HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 25

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
GCP-2 cis Discovery rs16850073 4:74,703,999 C/T 0.38 984 0.888 0.038 9.7×10-98 1.350 7.7×10-78 7×10-11
GCP-2 cis Replication rs16850073 4:74,703,999 G/A 0.23 337 0.606 0.060 4.6×10-21 1.430 1.2×10-17 0.241

 

Regional association plots

 

Boxplots and histograms for top associations

C-X-C motif chemokine 6 (GCP-2)

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

C-X-C motif chemokine 6 (GCP-2)

Target (abbrv.) GCP-2
Target (full name) C-X-C motif chemokine 6
Somalogic ID (Sequence ID) SL003172 (3495-15_2)
Entrez Gene Symbol CXCL6
UniProt ID P80162
UniProt Comment
  • Chemotactic for neutrophil granulocytes. Signals through binding and activation of its receptors (CXCR1 and CXCR2). In addition to its chemotactic and angiogenic properties, it has strong antibacterial activity against Gram-positive and Gram-negative bacteria (90-fold-higher when compared to CXCL5 and CXCL7).
Biomarker applications (based on IPA annotation)
  • unspecified application
Reactome
  • Chemokine receptors bind chemokines
  • G alpha (i) signalling events
Pathway Studio
  • IL8R → CREB/EGR signaling

All locus annotations are based on the sentinel SNP (rs16850073) and 1 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
  • CXCL6 chemokine (C-X-C motif) ligand 6
eQTL genes
  • CXCL6 chemokine (C-X-C motif) ligand 6
  • PF4V1 platelet factor 4 variant 1

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of PF4V1 in peripheral blood monocytes 1.3×10-17 20502693 (PMID) GRASP2 eQTL