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Table 1 Penalized regression-based fine-mapping identifies eQTLs in established platelet trait GWAS loci that overlie GATA binding sites. Listed SNPs are within platelet trait GWAS LD blocks (EUR r2 > 0.7), scored in the top 5% by our platelet trait model and by GWAVA [17], overlap canonical or near-canonical GATA binding sites, and are eQTLs for at least 1 gene [41] (GTEx V7). Associated gChromVAR posterior probabilities of being causal for platelet count trait association (PP PLT) are shown [1]. Genes in boldface have known hematopoietic function. SNP rsIDs and locations refer to hg19 genome

From: Tropomyosin 1 genetically constrains in vitro hematopoiesis

rsID Chr Pos (Mb) Platelet score (percentile) GWAVA score (percentile) gChromVAR (PP PLT) Nearest gene eQTL gene(s)
rs11240368 1 205.1 1.12 (97th) 0.52 (95th)   DSTYK CNTN2, TMEM81
rs3771535 2 70.0 0.94 (95th) 0.53 (95th) 0.01 ANXA4 GMCL1, SNRNP27
rs10180681 2 121.0 1.41 (98th) 0.63 (97th) 0.01 RALB EPB41L5, PTPN4 [42], RALB [43]
rs10180682 2 121.0 1.41 (98th) 0.64 (97th) 0.01 RALB EPB41L5, PTPN4 [42], RALB [43]
rs9646785 2 172.0 1.27 (98th) 0.58 (96th)   TLK1 GAD1, GORASP2
rs6771578 3 167.4 1.14 (97th) 0.60 (96th) 0.003 PDCD10 PDCD10 [44], SERPINI1, WDR49
rs12652692 5 77.8 3.62 (99th) 0.57 (96th) 0.01 LHFPL2 LHFPL2, SCAMP1
rs72793280 5 131.6 2.73 (99th) 0.89 (99th) 0.001 P4HA2 ACSL6, P4HA2 [45, 46], PDLIM4 [47], SLC22A4, SLC22A5
rs1741820 6 122.8 1.75 (99th) 0.55 (96th)   HSF2 HSF2, PKIB
rs342293 7 106.4 1.80 (99th) 0.94 (99th) 0.99 CC71L PIK3CG [12]*
rs13265995 8 56.7 1.75 (99th) 0.60 (96th)   TMEM68 LYN [48, 49], TGS, TMEM68
rs9704108 11 0.3 1.12 (97th) 0.85 (99th) 0.087 IFITM2 IFITM2
rs11071720 15 63.3 1.53 (98th) 0.58 (96th) 0.98 TPM1 APH1B, LACTB, RAB8B, TPM1 [5]**
rs2316513 17 2.0 0.92 (95th) 0.54 (95th) 0.005 EST1A DPH1, SMG6, SRR [50]
rs1654439 19 55.6 2.69 (99th) 0.58 (96th) 0.002 RDH13 GP6 [49, 51], NLRP2, RDH13 [52]
  1. *eQTL in human platelets [12], but not in GTEx tissues [41]
  2. **Function suggested by D. rerio morpholino experiments [5]
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