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

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Locus annotations

Locus 86

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Haptoglobin, Mixed Type cis Discovery rs2000999 16:72,108,093 G/A 0.19 996 -0.758 0.051 7.4×10-45 -1.480 4.6×10-42 1.8×10-40
Heparin cofactor II trans Discovery rs2000999 16:72,108,093 G/A 0.19 996 -0.458 0.054 8.3×10-17 -1.090 6.7×10-18 2.6×10-16
Hemoglobin trans Discovery rs2000999 16:72,108,093 G/A 0.19 996 0.369 0.053 5.3×10-12 1.210 8.2×10-11 0.035

 

Regional association plots

 

Boxplots and histograms for top associations

Haptoglobin (Haptoglobin, Mixed Type)

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

Heparin cofactor 2 (Heparin cofactor II)

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

Hemoglobin

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

Haptoglobin (Haptoglobin, Mixed Type)

Target (abbrv.) Haptoglobin, Mixed Type
Target (full name) Haptoglobin
Somalogic ID (Sequence ID) SL000437 (3054-3_2)
Entrez Gene Symbol HP
UniProt ID P00738
UniProt Comment
  • As a result of hemolysis, hemoglobin is found to accumulate in the kidney and is secreted in the urine. Haptoglobin captures, and combines with free plasma hemoglobin to allow hepatic recycling of heme iron and to prevent kidney damage. Haptoglobin also acts as an Antimicrobial; Antioxidant, has antibacterial activity and plays a role in modulating many aspects of the acute phase response. Hemoglobin/haptoglobin complexes are rapidely cleared by the macrophage CD163 scavenger receptor expressed on the surface of liver Kupfer cells through an endocytic lysosomal degradation pathway.
Biomarker applications (based on IPA annotation)
  • diagnosis
  • efficacy
  • unspecified application
Reactome
  • Scavenging of heme from plasma

Heparin cofactor 2 (Heparin cofactor II)

Target (abbrv.) Heparin cofactor II
Target (full name) Heparin cofactor 2
Somalogic ID (Sequence ID) SL004466 (3316-58_1)
Entrez Gene Symbol SERPIND1
UniProt ID P05546
UniProt Comment
  • Thrombin inhibitor activated by the glycosaminoglycans, heparin or dermatan sulfate. In the presence of the latter, HC-II becomes the predominant thrombin inhibitor in place of antithrombin III (AT-III). Also inhibits chymotrypsin, but in a glycosaminoglycan-independent manner.
Targeted by drugs (based on IPA annotation)
  • ardeparin
  • glucuronyl glucosamine glycan sulfate
Biomarker applications (based on IPA annotation)
  • disease progression
Wiki Pathways
  • Complement and Coagulation Cascades
Reactome
  • Common Pathway of Fibrin Clot Formation
  • Intrinsic Pathway of Fibrin Clot Formation

Hemoglobin

Target (abbrv.) Hemoglobin
Target (full name) Hemoglobin
Somalogic ID (Sequence ID) SL000836 (4915-64_2)
Entrez Gene Symbol HBA1, HBB
UniProt ID P69905, P68871
UniProt Comment
  • P69905: Involved in oxygen transport from the lung to the various peripheral tissues.
  • P68871: Involved in oxygen transport from the lung to the various peripheral tissues.
Wiki Pathways
  • Folate Metabolism
  • Selenium Pathway
  • Vitamin B12 Metabolism
Reactome
  • Erythrocytes take up carbon dioxide and release oxygen
  • Erythrocytes take up oxygen and release carbon dioxide
  • Factors involved in megakaryocyte development and platelet production
  • Scavenging of heme from plasma

All locus annotations are based on the sentinel SNP (rs2000999) and 5 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
  • TXNL4B thioredoxin-like 4B
  • HP haptoglobin
  • HPR haptoglobin-related protein
  • DHX38 DEAH (Asp-Glu-Ala-His) box polypeptide 38
  • PMFBP1 polyamine modulated factor 1 binding protein 1