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

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Locus annotations

Locus 298

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Nidogen trans Discovery rs9651367 10:20,223,450 G/A 0.28 997 -0.355 0.045 1.2×10-14 -1.070 2.1×10-13 2.5×10-10
Nidogen trans Replication rs1018635 10:20,226,672 G/A 0.24 337 -0.247 0.081 0.003 -1.050 0.003 0.01

 

Regional association plots

 

Boxplots and histograms for top associations

Nidogen-1 (Nidogen)

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

Nidogen-1 (Nidogen)

Target (abbrv.) Nidogen
Target (full name) Nidogen-1
Somalogic ID (Sequence ID) SL000640 (3213-65_2)
Entrez Gene Symbol NID1
UniProt ID P14543
UniProt Comment
  • Sulfated glycoprotein widely distributed in basement membranes and tightly associated with laminin. Also binds to collagen IV and perlecan. It probably has a role in cell-extracellular matrix interactions.
Pathway Interaction Database
  • Beta1 integrin cell surface interactions
Reactome
  • Degradation of the extracellular matrix
  • Laminin interactions

All locus annotations are based on the sentinel SNP (rs9651367) and 8 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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Genes hit or close-by
  • PLXDC2 plexin domain containing 2

 

Results from other genome-wide association studies

Trait P Study Source
PE e (COOH) C16:3 (PE e (COOH) C16:3, PE e (OH) C18:3, PE ae (OH, COOH) C14:4, PE a C18:2) 5.2×10-5 19043545 (PMID) GRASP2 metabQTL
PC aa (OH, COOH) C30:4 1.7×10-4 19043545 (PMID) GRASP2 metabQTL
PC aa C34:3 3.5×10-4 19043545 (PMID) GRASP2 metabQTL
HDL cholesterol 4.4×10-4 19060906 (PMID) GRASP2 nonQTL

Possible link between cis-variants and protein levels of NID1 and NID2.

This locus harbours a non-replicated trans-pQTL to Nidogen-1 (NID1), and a nominal trans-pQTL in KORA with NID2 (p=1.2×10-8); both proteins are encoded at different loci.

The information gathered here is a result of an attempt to keep track of all interesting information that we encountered while investigating these loci. Please bear in mind that the annotation given here is neither complete nor free of errors, and that all information provided here should be confirmed by additional literature research before being used as a basis for firm conclusions or further experiments.