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

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Locus annotations

Locus 449

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
RANTES cis Discovery rs4239252 17:34,163,565 G/A 0.21 996 -0.346 0.053 7.8×10-11 -1.150 2.9×10-10 7.8×10-10
RANTES cis Replication rs55858632 17:34,099,741 A/G 0.24 337 -0.162 0.056 0.004 -1.140 0.007 0.011

 

Regional association plots

 

Boxplots and histograms for top associations

C-C motif chemokine 5 (RANTES)

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

C-C motif chemokine 5 (RANTES)

Target (abbrv.) RANTES
Target (full name) C-C motif chemokine 5
Somalogic ID (Sequence ID) SL000563 (2523-31_3)
Entrez Gene Symbol CCL5
UniProt ID P13501
UniProt Comment
  • Chemoattractant for blood monocytes, memory T-helper cells and eosinophils. Causes the release of histamine from basophils and activates eosinophils. May activate several chemokine receptors including CCR1, CCR3, CCR4 and CCR5. One of the major HIV-suppressive factors produced by CD8+ T-cells. Recombinant RANTES protein induces a dose-dependent inhibition of different strains of HIV-1, HIV-2, and simian immunodeficiency virus (SIV). The processed form RANTES(3-68) acts as a natural chemotaxis inhibitor and is a more potent inhibitor of HIV-1-infection. The second processed form RANTES(4-68) exhibits reduced chemotactic and HIV-suppressive activity compared with RANTES(1-68) and RANTES(3-68) and is generated by an unidentified enzyme associated with monocytes and neutrophils (PubMed:16791620, PubMed:1380064, PubMed:8525373, PubMed:9516414, PubMed:15923218). May also be an agonist of the G protein-coupled receptor GPR75, stimulating inositol trisphosphate production and calcium mobilization through its activation. Together with GPR75, may play a role in neuron survival through activation of a downstream signaling pathway involving the PI3, Akt and MAP kinases. By activating GPR75 may also play a role in insulin secretion by islet cells (PubMed:23979485).
Biomarker applications (based on IPA annotation)
  • diagnosis
  • efficacy
  • unspecified application

All locus annotations are based on the sentinel SNP (rs4239252) and 52 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
eQTL genes
  • CCL5 chemokine (C-C motif) ligand 5

 

Results from other genome-wide association studies

Trait P Study Source
cg08012672 (chr17:34258194) 6.4×10-25 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of CCL5 in CEU-CHB-JPT-YRI lymphoblastoid cell lines 4.2×10-17 17873874 (PMID) GRASP2 eQTL
Gene expression of RAD52B in CEU-CHB-JPT-YRI lymphoblastoid cell lines 5.7×10-14 17873874 (PMID) GRASP2 eQTL
Gene expression of NFS1 in peripheral blood monocytes 1.1×10-13 20502693 (PMID) GRASP2 eQTL
Gene expression of CCL5 in peripheral blood monocytes 3.7×10-13 20502693 (PMID) GRASP2 eQTL
Gene expression of NPSR1 in peripheral blood monocytes 2.8×10-11 20502693 (PMID) GRASP2 eQTL
Gene expression of ZKSCAN2 in peripheral blood monocytes 3.7×10-11 20502693 (PMID) GRASP2 eQTL
Gene expression of probe 241885_at in lymphoblastoid cell lines 1×10-9 17873877 (PMID) GRASP2 eQTL
Gene expression of CCL5 in blood 4.3×10-8 21829388 (PMID) GRASP2 eQTL
cg11915366 (chr17:34139095) 4×10-7 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of KRTAP20-2 in peripheral blood monocytes 3.8×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of CD3D in peripheral blood monocytes 9.1×10-6 20502693 (PMID) GRASP2 eQTL
cg16983627 (chr17:34238362) 1.2×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg13376404 (chr17:34077317) 1.3×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Cup-to-disc ratio (taken at worst eye) 2.5×10-5 22605921 (PMID) GRASP2 nonQTL
cg04932840 (chr17:34077117) 3.5×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
N-acetylglycine 5.8×10-5 24816252 (PMID) gwas.eu via SNiPA
pyridoxate 9.6×10-5 24816252 (PMID) gwas.eu via SNiPA
"Gene expression of MMP28 [transcript NM_024302, probe A_23_P26890] in liver" 3.1×10-4 21637794 (PMID) GRASP2 eQTL