HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 102

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
CNTN2 cis Discovery rs4951168 1:205,053,219 T/C 0.15 993 0.785 0.057 2.1×10-39 1.250 2.1×10-39 7.8×10-27
CNTN2 cis Replication rs3820337 1:205,014,930 G/A 0.16 337 0.482 0.069 1.3×10-11 1.230 1.3×10-12 2.5×10-6

 

Regional association plots

 

Boxplots and histograms for top associations

Contactin-2 (CNTN2)

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

Contactin-2 (CNTN2)

Target (abbrv.) CNTN2
Target (full name) Contactin-2
Somalogic ID (Sequence ID) SL008623 (3296-92_2)
Entrez Gene Symbol CNTN2
UniProt ID Q02246
UniProt Comment
  • In conjunction with another transmembrane protein, CNTNAP2, contributes to the organization of axonal domains at nodes of Ranvier by maintaining voltage-gated potassium channels at the juxtaparanodal region. May be involved in cell adhesion.
Reactome
  • L1CAM interactions
  • NCAM1 interactions
  • NrCAM interactions

All locus annotations are based on the sentinel SNP (rs4951168) and 54 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
Potentially regulated genes
  • CNTN2 contactin 2 (axonal)
  • DSTYK dual serine/threonine and tyrosine protein kinase
  • RBBP5 retinoblastoma binding protein 5
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of RIPK5 in peripheral blood monocytes 4.8×10-31 20502693 (PMID) GRASP2 eQTL
cg03142956 (chr1:205012325) 5.6×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg25603742 (chr1:205014754) 7.6×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg24931168 (chr1:204966037) 5.6×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Serum ratio of (trigonelline (N'-methylnicotinate))/(ursodeoxycholate) 8.3×10-6 21886157 (PMID) GRASP2 metabQTL
Serum ratio of (1-methylxanthine)/(taurochenodeoxycholate) 1.5×10-5 21886157 (PMID) GRASP2 metabQTL
Waist circumference 7.7×10-5 pha003024 (dbGaP) dbGaP via SNiPA
Serum ratio of (bilirubin (E,Z or Z,E)*)/(tetradecanedioate) 8.3×10-5 21886157 (PMID) GRASP2 metabQTL
Frontotemporal lobar degeneration with TDP-43 inclusions (GRN mutation negative) 9×10-5 20154673 (PMID) GRASP2 nonQTL
Body weight 9.9×10-5 pha003026 (dbGaP) dbGaP via SNiPA
Serum ratio of (hexanoylcarnitine)/(tetradecanedioate) 1.4×10-4 21886157 (PMID) GRASP2 metabQTL
Stroke 2×10-4 pha002886 (dbGaP) dbGaP via SNiPA