HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 323

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
GPNMB cis Discovery rs5850 7:23,314,547 C/T 0.39 996 -0.337 0.044 8.1×10-14 -1.070 1.3×10-13 1.8×10-12
GPNMB cis Replication rs10085838 7:23,298,415 C/A 0.31 337 -0.141 0.059 0.018 -1.030 0.084 0.059

 

Regional association plots

Transmembrane glycoprotein NMB (GPNMB)

 

Boxplots and histograms for top associations

Transmembrane glycoprotein NMB (GPNMB)

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

Transmembrane glycoprotein NMB (GPNMB)

Target (abbrv.) GPNMB
Target (full name) Transmembrane glycoprotein NMB
Somalogic ID (Sequence ID) SL007429 (5080-131_3)
Entrez Gene Symbol GPNMB
UniProt ID Q14956
UniProt Comment
  • Could be a melanogenic enzyme.
Biomarker applications (based on IPA annotation)
  • unspecified application

All locus annotations are based on the sentinel SNP (rs5850) and 20 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
  • GPNMB glycoprotein (transmembrane) nmb
eQTL genes

 

Results from other genome-wide association studies

Trait P Study Source
Gene expression of GPNMB in peripheral blood monocytes 3.1×10-41 20502693 (PMID) GRASP2 eQTL
Gene expression of NUPL2 in peripheral blood monocytes 1.1×10-39 20502693 (PMID) GRASP2 eQTL
Gene expression of NUPL2 in blood 1.3×10-24 21829388 (PMID) GRASP2 eQTL
cg20723844 (chr7:23221021) 3.5×10-23 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of GPNMB (probeID ILMN_1801205) in cerebellum in Alzheimer's disease cases and controls 6.8×10-21 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_2407389) in cerebellum in Alzheimer's disease cases and controls 3.7×10-19 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_2407389) in temporal cortex in Alzheimer's disease cases and controls 1.1×10-17 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB in Frontal cortex 3.4×10-16 20485568 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_1801205) in temporal cortex in Alzheimer's disease cases and controls 3.8×10-14 22685416 (PMID) GRASP2 eQTL
Gene expression of NUPL2 (probeID ILMN_2115154) in cerebellum in Alzheimer's disease cases and controls 9.5×10-12 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_2407389) in cerebellum in Alzheimer's disease cases 2.5×10-11 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_1801205) in cerebellum in Alzheimer's disease cases 9.3×10-11 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_1801205) in cerebellum in non-Alzheimer's disease samples 1×10-10 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB in CHB-JPT lymphoblastoid cell lines 1.1×10-9 17873874 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_2407389) in cerebellum in non-Alzheimer's disease samples 1.7×10-9 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_2407389) in temporal cortex in Progressive Supranuclear Palsy cases 2.7×10-9 22685416 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992828] in brain cortex 3.3×10-9 19222302 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_2407389) in temporal cortex in Alzheimer's disease cases 1.3×10-8 22685416 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992840] in brain cortex 1.8×10-8 19222302 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_1801205) in temporal cortex in Alzheimer's disease cases 4.8×10-8 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB [probe 2992814] in brain cortex 7×10-8 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992831] in brain cortex 2.1×10-7 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992848] in brain cortex 2.2×10-7 19222302 (PMID) GRASP2 eQTL
Gene expression of NUPL2 (probeID ILMN_2115154) in temporal cortex in Alzheimer's disease cases and controls 3.4×10-7 22685416 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992845] in brain cortex 3.5×10-7 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992847] in brain cortex 4.1×10-7 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992825] in brain cortex 4.3×10-7 19222302 (PMID) GRASP2 eQTL
Gene expression of NUPL2 (probeID ILMN_2115154) in cerebellum in Alzheimer's disease cases 6.1×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_1801205) in cerebellum in Progressive Supranuclear Palsy cases 6.2×10-7 22685416 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992832] in brain cortex 1.1×10-6 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992842] in brain cortex 1.6×10-6 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992827] in brain cortex 6.7×10-6 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992826] in brain cortex 6.9×10-6 19222302 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_2407389) in cerebellum in Progressive Supranuclear Palsy cases 1.1×10-5 22685416 (PMID) GRASP2 eQTL
Gene expression of NUPL2 (probeID ILMN_2115154) in cerebellum in non-Alzheimer's disease samples 1.5×10-5 22685416 (PMID) GRASP2 eQTL
Gene expression of GPNMB (probeID ILMN_1801205) in temporal cortex in Progressive Supranuclear Palsy cases 3.5×10-5 22685416 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992816] in brain cortex 3.9×10-5 19222302 (PMID) GRASP2 eQTL
Differential exon level expression of GPNMB [probe 2992841] in brain cortex 4.3×10-5 19222302 (PMID) GRASP2 eQTL
Gene expression of C7orf30 in blood 1.3×10-4 21829388 (PMID) GRASP2 eQTL
Parkinson's disease 1.9×10-4 22451204 (PMID) GRASP2 nonQTL
Gene expression of GPNMB (ENSG00000136235) in dendritic cells 2.3×10-4 22233810 (PMID) GRASP2 eQTL