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 |
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)
Genes hit or close-by | |
Potentially regulated genes |
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eQTL genes |
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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 |
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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.