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

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Locus annotations

Locus 87

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
PARC cis Discovery rs9904601 17:34,372,006 G/A 0.12 996 0.863 0.060 2.5×10-43 1.440 8.3×10-44 2.1×10-37
PARC cis Replication rs972317 17:34,371,659 A/C 0.14 337 0.644 0.097 1.5×10-10 1.300 1.8×10-10 9.9×10-9
MIP-1a cis Discovery rs9904601 17:34,372,006 G/A 0.12 996 0.571 0.066 1.2×10-17 1.130 1.2×10-10 0.663
MIP-1a cis Replication rs972317 17:34,371,659 A/C 0.14 337 0.440 0.099 1.1×10-5 1.150 1.4×10-4 0.099

 

Regional association plots

 

Boxplots and histograms for top associations

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 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 (rs9904601).
However, the sentinel SNP is not contained in SNiPA's database (1000 Genomes Project, phase 3 version 5, European population). Thus, no information about linked genes or further functional annotation is available.

 

Results from other genome-wide association studies


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No associations available.

Genetic variation can inform relationship between different chemokines encoded at the chr7-cluster.

This locus includes two replicated cis-associations, with C-C motif chemokine 18 (CCL18, aka PARC) and C-C motif chemokine 3 (CCL3, aka MIP-1a). Note that there are multiple C-C motif chemokines encoded at this locus, including CCL3/4/5/7/14/15/16/18/23. See also Locus 88.

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.