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WCMC

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

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Locus annotations

Locus 9

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Cripto cis Discovery rs3806701 3:46,617,337 G/A 0.27 997 1.106 0.036 3.8×10-145 1.230 3.7×10-84 2.8×10-28
Cripto cis Replication rs3806702 3:46,617,502 A/G 0.22 337 1.050 0.070 3.3×10-39 1.210 1×10-32 1.2×10-20

 

Regional association plots

Teratocarcinoma-derived growth factor 1 (Cripto)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Teratocarcinoma-derived growth factor 1 (Cripto)

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

Teratocarcinoma-derived growth factor 1 (Cripto)

Target (abbrv.) Cripto
Target (full name) Teratocarcinoma-derived growth factor 1
Somalogic ID (Sequence ID) SL005155 (2672-60_1)
Entrez Gene Symbol TDGF1
UniProt ID P13385
UniProt Comment
  • Could play a role in the determination of the epiblastic cells that subsequently give rise to the mesoderm.
Biomarker applications (based on IPA annotation)
  • diagnosis

All locus annotations are based on the sentinel SNP (rs3806701) and 8 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
Potentially regulated genes
eQTL genes
  • ALS2CL ALS2 C-terminal like
  • TDGF1 teratocarcinoma-derived growth factor 1
  • LRRC2 leucine rich repeat containing 2
  • LRRC2-AS1 LRRC2 antisense RNA 1

 

Results from other genome-wide association studies

Trait P Study Source
cg00285902 (chr3:46605640) 8.8×10-35 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
P13385 protein abundance levels 7.1×10-13 22595970 (PMID) GRASP2 pQTL
Gene expression of LRRC2 (probeID ILMN_1755047) in cerebellum in Alzheimer's disease cases and controls 5.3×10-12 22685416 (PMID) GRASP2 eQTL
Gene expression of LRRC2 (probeID ILMN_1755047) in cerebellum in Alzheimer's disease cases 9.2×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of LRRC2 (probeID ILMN_1755047) in cerebellum in non-Alzheimer's disease samples 2.1×10-6 22685416 (PMID) GRASP2 eQTL