Table 1:
GWAS variants nominated for functional causality by MPRAu.
| MPRAu Tested SNP | tag SNP | Gene | Trait | PMID | OR/Beta | tamVar log2FC | tamVar P value |
|---|---|---|---|---|---|---|---|
| rs1056801# | rs3771570 | SEPT2 | Prostate cancer | 23535732 | 1.12 | −1.2 | 7.7x10-12 |
| rs1140711 | rs10835187 | LIN7C | Bone mineral density | 24945404 | 0.127 | −0.43 | 0.061 |
| rs12190287# | rs12190287 | TCF21 | Coronary heart disease | 21378990 | 1.08 | 0.47 | 0.0021 |
| rs13702# | rs10105606 | LPL | Triglycerides | 20864672 | 0.07 | 0.31 | 1.00E-08 |
| rs13702# | rs331 | LPL | HDLC | 19936222 | 1.459 | 0.31 | 1.00E-08 |
| rs5891007 | rs16887244 | LSM1 | Schizophrenia | 22037555 | 1.19 | 0.36 | 0.004 |
| rs705866# | rs7803454 | PILRB | Age-related macular degeneration | 26691988 | 1.13 | 0.3 | 0.083 |
| rs708723 | rs823118 | RAB7L1 | Parkinson’s disease | 25064009 | 1.122 | 0.37 | 0.067 |
| rs71396950 | rs1805007 | SPATA33 | Freckles | 17952075 | 4.37 | −0.43 | 0.095 |
| rs71396950 | rs1805007 | SPATA33 | Red hair color | 17952075 | 12.47 | −0.43 | 0.095 |
| rs71396950 | rs35063026 | SPATA33 | Squamous cell carcinoma | 26829030 | 1.33 | −0.43 | 0.095 |
| rs8066731 | rs9902453 | SLC6A4 | Coffee consumption | 25288136 | 0.03 | −0.65 | 0.0039 |
| rs35274349‡ | rs10948363 | CD2AP | Alzheimer’s disease | 24162737 | 1.1 | 0.48 | 6.30E-10 |
(Most significant adjusted p-value, and its corresponding log2FC, from the MPRAu screen is shown)
#
denotes variant perturbation of a top 100 expressed miRNA,
‡
denotes variant perturbation of a potential RBP motif within an eCLIP-seq peak region.