HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 184

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
TSG-6 cis Discovery rs289828 2:152,137,181 T/C 0.43 994 0.395 0.041 2.1×10-21 1.120 8.3×10-19 2.3×10-11
TSG-6 cis Replication rs2278089 2:152,146,672 A/C 0.37 337 0.441 0.053 1.5×10-15 1.160 3.2×10-15 2.5×10-13

 

Regional association plots

Tumor necrosis factor-inducible gene 6 protein (TSG-6)

 

Boxplots and histograms for top associations

Tumor necrosis factor-inducible gene 6 protein (TSG-6)

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

Tumor necrosis factor-inducible gene 6 protein (TSG-6)

Target (abbrv.) TSG-6
Target (full name) Tumor necrosis factor-inducible gene 6 protein
Somalogic ID (Sequence ID) SL004782 (5036-50_1)
Entrez Gene Symbol TNFAIP6
UniProt ID P98066
UniProt Comment
  • Possibly involved in cell-cell and cell-matrix interactions during inflammation and tumorigenesis.
Biomarker applications (based on IPA annotation)
  • unspecified application

All locus annotations are based on the sentinel SNP (rs289828) and 39 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
  • RBM43 RNA binding motif protein 43
  • NMI N-myc (and STAT) interactor
eQTL genes
  • RBM43 RNA binding motif protein 43
  • RIF1 replication timing regulatory factor 1
  • NMI N-myc (and STAT) interactor
  • TNFAIP6 tumor necrosis factor, alpha-induced protein 6

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of TNFAIP6 in blood 5.4×10-101 21829388 (PMID) GRASP2 eQTL
Gene expression of TNFAIP6 in peripheral blood monocytes 3.6×10-63 20502693 (PMID) GRASP2 eQTL
Gene expression of RBM43 in blood 8.4×10-53 21829388 (PMID) GRASP2 eQTL
Gene expression of NMI in blood 8.4×10-23 21829388 (PMID) GRASP2 eQTL
cg19350357 (chr2:152118859) 1.5×10-13 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of NMI in normal prepouch ileum 3.9×10-12 23474282 (PMID) GRASP2 eQTL
Differential exon level expression of NMI [probe 2580969] in peripheral blood mononuclear cells 3.5×10-6 19222302 (PMID) GRASP2 eQTL
Gene expression of NMI [probe ILMN_3552] in osteoblasts treated with PGE2 4.7×10-6 21283786 (PMID) GRASP2 eQTL
Gene expression of NMI [probe ILMN_3552] in untreated osteoblasts 1.1×10-5 21283786 (PMID) GRASP2 eQTL
Smoking behaviour, Ever smoked 3.2×10-5 20418890 (PMID) Supplemental file
Gene expression of TNFAIP6 in blood cells in Celiac disease 7.5×10-5 19128478 (PMID) GRASP2 eQTL
Obsessive-compulsive disorder (OCD) 3.6×10-4 22889921 (PMID) GRASP2 nonQTL
Serum ratio of (alpha-ketoglutarate)/(alpha-tocopherol) 4.5×10-4 21886157 (PMID) GRASP2 metabQTL
Triglycerides 4.9×10-4 20686565 (PMID) GRASP2 nonQTL