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

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Locus annotations

Locus 54

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
G-CSF trans Discovery rs5167 19:45,448,465 T/G 0.35 997 0.750 0.039 2.1×10-69 1.200 1.2×10-28 0.117
G-CSF trans Replication rs5167 19:45,448,465 A/C 0.36 337 0.334 0.074 9.5×10-6 1.050 0.165 0.273

 

Regional association plots

Granulocyte colony-stimulating factor (G-CSF)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Granulocyte colony-stimulating factor (G-CSF)

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

Granulocyte colony-stimulating factor (G-CSF)

Target (abbrv.) G-CSF
Target (full name) Granulocyte colony-stimulating factor
Somalogic ID (Sequence ID) SL001729 (4840-73_1)
Entrez Gene Symbol CSF3
UniProt ID P09919
UniProt Comment
  • Granulocyte/macrophage colony-stimulating factors are cytokines that act in hematopoiesis by controlling the production, differentiation, and function of 2 related white cell populations of the blood, the granulocytes and the monocytes-macrophages. This CSF induces granulocytes.
Targeted by drugs (based on IPA annotation)
  • filgrastim
Biomarker applications (based on IPA annotation)
  • diagnosis
Wiki Pathways
  • Cytokines and Inflammatory Response
Pathway Studio
  • CSF3R → STAT signaling
  • Nociception-related IL1B expression targets

All locus annotations are based on the sentinel SNP (rs5167) and 11 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
  • CEACAM19 carcinoembryonic antigen-related cell adhesion molecule 19
  • BCL3 B-cell CLL/lymphoma 3
eQTL genes
  • APOE apolipoprotein E
  • CLPTM1 cleft lip and palate associated transmembrane protein 1
  • APOC1 apolipoprotein C-I

 

Results from other genome-wide association studies

Trait P Study Source
cg06736138 (chr19:45444836) 5.5×10-83 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Alzheimer's disease 2.5×10-18 24162737 (PMID) Supplemental file
HDL cholesterol 4.9×10-16 24097068 (PMID) Supplemental file
Late onset Alzheimer's disease 3.4×10-8 21460841 (PMID) GRASP2 nonQTL
Triglycerides 2.2×10-6 24097068 (PMID) Supplemental file
Differential exon level expression of CLPTM1 [probe 3835952] in brain cortex 6.1×10-6 19222302 (PMID) GRASP2 eQTL
Height 2×10-5 25282103 (PMID) Supplemental file
Total cholesterol 3.9×10-5 20686565 (PMID) GRASP2 nonQTL
Gene expression of BLOC1S3 [probe ILMN_4337] in osteoblasts treated with pge-2 1.3×10-4 21283786 (PMID) GRASP2 eQTL
Schizophrenia 2×10-4 23974872 (PMID) Supplemental file
Bipolar disorder vs. Schizophrenia 2.9×10-4 24280982 (PMID) Supplemental file
Hip circumfence, adjusted for BMI 4.7×10-4 25673412 (PMID) Supplemental file

APOC4 and CSF3 may interact.

This locus is located in the APOE/C1/C4/C2 cluster and harbours a replicated trans-association with Granulocyte colony-stimulating factor (CSF3). rs5167 is linked to rs35336243 (r2>0.8), which associates with Alzheimer's disease (p=2.55×10-18) in the International Genomics of Alzheimer's Project (IGAP) stage 1 data. From the data at hand it is however not possible to say whether this is an independent association signal with AD, or a spill-over from the main AD variant in APOE. This variant is an amino acid changing variant in APOC4 (L96R). Since rs5167 also shows the strongest association with CSF3 when using imputed SNPs, it is likely that this variant in APOC4 causes differential protein expression of CSF3.

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.