (PMID) GRASP2 nonQTL
Gene expression of RDBP in peripheral blood monocytes 2.5×10-15 20502693 (PMID) GRASP2 eQTL
Rheumatoid arthritis (ACPA-positive) 7.4×10-14 21156761 (PMID) GRASP2 nonQTL
Gene expression of SKIV2L in peripheral blood monocytes 1.2×10-12 20502693 (PMID) GRASP2 eQTL
Gene expression of CFB///RDBP in blood 1.8×10-11 21829388 (PMID) GRASP2 eQTL
Type 1 diabetes, Rheumatoid arthritis, Crohn's disease, combined case analysis 5.1×10-9 17554300 (PMID) GRASP2 nonQTL
cg17528127 (chr8:144332499) 2.6×10-7 10.1101/033084 (DOI) BIOS QTL trans-meQTLs
Age-related macular degeneration (extreme sampling) 3×10-7 23577725 (PMID) GWAS Catalog via SNiPA
Age-related macular degeneration (Stage 5 ARMD) 3.3×10-7 23577725 (PMID) GRASP2 nonQTL
Age-related macular degeneration in ever smokers 7.9×10-7 23577725 (PMID) GRASP2 nonQTL
Exudative age-related macular degeneration 2.1×10-6 21909106 (PMID) GRASP2 nonQTL
Gene expression of HLA-DRB1 in peripheral blood monocytes 3.9×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of SKIV2L in normal prepouch ileum 5.4×10-6 23474282 (PMID) GRASP2 eQTL
Gene expression of MICA in peripheral blood monocytes 8×10-6 20502693 (PMID) GRASP2 eQTL
Crohn's disease 2.7×10-5 Supplemental file
Gene expression of C4B [probe 214428_x_at] in prefrontal cortex 4×10-5 20351726 (PMID) GRASP2 eQTL
Longevity (exceptional longevity) 1.7×10-4 22279548 (PMID) GRASP2 nonQTL
Cervical cancer 2×10-4 21716314 (PMID) GRASP2 nonQTL
Coronary artery calcification (CAC) 2.3×10-4 23727086 (PMID) GRASP2 nonQTL
Systemic sclerosis 3.9×10-4 21750679 (PMID) GRASP2 nonQTL