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WCMC

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

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Locus annotations

Locus 142

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 rs4151669 6:31,915,144 G/A 0.04 997 -1.170 0.104 6.3×10-28 -1.170 1.3×10-29 3×10-26

 

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

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 (rs4151669) and 21 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.

Linked genes


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Genes hit or close-by
  • EHMT2 euchromatic histone-lysine N-methyltransferase 2
  • SLC44A4 solute carrier family 44, member 4
  • EHMT2-AS1 EHMT2 antisense RNA 1
  • ZBTB12 zinc finger and BTB domain containing 12
  • C2 complement component 2
  • XXbac-BPG116M5.17
  • C2-AS1 C2 antisense RNA 1
  • CFB complement factor B
  • NELFE negative elongation factor complex member E
  • MIR1236 microRNA 1236
  • DXO decapping exoribonuclease
  • STK19 serine/threonine kinase 19
  • C4A complement component 4A (Rodgers blood group)
eQTL genes
  • DXO decapping exoribonuclease
  • C6orf48 chromosome 6 open reading frame 48
  • XXbac-BPG246D15.9
  • HLA-DOB major histocompatibility complex, class II, DO beta
  • HLA-B major histocompatibility complex, class I, B

 

Results from other genome-wide association studies

Trait P Study Source
Age-related macular degeneration 2×10-23 21665990 (PMID) GWAS Catalog via SNiPA
Advanced age-related macular degeneration 2.4×10-23 21665990 (PMID) GRASP2 nonQTL
Gene expression of FFAR2 in liver 3.5×10-20 18462017 (PMID) GRASP2 eQTL
Gene expression of HSS00126305 in liver 4.8×10-16 18462017 (PMID) GRASP2 eQTL
Rheumatoid arthritis 6.3×10-15 22446960 (PMID) Supplemental file
Advanced age-related macular degeneration (choroidal neovascularization) vs. no AMD 4.7×10-13 23455636 (PMID) GRASP2 nonQTL
Serum myeloperoxidase levels 4.8×10-10 23620142 (PMID) GRASP2 nonQTL
Macular degeneration 6.1×10-10 pha002869 (dbGaP) dbGaP via SNiPA
Gene expression of DOM3Z (probeID ILMN_1726990) in cerebellum in Alzheimer's disease cases and controls 6.3×10-9 22685416 (PMID) GRASP2 eQTL
Age-related macular degeneration (CNV) 2×10-8 22705344 (PMID) GWAS Catalog via SNiPA
Gene expression of DOM3Z (probeID ILMN_1726990) in temporal cortex in Alzheimer's disease cases and controls 5.3×10-8 22685416 (PMID) GRASP2 eQTL
Advanced age-related macular degeneration (geographic atrophy) 1.7×10-7 23455636 (PMID) GRASP2 nonQTL
Age-related macular degeneration (GA) 1×10-6 22705344 (PMID) GWAS Catalog via SNiPA
Gene expression of DOM3Z (probeID ILMN_1726990) in cerebellum in non-Alzheimer's disease samples 3.6×10-6 22685416 (PMID) GRASP2 eQTL
Gene expression of CREBL1 [probe ILMN_21310] in osteoblasts treated with PGE2 4.7×10-5 21283786 (PMID) GRASP2 eQTL
Exudative age-related macular degeneration 2×10-4 21909106 (PMID) GRASP2 nonQTL
Total cholesterol 2.2×10-4 24097068 (PMID) Supplemental file