Overlap between prior published GWAS catalog variants for platelet-related traits and significant eGenes in the platelet and/or MK analyses
| Chromosome . | SNP position . | eGene(s) in MKs . | eGene(s) in platelets . | GWAS phenotypes from GWAS catalog . |
|---|---|---|---|---|
| chr1 | 25561667 | TMEM50A (9.58 × 10−5) | TMEM50A (8.59 × 10−10) | Plateletcrit |
| chr1 | 25561667 | RHD (1.03 × 10−22) | RHD (7.88 × 10−37) | Plateletcrit |
| chr1 | 156869714 | PEAR1 (3.62 × 10−2) | PEAR1 (1.51 × 10−9) |
|
| chr1 | 8917102 | — | ENO1 (2.16 × 10−27) | Plateletcrit |
| chr1 | 10271688 | — | KIF1B (1.54 × 10−19) | Mean platelet volume |
| chr1 | 202909974 | — | ADIPOR1 (2.90 × 10−3) | Mean platelet volume |
| chr1 | 247712303 | — | GCSAML (5.07 × 10−11) |
|
| chr2 | 224874874 | SERPINE2 (2.22 × 10−12) | SERPINE2 (3.16 × 10−95) |
|
| chr2 | 31477838 | — | EHD3 (1.61 × 10−6) |
|
| chr3 | 56849749 | ARHGEF3 (7.46 × 10−24) | — |
|
| chr3 | 122833003 | PDIA5 (1.21 × 10−92) | — |
|
| chr4 | 6883012 | TBC1D14 (6.08 × 10−5) | — | Platelet count |
| chr4 | 6857278 | — | TBC1D14 (2.25 × 10−6) | Platelet count |
| chr4 | 57767327 | — | POLR2B (5.81 × 10−3) | Platelet count |
| chr7 | 106372219 | CCDC71L (7.34 × 10−20) | — |
|
| chr8 | 144996029 | PLEC (1.65 × 10−13) | — | Platelet count |
| chr9 | 99192919 | HABP4 (4.41 × 10−44) | HABP4 (4.55 × 10−45) |
|
| chr11 | 200343 | — | BET1L (5.93 × 10−12) | Plateletcrit |
| chr11 | 126285301 | — | ST3GAL4-AS1 (2.42 × 10−9) |
|
| chr11 | 126285301 | — | ST3GAL4 (6.39 × 10−36) |
|
| chr12 | 122216910 | — | TMEM120B (3.90 × 10−2) |
|
| chr12 | 122216910 | RHOF (5.33 × 10−12) | RHOF (3.87 × 10−54) |
|
| chr15 | 63341996 | — | TPM1 (2.70 × 10−28) |
|
| chr20 | 1819280 | SIRPA (1.35 × 10−3) | — |
|
| Chromosome . | SNP position . | eGene(s) in MKs . | eGene(s) in platelets . | GWAS phenotypes from GWAS catalog . |
|---|---|---|---|---|
| chr1 | 25561667 | TMEM50A (9.58 × 10−5) | TMEM50A (8.59 × 10−10) | Plateletcrit |
| chr1 | 25561667 | RHD (1.03 × 10−22) | RHD (7.88 × 10−37) | Plateletcrit |
| chr1 | 156869714 | PEAR1 (3.62 × 10−2) | PEAR1 (1.51 × 10−9) |
|
| chr1 | 8917102 | — | ENO1 (2.16 × 10−27) | Plateletcrit |
| chr1 | 10271688 | — | KIF1B (1.54 × 10−19) | Mean platelet volume |
| chr1 | 202909974 | — | ADIPOR1 (2.90 × 10−3) | Mean platelet volume |
| chr1 | 247712303 | — | GCSAML (5.07 × 10−11) |
|
| chr2 | 224874874 | SERPINE2 (2.22 × 10−12) | SERPINE2 (3.16 × 10−95) |
|
| chr2 | 31477838 | — | EHD3 (1.61 × 10−6) |
|
| chr3 | 56849749 | ARHGEF3 (7.46 × 10−24) | — |
|
| chr3 | 122833003 | PDIA5 (1.21 × 10−92) | — |
|
| chr4 | 6883012 | TBC1D14 (6.08 × 10−5) | — | Platelet count |
| chr4 | 6857278 | — | TBC1D14 (2.25 × 10−6) | Platelet count |
| chr4 | 57767327 | — | POLR2B (5.81 × 10−3) | Platelet count |
| chr7 | 106372219 | CCDC71L (7.34 × 10−20) | — |
|
| chr8 | 144996029 | PLEC (1.65 × 10−13) | — | Platelet count |
| chr9 | 99192919 | HABP4 (4.41 × 10−44) | HABP4 (4.55 × 10−45) |
|
| chr11 | 200343 | — | BET1L (5.93 × 10−12) | Plateletcrit |
| chr11 | 126285301 | — | ST3GAL4-AS1 (2.42 × 10−9) |
|
| chr11 | 126285301 | — | ST3GAL4 (6.39 × 10−36) |
|
| chr12 | 122216910 | — | TMEM120B (3.90 × 10−2) |
|
| chr12 | 122216910 | RHOF (5.33 × 10−12) | RHOF (3.87 × 10−54) |
|
| chr15 | 63341996 | — | TPM1 (2.70 × 10−28) |
|
| chr20 | 1819280 | SIRPA (1.35 × 10−3) | — |
|
The GWAS catalog was examined for the following phenotypes: cardiometabolic and hematological traits, mean platelet volume, platelet count, platelet distribution width, platelet-derived growth factor BB levels, and Plateletcrit (see supplemental Methods for specific references). SNPs within the catalog were limited to those with P value <5 × 10−8, and all eGenes for this full set of curated variants are listed in this table. A total of 1065 variants were looked up, and 24 variants had a significant eGene in one or both tissues (q-values shown in parentheses).