Connecting genetic risk to disease endpoints through the human blood plasma proteome
ONLINE SUPPLEMENTARY INFORMATION
Locus annotations
Locus 48
Top associations per target
| Target | cis/trans | Study | SNP | SNP location | Maj/min allele | MAF | N | βinv | seinv | Pinv | fclog | Plog | Praw |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ILT-4 | cis | Discovery | rs103294 | 19:54,797,848 | C/T | 0.19 | 995 | -0.943 | 0.048 | 1.7×10-73 | -1.230 | 3.6×10-80 | 2.8×10-64 |
| ILT-4 | cis | Replication | rs798888 | 19:54,793,239 | G/A | 0.13 | 337 | -0.832 | 0.089 | 1×10-18 | -1.300 | 1.7×10-16 | 7.7×10-10 |
Regional association plots
Leukocyte immunoglobulin-like receptor subfamily B member 2 (ILT-4)
Boxplots and histograms for top associations
Leukocyte immunoglobulin-like receptor subfamily B member 2 (ILT-4)
| Target (abbrv.) | ILT-4 |
| Target (full name) | Leukocyte immunoglobulin-like receptor subfamily B member 2 |
| Somalogic ID (Sequence ID) | SL005191 (5091-28_3) |
| Entrez Gene Symbol | LILRB2 |
| UniProt ID | Q8N423 |
| UniProt Comment |
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| Reactome |
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All locus annotations are based on the sentinel SNP (rs103294) and 24 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 |
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| eQTL genes |
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Results from other genome-wide association studies
| Trait | P | Study | Source |
|---|---|---|---|
| Gene expression of LILRA3 in peripheral blood monocytes | Warning: Division by zero in /var/www/html/pGWAS/locuscard.php on line 7 Warning: Division by zero in /var/www/html/pGWAS/locuscard.php on line 7 INF×10-324 |
20502693 (PMID) | GRASP2 eQTL |
| Gene expression of LILRA3///LILRA1 in blood | 9.8×10-198 | 21829388 (PMID) | GRASP2 eQTL |
| Gene expression of LILRA3 in blood | 3.5×10-157 | 21829388 (PMID) | GRASP2 eQTL |
| LILRA3 gene expression | 1.1×10-48 | 21798870 (PMID) | GRASP2 eQTL |
| HDL cholesterol | 4×10-30 | 24097068 (PMID) | Supplemental file |
| Gene expression of LILRA5 in blood | 1.2×10-22 | 21829388 (PMID) | GRASP2 eQTL |
| PROSTATE CANCER | 5×10-16 | 23023329 (PMID) | GWAS Catalog via SNiPA |
| Prostate cancer | 5.3×10-16 | 23023329 (PMID) | GRASP2 nonQTL |
| "Gene expression of LILRA3 [transcript NM_006865, probe A_23_P79094] in liver" | 4.9×10-15 | 21637794 (PMID) | GRASP2 eQTL |
| Gene expression of LILRA3 in blood cells in Celiac disease | 1.4×10-13 | 19128478 (PMID) | GRASP2 eQTL |
| Differential exon level expression of LILRB3 [probe 3870669] in peripheral blood mononuclear cells | 4.9×10-12 | 19222302 (PMID) | GRASP2 eQTL |
| Gene expression of LILRA3 [probe ILMN_1661631] in peripheral leukocytes | 4.9×10-12 | 19966804 (PMID) | GRASP2 eQTL |
| LILRA3 gene expression in human liver | 9×10-12 | 20686565 (PMID) | GRASP2 nonQTL |
| Triglycerides | 2.3×10-11 | 24097068 (PMID) | Supplemental file |
| Differential exon level expression of LILRB3 [probe 3870671] in peripheral blood mononuclear cells | 4.6×10-11 | 19222302 (PMID) | GRASP2 eQTL |
| Differential exon level expression of LILRB3 [probe 3870663] in peripheral blood mononuclear cells | 5.9×10-11 | 19222302 (PMID) | GRASP2 eQTL |
| Differential exon level expression of LILRB3 [probe 3870667] in peripheral blood mononuclear cells | 1.1×10-10 | 19222302 (PMID) | GRASP2 eQTL |
| Differential exon level expression of LILRB3 [probe 3870670] in peripheral blood mononuclear cells | 2.1×10-10 | 19222302 (PMID) | GRASP2 eQTL |
| Differential exon level expression of LILRB3 [probe 3870674] in peripheral blood mononuclear cells | 4.8×10-10 | 19222302 (PMID) | GRASP2 eQTL |
| Gene expression of LILRB3 [probe 3870611] in peripheral blood mononuclear cells | 1.9×10-9 | 19222302 (PMID) | GRASP2 eQTL |
| Differential exon level expression of LILRB3 [probe 3870673] in peripheral blood mononuclear cells | 6.3×10-9 | 19222302 (PMID) | GRASP2 eQTL |
| Gene expression of LILRA3 (ENSG00000170866) in dendritic cells treated with Mycobacterium tuberculosis | 7.7×10-9 | 22233810 (PMID) | GRASP2 eQTL |
| Gene expression of TSEN34 in blood | 9.7×10-9 | 21829388 (PMID) | GRASP2 eQTL |
| cg02477834 (chr19:475551) | 2.6×10-8 | 10.1101/033084 (DOI) | BIOS QTL trans-meQTLs |
| Gene expression of LILRA3 [probeset 206881_s_at] in sputum | 5.9×10-8 | 21949713 (PMID) | GRASP2 eQTL |
| "Gene expression of LILRB3 [transcript NM_001081450, probe A_23_P368711] in liver" | 9.3×10-8 | 21637794 (PMID) | GRASP2 eQTL |
| Gene expression of LILRB5 in peripheral blood monocytes | 6.4×10-7 | 20502693 (PMID) | GRASP2 eQTL |
| Differential exon level expression of LILRB3 [probe 3870664] in peripheral blood mononuclear cells | 2.5×10-6 | 19222302 (PMID) | GRASP2 eQTL |
| Gene expression of LILRA3 in T cells | 1.2×10-5 | 19644074 (PMID) | GRASP2 eQTL |
| cg15441416 (chr19:54972071) | 1.6×10-5 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Behcet's disease | 2.2×10-5 | 23001997 (PMID) | GRASP2 nonQTL |
| "Gene expression of LILRA4 [transcript NM_012276, probe A_23_P90497] in liver" | 2.3×10-5 | 21637794 (PMID) | GRASP2 eQTL |
| Advanced age-related macular degeneration (choroidal neovascularization) vs. no AMD | 2.4×10-5 | 23455636 (PMID) | GRASP2 nonQTL |
| Advanced age-related macular degeneration | 6.6×10-5 | 23455636 (PMID) | GRASP2 nonQTL |
| Total cholesterol | 1.1×10-4 | 20686565 (PMID) | GRASP2 nonQTL |
| Gene expression of LILRA3 (probeID ILMN_1661631) in breast tumors | 1.7×10-4 | 22522925 (PMID) | GRASP2 eQTL |
Prostate cancer related.
This is a replicated cis-pQTL to Leukocyte immunoglobulin-like receptor subfamily B member 2 (LILRB2). It is a risk-locus for prostate cancer [PubMed]. SNP rs103294 is in strong linkage equilibrium with a 6.7-kb germline deletion that removes the first six of seven exons in LILRA3 – reported in Chinese. Imputing yields much stronger associations, i.e. with coding variant rs386056.
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.