Table 2.
Intersection of highly significant allelic imbalance SNPs with published genome‐wide association data sets of minimal JSW and hip OAa
| Allelic imbalance | Genome‐wide association | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Positional gene | Meta‐φ | FDR | SNP | R2 | Minimal JSW | Hip OA | ||||||||||
| AA | AAF | EA | EAF | Beta | SEM | P | EA | EAF | Beta | SEM | P | ||||||
| rs4744 | PLA2G2A | A | 0.11 | 0.46 | 8.1 × 10−134 | rs11677 | 1.0 | A | 0.11 | −0.05 | 0.02 | 0.0091 | A | 0.12 | 0.00 | 0.04 | 0.9360 |
| rs4605 | FMOD | C | 0.70 | 0.49 | 0.000 | rs4605 | NA | C | 0.52 | −0.03 | 0.01 | 0.0679 | C | 0.46 | −0.09 | 0.03 | 0.0057 |
| rs3190 | PPP1CB | G | 0.56 | 0.59 | 6.3 × 10−10 | rs3190 | NA | G | 0.57 | 0.03 | 0.01 | 0.0076 | G | 0.57 | −0.00 | 0.02 | 0.8820 |
| rs1054629 | IBSP | T | 0.18 | 0.41 | 1.0 × 10−24 | rs13144371 | 1.0 | A | 0.24 | 0.03 | 0.01 | 0.0340 | A | 0.24 | −0.05 | 0.03 | 0.0801 |
| rs6546 | C1QTNF3 | G | 0.30 | 0.39 | 4.8 × 10−13 | rs840385 | 0.88 | C | 0.40 | −0.03 | 0.01 | 0.0168 | C | 0.39 | −0.03 | 0.03 | 0.2361 |
| rs3549 | SPARC | C | 0.39 | 0.45 | 1.1 × 10−58 | rs1059829 | 1.0 | A | 0.53 | 0.03 | 0.01 | 0.0284 | A | 0.53 | −0.02 | 0.02 | 0.3896 |
| rs3829078 | CA9 | G | 0.05 | 0.59 | 2.5 × 10−14 | rs3829078 | NA | G | 0.11 | 0.04 | 0.02 | 0.0495 | G | 0.11 | −0.04 | 0.04 | 0.2710 |
| rs13321 | TNC | G | 0.67 | 0.53 | 2.4 × 10−16 | rs12347433 | 0.1 | T | 0.72 | −0.02 | 0.01 | 0.1487 | T | 0.72 | 0.06 | 0.03 | 0.0256 |
| rs1871452 | CHST3 | A | 0.60 | 0.42 | 5.4 × 10−25 | rs731027 | 1.0 | T | 0.52 | 0.01 | 0.01 | 0.3073 | T | 0.50 | −0.06 | 0.02 | 0.0087 |
| rs3133187 | RPS3 | G | 0.12 | 0.42 | 5.0 × 10−9 | rs3133187 | NA | G | 0.06 | −0.04 | 0.03 | 0.1420 | G | 0.06 | 0.18 | 0.05 | 0.0011 |
| rs1800801 | MGP | T | 0.74 | 0.41 | 2.6 × 10−26 | rs4236 | 0.9 | T | 0.61 | −0.03 | 0.01 | 0.0433 | T | 0.60 | 0.03 | 0.03 | 0.2068 |
| rs3737548 | COL2A1 | T | 0.23 | 0.53 | 5.1 × 10−72 | rs1635553 | 0.4 | G | 0.46 | −0.02 | 0.01 | 0.2290 | G | 0.46 | −0.06 | 0.03 | 0.0161 |
| rs6647 | SERPINA1 | G | 0.75 | 0.41 | 7.2 × 10−283 | rs6647 | NA | G | 0.77 | −0.03 | 0.01 | 0.0848 | A | 0.76 | 0.06 | 0.03 | 0.0388 |
| rs1052429 | WWP2 | A | 0.86 | 0.56 | 3.4 × 10−55 | rs1566452 | 0.9 | A | 0.73 | −0.04 | 0.01 | 0.0028 | A | 0.71 | −0.05 | 0.03 | 0.0656 |
| rs2646108 | CRISPLD2 | A | 0.18 | 0.63 | 2.6 × 10−9 | rs2646108 | NA | A | 0.20 | −0.01 | 0.02 | 0.7410 | A | 0.19 | 0.09 | 0.03 | 0.0053 |
| rs6554 | UBA52 | T | 0.70 | 0.43 | 1.1 × 10−53 | rs6554 | NA | T | 0.60 | 0.00 | 0.01 | 0.9300 | T | 0.61 | 0.05 | 0.03 | 0.0416 |
| rs7499 | COL18A1 | A | 0.47 | 0.63 | 2.0 × 10−11 | rs7499 | NA | A | 0.40 | −0.01 | 0.01 | 0.3528 | A | 0.40 | −0.05 | 0.03 | 0.0332 |
| rs3088026 | COL6A2 | T | 0.07 | 0.53 | 5.5 × 10−3 | rs3088026 | NA | T | 0.09 | −0.02 | 0.02 | 0.4125 | T | 0.09 | −0.12 | 0.04 | 0.0055 |
a
SNPs = single‐nucleotide polymorphisms; JSW = joint space width; OA = osteoarthritis; AA = alternative allele; AAF = alternative allele frequency; φ = count fraction of the alternative allele reads among the total number of reads; FDR = false discovery rate relative to median φ = 0.49 as reference; R2 = measure of linkage disequilibrium of proxy SNP with allelic imbalance SNP; EA = effect allele; EAF = effect allele frequency; NA = not applicable.