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

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Locus annotations

Locus 241

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
FCN1 cis Discovery rs10858300 9:137,842,500 C/T 0.25 994 0.409 0.048 6.2×10-17 1.130 1.7×10-11 0.063
FCN1 cis Replication rs60008355 9:137,843,955 A/G 0.27 337 0.366 0.081 9.3×10-6 1.120 0.011 0.399

 

Regional association plots

 

Boxplots and histograms for top associations

Ficolin-1 (FCN1)

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

Ficolin-1 (FCN1)

Target (abbrv.) FCN1
Target (full name) Ficolin-1
Somalogic ID (Sequence ID) SL010462 (3613-62_5)
Entrez Gene Symbol FCN1
UniProt ID O00602
UniProt Comment
  • Extracellular lectin functioning as a pattern-recognition receptor in innate immunity. Binds the sugar moieties of pathogen-associated molecular patterns (PAMPs) displayed on microbes and activates the lectin pathway of the complement system. May also activate monocytes through a G protein-coupled receptor, FFAR2, inducing the secretion of interleukin-8/IL-8 (PubMed:21037097). Binds preferentially to 9-O-acetylated 2-6-linked sialic acid derivatives and to various glycans containing sialic acid engaged in a 2-3 linkage.
Reactome
  • Ficolins bind to repetitive carbohydrate structures on the target cell surface
  • Initial triggering of complement
  • Lectin pathway of complement activation

All locus annotations are based on the sentinel SNP (rs10858300) and 22 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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eQTL genes
  • OLFM1 olfactomedin 1
  • RP11-447M12.2
  • FCN1 ficolin (collagen/fibrinogen domain containing) 1
  • NELFB negative elongation factor complex member B

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of OLFM1 in peripheral blood monocytes 2.3×10-70 20502693 (PMID) GRASP2 eQTL
cg06244417 (chr9:137809604) 1.2×10-62 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of OLFM1 in blood 5.7×10-46 21829388 (PMID) GRASP2 eQTL
cg17357062 (chr9:137810324) 3.4×10-39 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
OLFM1 gene expression 3.5×10-13 21798870 (PMID) GRASP2 eQTL
cg13639452 (chr9:137623806) 1.8×10-12 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of OLFM1 (probeID ILMN_1714709) in whole blood 6.3×10-10 22692066 (PMID) GRASP2 eQTL
cg13709646 (chr9:137813921) 2.1×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg21212713 (chr9:137709405) 2.6×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Coronary artery disease (CAD) 1.6×10-8 23364394 (PMID) GRASP2 nonQTL
Gene expression of FCN1 in blood 1.9×10-6 21829388 (PMID) GRASP2 eQTL
cg05328939 (chr9:137731049) 6.4×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of OLFM1 in blood cells in Celiac disease 7×10-6 19128478 (PMID) GRASP2 eQTL
cg13749670 (chr9:137611670) 9.5×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg00155846 (chr9:138011542) 2.5×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg14377171 (chr9:138022155) 2.7×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
FCN1 gene expression 1×10-4 21798870 (PMID) GRASP2 eQTL