HelmholtzZentrum munich
WCMC

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

ONLINE SUPPLEMENTARY INFORMATION

Ideogram
Proteome annotation
Locus annotations

Locus 45

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
Granulysin cis Discovery rs12151621 2:85,934,499 C/A 0.21 995 0.902 0.045 5.8×10-76 1.380 1.4×10-74 3.1×10-78
Granulysin cis Replication rs7577293 2:85,935,282 G/A 0.23 337 0.732 0.081 1.1×10-17 1.360 1.3×10-17 8.8×10-18

 

Regional association plots

 

Boxplots and histograms for top associations

Granulysin

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

Granulysin

Target (abbrv.) Granulysin
Target (full name) Granulysin
Somalogic ID (Sequence ID) SL000678 (3195-50_2)
Entrez Gene Symbol GNLY
UniProt ID P22749
UniProt Comment
  • Antimicrobial protein that kills intracellular pathogens. Active against a broad range of microbes, including Gram-positive and Gram-negative bacteria, fungi, and parasites. Kills Mycobacterium tuberculosis.

All locus annotations are based on the sentinel SNP (rs12151621) 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

Potentially regulated genes
  • CAPG capping protein (actin filament), gelsolin-like
  • AC105053.3
  • IMMT inner membrane protein, mitochondrial
  • TMEM150A transmembrane protein 150A
  • TGOLN2 trans-golgi network protein 2
  • USP39 ubiquitin specific peptidase 39
  • MRPL35 mitochondrial ribosomal protein L35
  • VAMP8 vesicle-associated membrane protein 8
  • POLR1A polymerase (RNA) I polypeptide A, 194kDa
  • SFTPB surfactant protein B
  • SH2D6 SH2 domain containing 6
  • MAT2A methionine adenosyltransferase II, alpha
  • VAMP5 vesicle-associated membrane protein 5
  • PTCD3 pentatricopeptide repeat domain 3
eQTL genes
  • VAMP8 vesicle-associated membrane protein 8
  • ATOH8 atonal homolog 8 (Drosophila)
  • AC012454.4
  • GGCX gamma-glutamyl carboxylase
  • GNLY granulysin
  • MLH3 mutL homolog 3

 

Results from other genome-wide association studies

Trait P Study Source
cg19805943 (chr2:85933093) 3.3×10-310 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg11752275 (chr2:85921060) 1.7×10-127 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of ATOH8 in peripheral blood monocytes 4×10-73 20502693 (PMID) GRASP2 eQTL
cg21473183 (chr2:85925725) 3.7×10-40 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of GNLY in peripheral blood monocytes 2.1×10-23 20502693 (PMID) GRASP2 eQTL
Gene expression of ATOH8 (probeID ILMN_1654065) in whole blood 9.5×10-23 22692066 (PMID) GRASP2 eQTL
GNLY gene expression 1.6×10-20 21798870 (PMID) GRASP2 eQTL
Gene expression of GNLY (probeID ILMN_1708645) in whole blood 2.2×10-13 22692066 (PMID) GRASP2 eQTL
Gene expression of GNLY [probe ILMN_1654065] in peripheral leukocytes 4.6×10-13 19966804 (PMID) GRASP2 eQTL
cg21512179 (chr2:85971572) 1.2×10-10 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg25651505 (chr2:85812047) 1.7×10-9 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of SENP3 in peripheral blood monocytes 4.8×10-9 20502693 (PMID) GRASP2 eQTL
Gene expression of GGCX in peripheral blood monocytes 1.2×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of DYNLRB2 in peripheral blood monocytes 1.9×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of MLH3 in peripheral blood monocytes 7.6×10-8 20502693 (PMID) GRASP2 eQTL
Gene expression of FAM26C in peripheral blood monocytes 3.1×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of SLC39A7 in peripheral blood monocytes 3.9×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of DEFB131 in peripheral blood monocytes 4.6×10-7 20502693 (PMID) GRASP2 eQTL
"Gene expression of GNLY [transcript NM_012483, probe A_23_P209954] in liver" 9.4×10-7 21637794 (PMID) GRASP2 eQTL
Gene expression of GNLY in CD4+ lymphocytes 1.7×10-6 20833654 (PMID) GRASP2 eQTL
P22749 protein abundance levels 4.9×10-6 22595970 (PMID) GRASP2 pQTL
Gene expression of B4GALNT1 in peripheral blood monocytes 9.6×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of ATOH8 in CD4+ lymphocytes 1.1×10-5 20833654 (PMID) GRASP2 eQTL
cg17415111 (chr2:86035381) 1.1×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg26337070 (chr2:85999849) 6.4×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg21946195 (chr2:86012249) 6.7×10-5 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Serum concentration of indoleacetate 1.2×10-4 21886157 (PMID) GRASP2 metabQTL
Gene expression of ATOH8 [probeset 228890_at] in sputum 1.9×10-4 21949713 (PMID) GRASP2 eQTL