Connecting genetic risk to disease endpoints through the human blood plasma proteome
ONLINE SUPPLEMENTARY INFORMATION
Locus annotations
Locus 64
Top associations per target
| Target | cis/trans | Study | SNP | SNP location | Maj/min allele | MAF | N | βinv | seinv | Pinv | fclog | Plog | Praw |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| FCRL3 | cis | Discovery | rs7522061 | 1:157,668,390 | T/C | 0.43 | 994 | 0.676 | 0.040 | 5.4×10-57 | 1.100 | 1.2×10-15 | 0.112 |
| FCRL3 | cis | Replication | rs7522061 | 1:157,668,390 | A/G | 0.45 | 337 | 0.426 | 0.065 | 2.7×10-10 | 1.100 | 1.3×10-4 | 0.062 |
Regional association plots
Fc receptor-like protein 3 (FCRL3)
Boxplots and histograms for top associations
All locus annotations are based on the sentinel SNP (rs7522061) and 12 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 |
|---|---|---|---|
| cg17134153 (chr1:157670352) | 3.3×10-310 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg25259754 (chr1:157670196) | 3.3×10-310 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg19602479 (chr1:157670845) | 1.4×10-278 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg08786003 (chr1:157670686) | 2.1×10-169 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of FCRL3 in blood | 6.8×10-74 | 21829388 (PMID) | GRASP2 eQTL |
| Gene expression of [probe 70754 centered at chr1:155915082] in blood | 9.1×10-56 | 21829388 (PMID) | GRASP2 eQTL |
| cg07184316 (chr1:157669087) | 2.9×10-46 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of [probe 620167 centered at chr1:155914668] in blood | 2×10-30 | 21829388 (PMID) | GRASP2 eQTL |
| Positivity for ZnT8A in Type 1 diabetes | 1.1×10-16 | 22526605 (PMID) | GRASP2 nonQTL |
| Grave's disease | 1.5×10-13 | 21841780 (PMID) | GRASP2 nonQTL |
| Graves' disease | 2×10-13 | 21841780 (PMID) | GWAS Catalog via SNiPA |
| Positivity for ZnT8WA in Type 1 diabetes | 8.1×10-12 | 22526605 (PMID) | GRASP2 nonQTL |
| Insulinoma-associated antigen 2 positive (IA-2A) Type 1 diabetes | 8.3×10-12 | 21829393 (PMID) | GRASP2 nonQTL |
| Type 1 diabetes autoantibodies | 1×10-11 | 21829393 (PMID) | GWAS Catalog via SNiPA |
| Positivity for ZnT8RA in Type 1 diabetes | 1.7×10-11 | 22526605 (PMID) | GRASP2 nonQTL |
| Gene expression of FCRL3 [probe 231093_at] in lymphoblastoid cell lines | 1×10-10 | 17873877 (PMID) | GRASP2 eQTL |
| Gene expression of FCRL3 in CD4+ lymphocytes | 4×10-10 | 20833654 (PMID) | GRASP2 eQTL |
| Gene expression of FCRL3 in peripheral blood monocytes | 4.5×10-10 | 20502693 (PMID) | GRASP2 eQTL |
| Persistent TRAb autoantibody positive Grave's disease | 1×10-9 | 21841780 (PMID) | GRASP2 nonQTL |
| cg15761405 (chr1:157746429) | 5.7×10-8 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of FCRL3 in liver | 1.7×10-7 | 18462017 (PMID) | GRASP2 eQTL |
| Multiple sclerosis | 9.9×10-7 | 21833088 (PMID) | GRASP2 nonQTL |
| Monocyte count | 1.1×10-6 | 21738479 (PMID) | GRASP2 nonQTL |
| Gene expression of PLXNB2 in liver | 3×10-6 | 18462017 (PMID) | GRASP2 eQTL |
| Major depressive disorder | 3.2×10-6 | 20673876 (PMID) | GRASP2 nonQTL |
| Serum ratio of (hydroxyisovaleroyl carnitine)/(threitol) | 7.3×10-6 | 21886157 (PMID) | GRASP2 metabQTL |
| Gene expression of IQUB in peripheral blood monocytes | 8.7×10-6 | 20502693 (PMID) | GRASP2 eQTL |
| Graves' disease and Hashimoto's thyroiditis | 2.4×10-5 | 22922229 (PMID) | GRASP2 nonQTL |
| Alkaline phosphatase | 3.3×10-5 | pha001179 (dbGaP) | dbGaP via SNiPA |
| Persistent TRAb autoantibody negative Grave's disease | 6.2×10-5 | 21841780 (PMID) | GRASP2 nonQTL |
| Gene expression of FCRL3 in blood cells in Celiac disease | 8.6×10-5 | 19128478 (PMID) | GRASP2 eQTL |
| Autoantigen thyroid peroxidase positive (TPOA) Type 1 diabetes | 3.5×10-4 | 21829393 (PMID) | GRASP2 nonQTL |
| Serum ratio of (1-methylurate)/(biliverdin) | 3.9×10-4 | 21886157 (PMID) | GRASP2 metabQTL |
| Rheumatoid arthritis | 4.3×10-4 | 20453842 (PMID) | GRASP2 nonQTL |