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WCMC

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

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Locus annotations

Locus 152

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
PD-L2 cis Discovery rs16923189 9:5,510,644 A/G 0.28 996 0.524 0.048 1.6×10-26 1.090 8.9×10-23 6.6×10-19
PD-L2 cis Replication rs16923189 9:5,510,644 A/G 0.28 337 0.363 0.061 7.9×10-9 1.100 1.1×10-5 0.177

 

Regional association plots

Programmed cell death 1 ligand 2 (PD-L2)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Programmed cell death 1 ligand 2 (PD-L2)

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

Programmed cell death 1 ligand 2 (PD-L2)

Target (abbrv.) PD-L2
Target (full name) Programmed cell death 1 ligand 2
Somalogic ID (Sequence ID) SL004862 (3004-67_2)
Entrez Gene Symbol PDCD1LG2
UniProt ID Q9BQ51
UniProt Comment
  • Involved in the costimulatory signal, essential for T-cell proliferation and IFNG production in a PDCD1-independent manner. Interaction with PDCD1 inhibits T-cell proliferation by blocking cell cycle progression and cytokine production (By similarity).
Reactome
  • PD-1 signaling
Pathway Studio
  • Peripheral T-cell Tolerance Overview

All locus annotations are based on the sentinel SNP (rs16923189) and 6 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
  • PDCD1LG2 programmed cell death 1 ligand 2
Potentially regulated genes
eQTL genes
  • PDCD1LG2 programmed cell death 1 ligand 2

 

Results from other genome-wide association studies

Trait P Study Source
Methylation levels at chr9:5500447-5500497 [hg18 coord, probe cg07211259] in Temporal cortex 1.4×10-14 20485568 (PMID) GRASP2 meQTL
Methylation levels at chr9:5500447-5500497 [hg18 coord, probe cg07211259] in Frontal cortex 1.4×10-12 20485568 (PMID) GRASP2 meQTL
Methylation levels at chr9:5500447-5500497 [hg18 coord, probe cg07211259] in Caudal pons 2.6×10-9 20485568 (PMID) GRASP2 meQTL
Gene expression of PDCD1LG2 (probeID ILMN_2159272) in cerebellum in Alzheimer's disease cases and controls 4.5×10-9 22685416 (PMID) GRASP2 eQTL
Gene expression of PDCD1LG2 (probeID ILMN_2159272) in cerebellum in non-Alzheimer's disease samples 2.1×10-5 22685416 (PMID) GRASP2 eQTL
Gene expression of PDCD1LG2 [probe ILMN_3561] in osteoblasts treated with dexamethasone 7.7×10-5 21283786 (PMID) GRASP2 eQTL
Ulcerative collitis 8.6×10-5 Supplemental file
Gene expression of PDCD1LG2 (probeID ILMN_2159272) in temporal cortex in Alzheimer's disease cases 9.3×10-5 22685416 (PMID) GRASP2 eQTL