HelmholtzZentrum munich
WCMC

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

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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


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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