HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 304

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
CLM6 trans Discovery rs722414 12:89,937,437 G/A 0.23 994 0.405 0.052 2.3×10-14 1.090 1.6×10-12 1.2×10-7
CLM6 trans Replication rs2230281 12:89,917,518 G/A 0.22 337 0.351 0.074 3.1×10-6 1.100 2.3×10-5 0.003

 

Regional association plots

 

Boxplots and histograms for top associations

CMRF35-like molecule 6 (CLM6)

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

CMRF35-like molecule 6 (CLM6)

Target (abbrv.) CLM6
Target (full name) CMRF35-like molecule 6
Somalogic ID (Sequence ID) SL014270 (5066-134_3)
Entrez Gene Symbol CD300C
UniProt ID Q08708
UniProt Comment
  • Cell membrane

All locus annotations are based on the sentinel SNP (rs722414) and 93 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
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
GALNT4 gene expression in monocytes 6.4×10-171 22100073 (PMID) GRASP2 nonQTL
cg07204479 (chr12:89915503) 9.7×10-163 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of GALNT4 in peripheral blood monocytes 5.8×10-111 20502693 (PMID) GRASP2 eQTL
Gene expression of WDR51B in blood 1.7×10-81 21829388 (PMID) GRASP2 eQTL
Gene expression of GALNT4 (probeID ILMN_1739297) in cerebellum in Alzheimer's disease cases and controls 5.6×10-15 22685416 (PMID) GRASP2 eQTL
Gene expression of GALNT4 in CEU-CHB-JPT-YRI lymphoblastoid cell lines 1.3×10-13 17873874 (PMID) GRASP2 eQTL
Gene expression of GALNT4 in CEU-CHB-JPT lymphoblastoid cell lines 6.3×10-12 17873874 (PMID) GRASP2 eQTL
Gene expression of GALNT4 (ENSG00000139323) in dendritic cells 4.7×10-9 22233810 (PMID) GRASP2 eQTL
Gene expression of GALNT4 (probeID ILMN_1739297) in cerebellum in non-Alzheimer's disease samples 8.9×10-9 22685416 (PMID) GRASP2 eQTL
Gene expression of GALNT4 [probe ILMN_15303] in untreated osteoblasts 4.6×10-8 21283786 (PMID) GRASP2 eQTL
Gene expression of GALNT4 (ENSG00000139323) in dendritic cells treated with Mycobacterium tuberculosis 4.9×10-8 22233810 (PMID) GRASP2 eQTL
Gene expression of ATP2B1 in blood 1.6×10-7 21829388 (PMID) GRASP2 eQTL
Gene expression of GALNT4 (probeID ILMN_1739297) in cerebellum in Alzheimer's disease cases 2.4×10-7 22685416 (PMID) GRASP2 eQTL
"Gene expression of GALNT4 [transcript NM_003774, probe A_23_P413576] in liver" 5×10-7 21637794 (PMID) GRASP2 eQTL
Gene expression of GALNT4 [probe ILMN_15303] in osteoblasts treated with BMP2 1.6×10-6 21283786 (PMID) GRASP2 eQTL
Height 2.1×10-6 25282103 (PMID) Supplemental file
Gene expression of GALNT4 [probe ILMN_15303] in osteoblasts treated with PGE2 2.9×10-6 21283786 (PMID) GRASP2 eQTL
Gene expression of LETMD1 in peripheral blood monocytes 3.1×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of MT1F in peripheral blood monocytes 4.2×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of GALNT4 [probe ILMN_15303] in osteoblasts treated with dexamethasone 4.6×10-6 21283786 (PMID) GRASP2 eQTL
Schizophrenia 5.4×10-6 25056061 (PMID) Supplemental file
Gene expression of C1QBP in peripheral blood monocytes 7.6×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of TMEM18 in peripheral blood monocytes 9.8×10-6 20502693 (PMID) GRASP2 eQTL
Hip circumfence, adjusted for BMI 1.2×10-5 25673412 (PMID) Supplemental file
1-linoleoylglycerophosphoethanolamine* 2×10-5 24816252 (PMID) gwas.eu via SNiPA
Gene expression of GALNT4 (probeID ILMN_1739297) in cerebellum in Progressive Supranuclear Palsy cases 6.9×10-5 22685416 (PMID) GRASP2 eQTL
ascorbate (Vitamin C) 9.1×10-5 24816252 (PMID) gwas.eu via SNiPA
Plasma aldosterone concentration 3.7×10-4 20877124 (PMID) GRASP2 nonQTL

Possible link between cis-variants and protein levels of CD300C.

This locus harbours a replicated trans-pQTL to CMRF35-like molecule 6 (CD300C).

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.