Table 1.
Summary of SNP2GENE Results for Lead Independent Significant GWAS SNPs and Associated Gene and eQTL Information
| Genomic Locus | a Lead IndSigSNP Chr:bp:alleles | rsID | GWAS P-value | Nearest Gene(s) | Type of Gene | Distance Nearest Gene bp | Functional Location | b N Pos Mapped SNVs | N eQTL SNPs | eQTL Database | c eQTL Type/genes influenced |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 3:16868616: A:T | rs1866862 | 3.49E-06 | PLCL2 | Protein coding | 0 | intronic | 41 | 63 | BIOSQTL BIOSQTL eQTLGen GTEx/v8 eQTLCat eQTLCat eQTLCat eQTLCat eQTLCat | 63 gene-level PLCL2 25 gene-level PLCL2:PLCL2-AS1 41 cis_eQTLs PLCL2 34 whole blood PLCL2 6 monocyte PLCL2 6 neutrophil PLCL2 5 neutrophil_CD15 PLCL2 5 blood PLCL2 6 fat PLCL2 |
| 2 | 3:138244928: C:G | rs9855074 | 5.38E-06 | CEP70 | Protein coding | 0 | intronic | 8 | 7 | eQTLGen BIOSQTL eQTLCat eQTLCat DICE | 7 cis-EQTL FAIM 2 gene level FAIM 2 monocyte CEP70 7 LCLd CEP70: FAIM 3 B cell naïve CEP70 |
| 3 | 5:111067185: C:CTAA | rs147647553 | 3.67E-06 | STARD4-AS1 NREP | Antisense Protein coding | 0 | ncRNA_ intronic intronic | 33 | 0 | nil | nil |
| 4 | 5:118132897: A:G | rs421765 | 7.48E-06 | CTC-448D22.1 | LincRNA | 11742 | intergenic | 63 | 64 | eQTLGen eQTLGen eQTLCat | 15 cis_eQTL DMXL1 49 cis_eQTL DTWD2 3 iPSC TNFAIP8 |
| 5 | 5:122006325: A:G | rs13180735 | 4.81E-06 | RP11-166A12.1 ARGFXP1 | LincRNA | 0 | ncRNA_ intronic | 6 | 2 | eQTLCat eQTLCat eQTLgen | 2 CEDAR_platelet SNX2 2 LCLd PPIC 2 cis-EQTL CTB-36H16.2 |
| 6 | 5:123136698: C:T | rs257141 | 6.61E-06 | KRT18P16 | Pseudogene | 163600 | intergenic | 10 | 0 | nil | nil |
| 7 | 5:124041059: C:G | rs6860814 | 8.10E-06 | ZNF608 | Protein coding | 0 | intronic | 3 | 0 | nil | nil |
| 8 | 5:126502084: A:G | rs10076402 | 4.71E-06 | CTB-88F18.2 | Pseudogene | 4142 | intergenic | 9 | 9 | eQTLGen BIOSQTL eQTLCat eQTLGen | 1 cis_eQTL C5orf63:MARCH3 3 gene level C5orf63:MARCH3 2 T cell C5orf63 3 cis_eQTL FBN2 |
| 9 | 5:142676404: G:T | rs258814 | 3.62E-06 | NR3C1 | Protein coding | 0 | intronic | 29 | 24 | BIOSQTL eQTLCat | 24 gene level NR3C1 18 blood NR3C1 |
| 10 | 5:143288470: C:G | rs13170657 | 1.83E-06 | CTB-57H20.1 | Sense overlapping | 80132 | intergenic | 62 | 0 | nil | nil |
| 11 | 5:152466290: C:T | rs11744443 | 9.06E-06 | AC091969.1 | LincRNA | 0 | ncRNA_ intronic | 20 | 0 | nil | nil |
| 12 | 5:160326888: A:G | rs10780120 | 3.31E-06 | RP11-109J4.1 | LincRNA | 31896 | intergenic | 57 | 57 | eQTLCat | 57 brain ATP10B |
| 13 | 6:21464051: C:G | rs9460636 | 8.59E-06 | RP11-204E9.1 | LincRNA | 58655 | intergenic | 7 | 0 | nil | nil |
| 14 | 6:38637538: A:G | rs62396381 | 4.95E-07 | GLO1:BTBD9 | Protein coding | 6162 | intergenic | 153 | 130 | eQTLGen eQTLGen eQTLGen eQTLGen eQTLGen eQTLGen BIOSQTL eQTLCat DICE | 61 cis_eQTL GLO1 30 cis_eQTL_GLO1:ZFAND3 7 cis_eQTL GLO1:MDGA1 17 cis_eQTL MDGA1:ZFAND3 6 cis_eQTL GLO1:MDGA1:ZFAND3 1 cis_eQTL MDGA1:ZFAND3:CCDC167 3 gene level GLO1 1 monocyte naïve GLO1 4 B cell naïve RP1–153P14.8 |
| 15 | 6:87510924: C:T | rs4291075 | 8.42E-06 | RP1-253B10.2 | Pseudogene | 32273 | intergenic | 8 | 0 | nil | nil |
| 16 | 16:6614413: A:G | rs2192643 | 9.33E-06 | RP11-420N3.2 RBFOX1 | Transcript Protein coding | 0 | ncRNA_ intronic | 16 | 0 | nil | nil |
| 17 | 19:59028585: A:G | rs11545185 | 5.30E-06 | ZBTB45 | Protein coding | 0 | exonic | 44 | 43 | eQTLCat eQTLCat eQTLCat eQTLCat eQTLCat | e 38 blood MZF1 43 monocytes CD14 MZF1 42 T cell CD4 MZF1 28 T cell CD8 MZF1 3 monocyte LPS MZF1 |
Note: More details of genomic loci are provided in Supplementary Table 3.
Abbreviations: a Lead IndSigSNP = GWAS top SNV; b Pos, positionally mapped SNVs for the locus from SNP2GENE analysis; c eQTL type/genes whose expression is associated with these eQTLs (note BIOSQTL = blood). d LCL, T cell leukemia cell line; e Many eQTLs associated with expression of numerous genes: ZNF584, ZNF132, CTD-2619J13.17, MZF1, AC016629.3, UBE2M, SLC27A5, CTD-2619J13.14, ZNF324, ZNF446, TRIM28, RP55, CHMP2A, ZNF544, A1BG-AS1, ZNF837, ZNF329, A1BG, MIR4754, AC010642.1, AC016629.8, CTD-2619J13.9, AC020915.1 (see Supplementary Figure 10), only those eQTLs associated with MZF1 gene expression are shown as the most plausible candidate in relation to cells relevant to OM.