Connecting genetic risk to disease endpoints through the human blood plasma proteome
ONLINE SUPPLEMENTARY INFORMATION
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
CMRF35-like molecule 6 (CLM6)
Boxplots and histograms for top associations
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.