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WCMC

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

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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


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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