Connecting genetic risk to disease endpoints through the human blood plasma proteome
ONLINE SUPPLEMENTARY INFORMATION
Locus annotations
Locus 95
Top associations per target
| Target | cis/trans | Study | SNP | SNP location | Maj/min allele | MAF | N | βinv | seinv | Pinv | fclog | Plog | Praw |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| TXD12 | trans | Discovery | rs11715835 | 3:48,770,732 | C/T | 0.10 | 996 | 0.943 | 0.068 | 2.2×10-40 | 1.260 | 2×10-37 | 2.1×10-42 |
| TXD12 | trans | Replication | rs9844757 | 3:49,343,601 | A/C | 0.05 | 337 | 0.865 | 0.154 | 4.2×10-8 | 1.260 | 5.1×10-7 | 9.9×10-7 |
Regional association plots
Thioredoxin domain-containing protein 12 (TXD12)
Boxplots and histograms for top associations
Thioredoxin domain-containing protein 12 (TXD12)
All locus annotations are based on the sentinel SNP (rs11715835) and 106 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 |
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| Potentially regulated genes |
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| eQTL genes |
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Results from other genome-wide association studies
| Trait | P | Study | Source |
|---|---|---|---|
| cg13063704 (chr3:48885689) | 3.5×10-118 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg16323609 (chr3:48885615) | 3.9×10-78 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg19472611 (chr3:48885464) | 2.4×10-57 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of WDR6 in peripheral blood monocytes | 4.1×10-37 | 20502693 (PMID) | GRASP2 eQTL |
| Gene expression of WDR6 in blood | 3.1×10-36 | 21829388 (PMID) | GRASP2 eQTL |
| Gene expression of C3orf62///USP4 in blood | 1.3×10-30 | 21829388 (PMID) | GRASP2 eQTL |
| Gene expression of USP4 in peripheral blood monocytes | 7×10-27 | 20502693 (PMID) | GRASP2 eQTL |
| cg08846852 (chr3:49314838) | 5.8×10-21 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg00675133 (chr3:48754922) | 6.9×10-19 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg24090938 (chr3:49211773) | 1.7×10-15 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Inflammatory bowel disease | 2×10-11 | Supplemental file | |
| cg03352189 (chr3:49236894) | 1.5×10-9 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of KLHDC8B///CCDC36 in blood | 1.7×10-9 | 21829388 (PMID) | GRASP2 eQTL |
| Ulcerative collitis | 1.6×10-8 | Supplemental file | |
| Gene expression of WDR6 in normal prepouch ileum | 1.7×10-8 | 23474282 (PMID) | GRASP2 eQTL |
| Gene expression of NCKIPSD in blood | 4.2×10-8 | 21829388 (PMID) | GRASP2 eQTL |
| cg04581018 (chr3:49236784) | 4.4×10-8 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg08071130 (chr3:49228544) | 8.5×10-8 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of CELSR3 in blood | 8.8×10-8 | 21829388 (PMID) | GRASP2 eQTL |
| Gene expression of HYAL3 in peripheral blood monocytes | 2.3×10-7 | 20502693 (PMID) | GRASP2 eQTL |
| cg21950072 (chr3:48755000) | 3.1×10-7 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of NCKIPSD in peripheral blood monocytes | 3.2×10-7 | 20502693 (PMID) | GRASP2 eQTL |
| Differential exon level expression of CELSR3 [probe 2673630] in brain cortex | 1.8×10-6 | 19222302 (PMID) | GRASP2 eQTL |
| cg05726910 (chr3:48885413) | 3.3×10-6 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Crohn's disease | 3.7×10-6 | Supplemental file | |
| cg07109801 (chr3:49057685) | 3.9×10-6 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| cg03163443 (chr3:49209029) | 4.8×10-6 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Gene expression of ZFAT in peripheral blood monocytes | 4.8×10-6 | 20502693 (PMID) | GRASP2 eQTL |
| Gene expression of [probe 150692 centered at chr3:48638191] in blood | 1.3×10-5 | 21829388 (PMID) | GRASP2 eQTL |
| Gene expression of SLC25A20 (ENSG00000178537) in dendritic cells treated with Mycobacterium tuberculosis | 1.7×10-5 | 22233810 (PMID) | GRASP2 eQTL |
| Serum creatinine | 3.5×10-5 | 20383146 (PMID) | GRASP2 nonQTL |
| Gene expression of USP4 [probe ILMN_5953] in osteoblasts treated with BMP2 | 4×10-5 | 21283786 (PMID) | GRASP2 eQTL |
| cg02386575 (chr3:49068033) | 4.1×10-5 | 10.1101/033084 (DOI) | BIOS QTL cis-meQTLs |
| Differential exon level expression of CELSR3 [probe 2673639] in brain cortex | 5.1×10-5 | 19222302 (PMID) | GRASP2 eQTL |
| Gene expression of USP4 [probe 202681_at] in prefrontal cortex | 5.9×10-5 | 20351726 (PMID) | GRASP2 eQTL |
| Serum concentration of mannose | 1.2×10-4 | 21886157 (PMID) | GRASP2 metabQTL |
| Anorexia nervosa | 1.2×10-4 | 24514567 (PMID) | Supplemental file |
| Gene expression of IHPK2 in blood | 1.9×10-4 | 21829388 (PMID) | GRASP2 eQTL |
| Attention-deficit/hyperactivity disorder | 3.4×10-4 | 20732625 (PMID) | Supplemental file |
Poorly characterized protein, may be further investigated using information on cis-encoded genes and eQTLs.
Two SNPs that are 1.2 MB apart, each harbours a replicated trans-pQTLs with Thioredoxin domain-containing protein 12 (TXNDC12). This protein is poorly characterized. Multiple cis-encoded genes with strong eQTLs may be used to elucidate its biological role. rs11715835 tags a 20 order of magnitude stronger association on imputed variant rs143867864. rs143867864 is uncorrelated with rs4688759.
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.