Table 2.
Novel common BP SNPs associated with non-BP traits
| Locus* (Function) | dbSNPID | Chr:Position | CA/NCA | CAF | GWAS Trait† | Amino Acid Substitution |
Literature Lab Term(s)‡ |
|---|---|---|---|---|---|---|---|
| SNPs not previously reported in GWAS | |||||||
| PRDM16 (NS) | rs2493292 | 1:3328659 | T/C | 0.15 | n.a. | Pro633Leu | |
| SULT1C3 (NS) | rs6722745 | 2:108875244 | C/T | 0.34 | n.a. | Met194Thr | |
| HRCT1 (NS) | rs76452347 | 9:35906471 | T/C | 0.19 | n.a. | Arg63Trp | |
| ADO (NS) | rs10995311 | 10:64564934 | G/C | 0.38 | n.a. | Pro39Ala | |
| CERS5 (NS) | rs7302981 | 12:50537815 | A/G | 0.34 | n.a. | Cys75Arg | |
| TNRC6A (NS) | rs11639856 | 16:24788645 | A/T | 0.19 | n.a. | Asn185Lys | |
| DOT1L (NS) | rs2302061 | 19:2226772 | C/G | 0.16 | n.a. | Val1418Leu | |
| RGL3 (NS) | rs167479 | 19:11526765 | T/G | 0.448 | n.a. | Pro162His | |
| SNPs previously reported to be significant in GWAS of other traits§ | |||||||
| PABPC4 (IN) | rs4660293 | 1:40028180 | G/A | 0.21 | HDL | ||
| CSNK1G3 (IN) | rs4530754 | 5:122855416 | G/A | 0.41 | LDL and TC | ||
| C5orf56 (IN) | rs2188962 | 5:131770805 | T/C | 0.35 | Crohn’s Disease | ||
| rs926552 | 6:29548089 | T/C | 0.11 | T1D | |||
|
MSH5-SAPCD1 (IN) |
rs409558 | 6:31708147 | G/A | 0.18 | SLE | ||
| IGFBP3 | rs11977526 | 7:46008110 | A/G | 0.40 | IGFBP3 | Insulin, 9%, IGF-1 signaling, 55% | |
|
PHF19 (5’ near gene) |
rs1953126 | 9:123640500 | T/C | 0.33 | RA | ||
| rs900145 | 11:13293905 | G/A | 0.34 | Age at Menarche | |||
| KCNJ11 (NS) | rs5219 | 11:17409572 | T/C | 0.32 | T2D | Lys23Glu | Insulin, 0.6%, T2D, 2.5% |
| MYH6 (IN) | rs452036 | 14:23865885 | A/G | 0.40 | Resting Heart Rate | Heart Development, 73%, Hypertrophy model, 83%, Cardiac muscle contraction, 84% | |
| DPEP1 (NS) | rs1126464 | 16:89704365 | C/G | 0.22 | Homocysteine Concentration |
Glu351Gln | |
| TBX2 (IN) | rs8068318 | 17:59483766 | C/T | 0.35 | Creatinine and eGFR |
Heart development, 17.5% | |
| INSR (IN) | rs7248104 | 19:7224431 | A/G | 0.395 | TG | Insulin, 90%, IGF-1 signaling, 45%, T2D, 93%, Hypertrophy model, 5.4% | |
| ZNRF3 (UTR3) | rs4823006 | 22:29451671 | G/A | 0.424 | WHR | ||
| SNPs previously reported in patent filing, candidate gene or GWAS∥ | |||||||
| SLC22A7 (SYN) | rs2270860 | 6:43270151 | T/C | 0.37 | HTN (patent filing) | ||
| COL21A1 (IN) | rs1925153 | 6:56102780 | T/C | 0.45 | Bipolar disease traits | ||
| PHIP (IN) | rs10943605 | 6:79655477 | A/G | 0.46 | Colon cancer (patent filing) |
||
| HOXA3 (UTR5) | rs6969780 | 7:27159136 | C/G | 0.13 | Hypospadias | ||
| NOS3 (IN) | rs891511 | 7:150704843 | A/G | 0.37 | Endothelium-dependent vasodilation | Heart Development, 6.7%, T2D, 3.9%, Cardiac muscle contraction, 14.5% | |
| CYP2C19 (IN) | rs4494250 | 10:96563757 | A/G | 0.32 | Breast cancer | ||
SNPs included in this table are common SNPs in Table 1. CA/NCA, coded allele/non-coded allele; CAF, coded allele frequency; IN, intron; NS, nonsynonymous; UTR3, 3’ upstream; UTR5, 5’ upstream; HDL/LDL, high/low- density cholesterol; TC, total cholesterol; T1D/T2D, Type I/Type 2 diabetes; SLE, systemic lupus erythematosus; IGFBP3, insulin-like growth factor-binding protein 3; RA, rheumatoid arthritis; TG, triglyceride; WHR, waist/hip ratio.
Loci are named according to closest gene based on the position of the index SNP.
Indicates whether a SNP was reported in previous genome-wide association studies (GWAS). n.a., not available.
Reported results were part of identifying biological and biochemical terms that were significantly associated with the investigated gene set using Literature Lab database. Percent shows relative weight of references to a BP candidate gene in relation to associated pathways / terms for the full gene set. Out of three classes of significances (STRONG, MODERATE and POSITIVE) above we reported only STRONG class.
Reported to be significant in GWAS using P<5 × 10−8 or pre-specified significance levels in the reported study. Details of association direction were included in Supplementary Table 7.
P values were not mentioned or did not reach the specified significance level.