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

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Locus annotations

Locus 88

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
HCC-1 cis Discovery rs41341749 17:34,310,702 A/G 0.06 997 -1.171 0.081 3×10-43 -1.360 5×10-48 8.3×10-34
HCC-1 cis Replication rs41341749 17:34,310,702 A/G 0.07 337 -0.795 0.117 4.9×10-11 -1.370 4.5×10-10 7.8×10-6
MPIF-1 cis Discovery rs41341749 17:34,310,702 A/G 0.06 997 1.032 0.084 3.1×10-32 1.360 3.3×10-35 9.6×10-40
MPIF-1 cis Replication rs9892586 17:34,313,915 A/G 0.07 337 0.934 0.128 2.4×10-12 1.340 1.6×10-12 1.9×10-12
PARC cis Discovery rs41341749 17:34,310,702 A/G 0.06 997 0.755 0.083 6.3×10-19 1.390 2.6×10-20 4.1×10-22
PARC cis Replication rs41341749 17:34,310,702 A/G 0.07 337 0.212 0.144 0.142 1.080 0.173 0.25
MIP-1a cis Discovery rs41341749 17:34,310,702 A/G 0.06 997 0.544 0.088 1×10-9 1.100 2×10-4 0.981
MIP-1a cis Replication rs41341749 17:34,310,702 A/G 0.07 337 0.146 0.142 0.304 1.040 0.468 0.964

 

Regional association plots

 

Boxplots and histograms for top associations

C-C motif chemokine 14 (HCC-1)

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

C-C motif chemokine 23 (MPIF-1)

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

C-C motif chemokine 18 (PARC)

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

C-C motif chemokine 3 (MIP-1a)

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

C-C motif chemokine 14 (HCC-1)

Target (abbrv.) HCC-1
Target (full name) C-C motif chemokine 14
Somalogic ID (Sequence ID) SL003329 (2900-53_3)
Entrez Gene Symbol CCL14
UniProt ID Q16627
UniProt Comment
  • Has weak activities on human monocytes and acts via receptors that also recognize MIP-1 alpha. It induced intracellular Ca(2+) changes and enzyme release, but no chemotaxis, at concentrations of 100-1,000 nM, and was inactive on T-lymphocytes, neutrophils, and eosinophil leukocytes. Enhances the proliferation of CD34 myeloid progenitor cells. The processed form HCC-1(9-74) is a chemotactic factor that attracts monocytes eosinophils, and T-cells and is a ligand for CCR1, CCR3 and CCR5.
Pathway Studio
  • CCR1 → STAT signaling
  • CCR2/5 → STAT signaling
  • CCR5 → TP53 signaling
  • Nociception-related CCR1 expression targets
  • Summarized nociception-related expression targets

C-C motif chemokine 23 (MPIF-1)

Target (abbrv.) MPIF-1
Target (full name) C-C motif chemokine 23
Somalogic ID (Sequence ID) SL003302 (2913-1_2)
Entrez Gene Symbol CCL23
UniProt ID P55773
UniProt Comment
  • Shows chemotactic activity for monocytes, resting T-lymphocytes, and neutrophils, but not for activated lymphocytes. Inhibits proliferation of myeloid progenitor cells in colony formation assays. This protein can bind heparin. Binds CCR1. CCL23(19-99), CCL23(22-99), CCL23(27-99), CCL23(30-99) are more potent chemoattractants than the small-inducible cytokine A23.
Reactome
  • Formyl peptide receptors bind formyl peptides and many other ligands
  • G alpha (i) signalling events
  • G alpha (q) signalling events
Pathway Studio
  • CCR1 → STAT signaling
  • Nociception-related CCR1 expression targets
  • Summarized nociception-related expression targets

C-C motif chemokine 18 (PARC)

Target (abbrv.) PARC
Target (full name) C-C motif chemokine 18
Somalogic ID (Sequence ID) SL003323 (3044-3_2)
Entrez Gene Symbol CCL18
UniProt ID P55774
UniProt Comment
  • Chemotactic factor that attracts lymphocytes but not monocytes or granulocytes. May be involved in B-cell migration into B-cell follicles in lymph nodes. Attracts naive T-lymphocytes toward dendritic cells and activated macrophages in lymph nodes, has chemotactic activity for naive T-cells, CD4+ and CD8+ T-cells and thus may play a role in both humoral and cell-mediated immunity responses.
Biomarker applications (based on IPA annotation)
  • efficacy
  • safety

C-C motif chemokine 3 (MIP-1a)

Target (abbrv.) MIP-1a
Target (full name) C-C motif chemokine 3
Somalogic ID (Sequence ID) SL000519 (3040-59_1)
Entrez Gene Symbol CCL3
UniProt ID P10147
UniProt Comment
  • Monokine with inflammatory and chemokinetic properties. Binds to CCR1, CCR4 and CCR5. One of the major HIV-suppressive factors produced by CD8+ T-cells. Recombinant MIP-1-alpha induces a dose-dependent inhibition of different strains of HIV-1, HIV-2, and simian immunodeficiency virus (SIV).
Biomarker applications (based on IPA annotation)
  • diagnosis
  • efficacy
  • prognosis
Wiki Pathways
  • Regulation of toll-like receptor signaling pathway
  • Senescence and Autophagy
  • Toll-like receptor signaling pathway
Pathway Interaction Database
  • IL12-mediated signaling events
Reactome
  • Chemokine receptors bind chemokines
Pathway Studio
  • CCR1 → STAT signaling
  • CCR2/5 → STAT signaling
  • CCR5 → TP53 signaling
  • Nociception-related CCR1 expression targets
  • Summarized nociception-related expression targets

All locus annotations are based on the sentinel SNP (rs41341749) and 4 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