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Connecting genetic risk to disease endpoints through the human blood plasma proteome

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Locus annotations

Locus 91

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 rs4688759 3:50,008,118 T/C 0.10 997 0.959 0.067 1.8×10-42 1.270 1.4×10-39 9.2×10-46
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)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Thioredoxin domain-containing protein 12 (TXD12)

inverse-normalized probe levels log2 transformed probe levels raw probe levels
Discovery study
Replication study

Thioredoxin domain-containing protein 12 (TXD12)

Target (abbrv.) TXD12
Target (full name) Thioredoxin domain-containing protein 12
Somalogic ID (Sequence ID) SL016128 (4815-25_3)
Entrez Gene Symbol TXNDC12
UniProt ID O95881
UniProt Comment
  • Possesses significant protein thiol-disulfide oxidase activity.

All locus annotations are based on the sentinel SNP (rs4688759) and 19 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


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Genes hit or close-by
  • BSN bassoon presynaptic cytomatrix protein
  • AMIGO3 adhesion molecule with Ig-like domain 3
  • GMPPB GDP-mannose pyrophosphorylase B
  • RNF123 ring finger protein 123
  • IP6K1 inositol hexakisphosphate kinase 1
  • RP13-1056D16.2
  • TRAIP TRAF interacting protein
  • RN7SL217P RNA, 7SL, cytoplasmic 217, pseudogene
  • CAMKV CaM kinase-like vesicle-associated
  • AC139451.2
  • ACTBP13 actin, beta pseudogene 13
  • RBM6 RNA binding motif protein 6
  • RBM5 RNA binding motif protein 5
eQTL genes
  • NCKIPSD NCK interacting protein with SH3 domain
  • AMT aminomethyltransferase
  • WDR6 WD repeat domain 6
  • TMEM89 transmembrane protein 89
  • SEMA3F sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F
  • NICN1 nicolin 1
  • CCDC36 coiled-coil domain containing 36
  • SLC26A6 solute carrier family 26 (anion exchanger), member 6
  • RBM6 RNA binding motif protein 6
  • C3orf62 chromosome 3 open reading frame 62
  • RP11-3B7.1
  • USP4 ubiquitin specific peptidase 4 (proto-oncogene)
  • APEH acylaminoacyl-peptide hydrolase
  • UBA7 ubiquitin-like modifier activating enzyme 7
  • MIR5193 microRNA 5193
  • HYAL3 hyaluronoglucosaminidase 3
  • CCDC71 coiled-coil domain containing 71

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of WDR6 in peripheral blood monocytes 1.7×10-28 20502693 (PMID) GRASP2 eQTL
Gene expression of USP4 in peripheral blood monocytes 1.8×10-27 20502693 (PMID) GRASP2 eQTL
Gene expression of HYAL3 in peripheral blood monocytes 2×10-10 20502693 (PMID) GRASP2 eQTL
Inflammatory bowel disease 4.5×10-8 Supplemental file
Gene expression of WDR6 in normal prepouch ileum 9.6×10-7 23474282 (PMID) GRASP2 eQTL
Ulcerative collitis 8.8×10-6 Supplemental file
Crohn's disease 2.2×10-5 Supplemental file
Anorexia nervosa 1.2×10-4 24514567 (PMID) Supplemental file
"Gene expression of UBA7 [transcript NM_003335, probe A_23_P21207] in liver" 1.8×10-4 21637794 (PMID) GRASP2 eQTL
Attention-deficit/hyperactivity disorder 2.5×10-4 20732625 (PMID) Supplemental file
Total cholesterol 2.9×10-4 20339536 (PMID) GRASP2 nonQTL

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.