Table 1. Stage 2 genes and corresponding polymorphisms.
| SNP | No. | Coordinate | Minor allele | Minor allele frequency | Putative function |
|---|---|---|---|---|---|
| ACVR1B | |||||
| rs10431538 | 1 | 50605127 | A | 0.15 | Located in transcription factor-binding site (TFBS)/conserved |
| rs706824a | 2 | 50605518 | Located in TFBS | ||
| rs1979921 | 3 | 50606344 | T | 0.08 | Conserved |
| rs12230575a | 4 | 50608313 | Conserved | ||
| rs10783485 | 5 | 50622274 | A | 0.35 | Tagging SNP, genotyped stage 1 |
| rs746434 | 6 | 50628932 | A | 0.09 | Tagging SNP, genotyped stage 1 |
| rs808873a | 7 | 50634449 | C | 0 | Located in TFBS/conserved |
| rs11612312 | 8 | 50635355 | A | 0.22 | Conserved |
| rs12809597a | 9 | 50642590 | Conserved | ||
| rs10783486b | 10 | 50649053 | A | 0.27 | Tagging SNP, genotyped stage 1 |
| rs34488074c | 11 | 50656482 | C | 0 | Non-synonymous SNP (L/F) |
| rs2172603 | 12 | 50663079 | A | 0.02 | Located in TFBS |
| rs12296553a | 13 | 50663569 | Located in TFBS | ||
| rs2641516c | 14 | 50666953 | C | 0 | Synonymous SNP (G/G)/conserved/located in TFBS |
| rs928906a | 15 | 50666954 | Located in TFBS/non-synonymous (V/L) | ||
| rs34050429c | 16 | 50667165 | A | 0 | Non-synonymous SNP (H/R) |
| rs2854464 | 17 | 50675158 | G | 0.27 | Located in TFBS/miRNA-binding site |
| rs2714 | 18 | 50675551 | A | 0.10 | Conserved |
| rs11169974 | 19 | 50676563 | T | 0.04 | Located in TFBS |
| rs7955401a | 20 | 50685018 | Located in TFBS | ||
| INHBC | |||||
| rs7964492 | 1 | 56109852 | C | 0.25 | Tagging SNP/conserved |
| rs12826906 | 2 | 56114925 | G | 0.006 | 5′ UTR |
| rs12831855c | 3 | 56114969 | T | 0 | Synonymous SNP (L/L)/conserved |
| rs12809642c | 4 | 56115002 | G | 0 | Synonymous SNP (A/A) |
| rs560048 | 5 | 56115396 | T | 0.45 | Regulatory region intron 1 |
| rs533975 | 6 | 56118251 | A | 0.45 | Tagging SNP/conserved |
| rs2943693 | 7 | 56122232 | A | 0.22 | Tagging SNP, genotyped stage 1 |
| rs34137943c | 8 | 56129647 | T | 0 | Synonymous SNP (L/L) |
| rs2229357 | 9 | 56129978 | A | 0.26 | Non-synonymous SNP (Q/R), genotyped stage 1 |
| rs3741414 | 10 | 56130316 | A | 0.26 | Tagging SNP, genotyped stage 1 |
| rs34435057c | 11 | 56130855 | T | 0 | 3′ UTR |
| rs11172223c | 12 | 56132314 | A | 0 | 3′ conserved SNP |
| rs7136620c | 13 | 56132489 | A | 0 | 3′ conserved SNP |
The physical location of each SNP is based on NCBI Build 36. The putative function was derived from SNPselector and SNPseek output. All SNP genotype distributions are in Hardy–Weinberg equilibrium (P>0.001).
a
Failed iPLEX assay.
b
Failed iPLEX assay but also genotyped in stage 1.
c
Monomorphic SNPs.