HelmholtzZentrum munich
WCMC

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

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Locus annotations

Locus 432

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 rs41264869 1:205,030,862 C/T 0.17 997 -0.389 0.058 4×10-11 -1.110 5.1×10-10 2.3×10-6
CNTN2 cis Replication rs2242000 1:205,031,769 G/A 0.22 337 -0.426 0.065 2.7×10-10 -1.180 1.2×10-9 0.001

 

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 (rs41264869) 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
Potentially regulated genes
  • CNTN2 contactin 2 (axonal)
eQTL genes
  • RBBP5 retinoblastoma binding protein 5
  • DSTYK dual serine/threonine and tyrosine protein kinase
  • TMCC2 transmembrane and coiled-coil domain family 2
  • CNTN2 contactin 2 (axonal)

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of RIPK5 in peripheral blood monocytes 4.6×10-31 20502693 (PMID) GRASP2 eQTL
cg03936955 (chr1:205030956) 1.6×10-28 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg15460899 (chr1:205039107) 5×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of RBBP5 [probe 205169_at] in lymphoblastoid cell lines 7.5×10-8 17873877 (PMID) GRASP2 eQTL
Schizophrenia 2.4×10-6 25056061 (PMID) Supplemental file
cg15542880 (chr1:205114610) 5.7×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg20290360 (chr1:204956415) 8.1×10-6 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg23627436 (chr1:204996127) 4.3×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs