HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 312

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
RGM-C trans Discovery rs2236293 9:35,841,783 G/A 0.44 992 -0.328 0.043 4.6×10-14 -1.060 3.4×10-14 3.7×10-14
RGM-C trans Replication rs13292880 9:35,817,579 C/A 0.48 337 -0.110 0.055 0.048 -1.030 0.103 0.118

 

Regional association plots

 

Boxplots and histograms for top associations

Hemojuvelin (RGM-C)

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

Hemojuvelin (RGM-C)

Target (abbrv.) RGM-C
Target (full name) Hemojuvelin
Somalogic ID (Sequence ID) SL010469 (3332-57_1)
Entrez Gene Symbol HFE2
UniProt ID Q6ZVN8
UniProt Comment
  • Acts as a bone morphogenetic protein (BMP) coreceptor. Through enhancement of BMP signaling regulates hepcidin (HAMP) expression and regulates iron homeostasis.
Pathway Interaction Database
  • BMP receptor signaling
Reactome
  • Netrin-1 signaling

All locus annotations are based on the sentinel SNP (rs2236293) and 16 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
  • RP11-112J3.16
  • NPR2 natriuretic peptide receptor 2
  • SPAG8 sperm associated antigen 8
  • HINT2 histidine triad nucleotide binding protein 2
  • FAM221B family with sequence similarity 221, member B
  • TMEM8B transmembrane protein 8B
  • OR13E1P olfactory receptor, family 13, subfamily E, member 1 pseudogene
  • LINC00950 long intergenic non-protein coding RNA 950
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
cg12876594 (chr9:35791822) 3.3×10-310 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg13911801 (chr9:35860888) 2.5×10-135 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of CREB3///GBA2 in blood 5.8×10-19 21829388 (PMID) GRASP2 eQTL
Gene expression of SPAG8 in peripheral blood monocytes 6.9×10-12 20502693 (PMID) GRASP2 eQTL
Gene expression of GBA2 in peripheral blood monocytes 2.4×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of NUP153 in Temporal cortex 2.6×10-8 20485568 (PMID) GRASP2 eQTL
2-aminobutyrate 5.1×10-5 24816252 (PMID) gwas.eu via SNiPA
Weight in controls 9.2×10-5 17463246 (PMID) GRASP2 nonQTL
Gene expression of CA9///TPM2 in blood 2.5×10-4 21829388 (PMID) GRASP2 eQTL
Gene expression of TPM2 in blood 2.8×10-4 21829388 (PMID) GRASP2 eQTL