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WCMC

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

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Locus annotations

Locus 12

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Gro-a cis Discovery rs3117600 4:74,731,812 A/G 0.30 996 1.013 0.038 3.2×10-120 1.560 9.3×10-120 1.8×10-62
Gro-a cis Replication rs3117604 4:74,734,668 A/G 0.43 337 0.636 0.048 3.9×10-32 1.490 1.3×10-25 0.002

 

Regional association plots

Growth-regulated alpha protein (Gro-a)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Growth-regulated alpha protein (Gro-a)

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

Growth-regulated alpha protein (Gro-a)

Target (abbrv.) Gro-a
Target (full name) Growth-regulated alpha protein
Somalogic ID (Sequence ID) SL003173 (2985-35_1)
Entrez Gene Symbol CXCL1
UniProt ID P09341
UniProt Comment
  • Has chemotactic activity for neutrophils. May play a role in inflammation and exerts its effects on endothelial cells in an autocrine fashion. In vitro, the processed forms GRO-alpha(4-73), GRO-alpha(5-73) and GRO-alpha(6-73) show a 30-fold higher chemotactic activity.
Biomarker applications (based on IPA annotation)
  • disease progression
Wiki Pathways
  • Cytokines and Inflammatory Response
  • Senescence and Autophagy
Pathway Interaction Database
  • IL23-mediated signaling events
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 (rs3117600) 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

Genes hit or close-by
  • CXCL1 chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha)
Potentially regulated genes
  • EREG epiregulin
  • MTHFD2L methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2-like
  • AC112518.3
  • CXCL6 chemokine (C-X-C motif) ligand 6
  • AFM afamin
eQTL genes
  • PF4V1 platelet factor 4 variant 1

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of PF4V1 in blood 7.8×10-41 21829388 (PMID) GRASP2 eQTL
Gene expression of PF4V1 in peripheral blood monocytes 1.1×10-17 20502693 (PMID) GRASP2 eQTL
cg08161323 (chr4:74734786) 2.8×10-17 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg02029926 (chr4:74734898) 1×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
O-Acetylcarnitine:Taurine 3.5×10-6 21572414 (PMID) GRASP2 metabQTL
White blood cell count (WBC) 6.8×10-6 21738479 (PMID) GRASP2 nonQTL