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

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Locus annotations

Locus 450

Top associations per target

Target cis/​trans Study SNP SNP location Maj/​min allele MAF N βinv seinv Pinv fclog Plog Praw
MED-1 trans Discovery rs9462846 6:42,861,581 A/C 0.26 995 0.326 0.050 8.1×10-11 1.040 0.011 0.557
MED-1 trans Replication rs9471966 6:42,891,022 G/A 0.29 337 0.160 0.063 0.011 1.030 0.191 0.848

 

Regional association plots

Mediator of RNA polymerase II transcription subunit 1 (MED-1)

Download the association data used to generate this plot

 

Boxplots and histograms for top associations

Mediator of RNA polymerase II transcription subunit 1 (MED-1)

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

Mediator of RNA polymerase II transcription subunit 1 (MED-1)

Target (abbrv.) MED-1
Target (full name) Mediator of RNA polymerase II transcription subunit 1
Somalogic ID (Sequence ID) SL010328 (3892-21_2)
Entrez Gene Symbol MED1
UniProt ID Q15648
UniProt Comment
  • Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. Mediator is recruited to promoters by direct interactions with regulatory proteins and serves as a scaffold for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors (PubMed:10406464, PubMed:11867769, PubMed:12037571, PubMed:12218053, PubMed:12556447, PubMed:14636573, PubMed:15340084, PubMed:15471764, PubMed:15989967, PubMed:16574658, PubMed:9653119). Acts as a coactivator for GATA1-mediated transcriptional activation during erythroid differentiation of K562 erythroleukemia cells (PubMed:24245781).

All locus annotations are based on the sentinel SNP (rs9462846) and 70 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
  • GLTSCR1L GLTSCR1-like
  • RPL7L1 ribosomal protein L7-like 1
  • C6orf226 chromosome 6 open reading frame 226
  • PTCRA pre T-cell antigen receptor alpha
  • CNPY3 canopy FGF signaling regulator 3
Potentially regulated genes
  • CUL9 cullin 9
  • PRPH2 peripherin 2 (retinal degeneration, slow)
  • RP11-480N24.4
  • PTK7 protein tyrosine kinase 7 (inactive)
  • PTCRA pre T-cell antigen receptor alpha
eQTL genes
  • RPL7L1 ribosomal protein L7-like 1
  • PEX6 peroxisomal biogenesis factor 6
  • C6orf226 chromosome 6 open reading frame 226
  • RPL7P21 ribosomal protein L7 pseudogene 21

 

Results from other genome-wide association studies

Trait P Study Source
cg09645574 (chr6:42879358) 6.3×10-272 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg01075005 (chr6:42879433) 2.4×10-223 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
cg07647651 (chr6:42878955) 6×10-150 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of PEX6 in peripheral blood monocytes 7.9×10-57 20502693 (PMID) GRASP2 eQTL
cg01702009 (chr6:42883738) 1.4×10-39 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of GNMT///PEX6 in blood 7.1×10-25 21829388 (PMID) GRASP2 eQTL
Gene expression of GNMT in peripheral blood monocytes 3.4×10-18 20502693 (PMID) GRASP2 eQTL
Gene expression of PEX6 (probeID ILMN_1683279) in temporal cortex in Alzheimer's disease cases and controls 7.7×10-14 22685416 (PMID) GRASP2 eQTL
Gene expression of PEX6 (probeID ILMN_1683279) in cerebellum in Alzheimer's disease cases and controls 1.5×10-13 22685416 (PMID) GRASP2 eQTL
cg07710211 (chr6:42900099) 1.4×10-11 10.1101/033084 (DOI) BIOS QTL cis-meQTLs
Gene expression of PEX6 in normal prepouch ileum 3.1×10-10 23474282 (PMID) GRASP2 eQTL
Gene expression of PEX6 (probeID ILMN_1683279) in temporal cortex in Alzheimer's disease cases 1.6×10-9 22685416 (PMID) GRASP2 eQTL
Gene expression of PEX6 in CEU-CHB-JPT lymphoblastoid cell lines 1×10-8 17873874 (PMID) GRASP2 eQTL
Gene expression of PEX6 [probe 320_at] in lymphoblastoid cell lines 2.6×10-8 17873877 (PMID) GRASP2 eQTL
Gene expression of PEX6 [probe 204545_at] in lymphoblastoid cell lines 6.7×10-8 17873877 (PMID) GRASP2 eQTL
Gene expression of PEX6 (probeID ILMN_1683279) in cerebellum in non-Alzheimer's disease samples 2.7×10-7 22685416 (PMID) GRASP2 eQTL
Gene expression of MRPL2 in peripheral blood monocytes 4.5×10-7 20502693 (PMID) GRASP2 eQTL
Gene expression of CUL7///MRPL2 in blood 1.7×10-6 21829388 (PMID) GRASP2 eQTL
Gene expression of PEX6 (probeID ILMN_1683279) in cerebellum in Alzheimer's disease cases 2×10-6 22685416 (PMID) GRASP2 eQTL
Gene expression of CSNK1G2 in peripheral blood monocytes 2.5×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of UTP18 in peripheral blood monocytes 3.7×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of MAFF in peripheral blood monocytes 5.1×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of AL353716.18///RPL7L1 in blood 5.2×10-6 21829388 (PMID) GRASP2 eQTL
Gene expression of TMED2 in peripheral blood monocytes 7.9×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of SCOC in peripheral blood monocytes 9.8×10-6 20502693 (PMID) GRASP2 eQTL
Gene expression of KIAA0240 in liver 1×10-5 18462017 (PMID) GRASP2 eQTL
Hip circumfence, adjusted for BMI 1.1×10-5 25673412 (PMID) Supplemental file
Gene expression of RP3-475N16.5///AL353716.18 in blood 1.2×10-5 21829388 (PMID) GRASP2 eQTL
Estimated total intracranial volume (excluding patients with neuropsychiatric disorders) 2.4×10-5 22504417 (PMID) GRASP2 nonQTL
Serum creatinine 5×10-5 20383146 (PMID) GRASP2 nonQTL
Gene expression of RPL7L1 in liver 1.2×10-4 21637794 (PMID) GRASP2 eQTL
Gene expression of RPL7L1///AL035587.5///AL353716.18 in blood 2.2×10-4 21829388 (PMID) GRASP2 eQTL
Hip bone mineral density (BMD) 3.1×10-4 18445777 (PMID) GRASP2 nonQTL
Gene expression of PEX6 (probeID ILMN_1683279) in cerebellum in Progressive Supranuclear Palsy cases 4.9×10-4 22685416 (PMID) GRASP2 eQTL