Table 1.
Results of the association tests between 41 validation SNPs and two sperm morphology traits, % normal morphology and morphology classification
| SNP | Chr | Position | Closest gene(s) | Relationship to the closest gene | Dist (kb) | Chicago validation sample | Hutterite men | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Allele: genotype count (2/1/0 copies) | Freq | % normal morphology P-value | Morphology classification P-value | Assoc. trait | P-value | Model | ||||||
| rs2991396 | 13 | 66,787,387 | PCDH9 | upst. | 84.9 | G: 14/53/55 | 0.33 | 1.27E-01 | 1.25E-01 | FS | 4.43E-06 | additive |
| rs10966811 | 9 | 25,223,484 | TUSC1 | dwnst. | 445.4 | T: 23/49/47 | 0.40 | 9.70E-01 | 9.21E-01 | FS | 5.57E-06 | recessive |
| rs11144790 | 9 | 78,002,292 | PCSK5 | dwnst. | 4.1 | A: 1/11/106 | 0.06 | 9.85E-01 | 9.68E-01 | FS | 6.45E-06 | additive |
| rs2423942 | 20 | 15,271,282 | MACROD2 | intron | — | T: 12/50/54 | 0.32 | 7.97E-01 | 8.24E-01 | FS | 9.26E-06 | recessive |
| rs7867029 | 9 | 80,210,238 | PSAT1 | dwnst. | 75.4 | G: 9/38/65 | 0.25 | 3.53E-01 | 2.97E-01 | FS | 1.04E-05 | recessive |
| rs4753939 | 11 | 98,493,518 | CNTN5 | intron | — | T: 26/56/40 | 0.44 | 8.88E-01 | 9.37E-01 | FS | 1.05E-05 | recessive |
| rs12339229 | 9 | 28,083,232 | LINGO2 | intron | — | A: 1/18/102 | 0.08 | 8.45E-01 | 7.63E-01 | FS | 1.23E-05 | additive |
| rs9851460 | 3 | 156,384,950 | MME | dwnst. | 0.7 | A: 11/53/58 | 0.31 | 8.69E-01 | 8.81E-01 | FS | 1.24E-05 | recessive |
| rs1152948 | 12 | 68,678,852 | RAB3IP | dwnst. | 175.6 | A: 11/52/59 | 0.30 | 9.96E-01 | 9.94E-01 | FS | 1.24E-05 | recessive |
| rs1472272 | 7 | 97,950,910 | BAIAP2L1 | upst. | 82.6 | G: 6/41/72 | 0.22 | 4.03E-01 | 1.76E-01 | FS | 1.44E-05 | recessive |
| rs12870438 | 13 | 42,378,205 | EPSTI1 | intron | — | A: 5/32/85 | 0.17 | 3.20E-01 | 3.98E-01 | FS | 2.07E-05 | recessive |
| rs1507417 | 3 | 78,733,335 | ROBO1 | intron | — | C: 11/40/71 | 0.25 | 3.99E-01 | 5.94E-01 | FS | 2.41E-05 | additive |
| rs12088543 | 1 | 84,490,571 | PRKACB | dwnst. | 13.8 | G: 11/46/64 | 0.28 | 5.29E-01 | 6.32E-01 | FS | 3.31E-05 | additive |
| rs7174015 | 15 | 48,504,360 | USP8 | intron | — | C: 24/52/39 | 0.43 | 3.31E-01 | 1.85E-01 | FS | 3.57E-05 | recessive |
| rs11723705 | 4 | 55,445,828 | KIT, KDR | dwnst. | 144.2, 193.6 | T: 2/24/92 | 0.12 | 7.66E-01 | 8.91E-01 | FS | 3.63E-05 | additive |
| rs10129954 | 14 | 72,220,454 | DPF3 | intron | — | C: 12/60/50 | 0.34 | 2.33E-02 | 9.88E-02 | FS | 3.86E-05 | recessive |
| rs7106789 | 11 | 21,526,300 | NELL1 | intron | — | A: 18/67/35 | 0.43 | 6.17E-01 | 6.85E-01 | FS | 4.36E-05 | recessive |
| rs1514673 | 12 | 41,930,420 | ADAMTS20 | dwnst. | 103.9 | T: 7/40/73 | 0.23 | 9.81E-01 | 9.86E-01 | FS | 7.18E-05 | additive |
| rs1487933 | 21 | 20,593,873 | BC047405 | dwnst. | 442.9 | G: 20/61/39 | 0.42 | 3.28E-01 | 1.78E-01 | FS | 5.18E-05 | recessive |
| rs6471590 | 8 | 143,795,554 | LY6K, C8orf55 | dwnst. | 12.9, 10.1 | C: 7/41/73 | 0.23 | 8.42E-01 | 6.33E-01 | FS | 5.32E-05 | recessive |
| rs11956144 | 5 | 160,248,178 | ATP10B | upst. | 36.4 | G: 1/30/81 | 0.14 | 5.83E-01 | 4.46E-01 | FS | 5.96E-05 | additive |
| rs10893363 | 11 | 124,670,989 | PKNOX2 | intron | — | G: 0/17/104 | 0.07 | 1.46E-01 | 9.06E-02 | FS | 7.16E-05 | additive |
| rs17088625 | 8 | 22,703,795 | PEBP4 | intron | — | C: 15/56/51 | 0.35 | 9.14E-01 | 9.65E-01 | FS | 7.20E-05 | additive |
| rs2330929 | 22 | 23,549,930 | SGSM1 | intron | — | C: 29/51/39 | 0.46 | 8.84E-01 | 8.10E-01 | FS | 7.91E-05 | additive |
| rs16917898 | 9 | 32,106,520 | ACO1 | upst. | 268.1 | T: 0/16/107 | 0.07 | 5.80E-01 | 2.72E-01 | FS | 7.99E-05 | recessive |
| rs11794651 | 9 | 38,728,489 | ANKRD18A | upst. | 117.8 | G: 3/31/88 | 0.15 | 5.50E-01 | 9.06E-01 | FS | 9.48E-05 | additive |
| rs1745689 | 14 | 57,140,645 | SLC35F4 | upst. | 7.3 | A: 16/45/62 | 0.31 | 3.63E-01 | 2.30E-01 | FS | 9.66E-05 | additive |
| rs9422913 | 10 | 127,335,597 | C10orf22 | intron | — | G: 22/58/37 | 0.44 | 3.82E-01 | 4.71E-01 | FS | 9.89E-05 | additive |
| rs433406 | 11 | 130,876,229 | NTM | intron | — | G: 32/51/32 | 0.50 | 4.06E-01 | 6.78E-01 | BR | 3.36E-06 | additive |
| rs4936891 | 11 | 123,425,855 | OR10G7 | upst. | 10.9 | C: 11/38/59 | 0.28 | 2.26E-01 | 8.78E-02 | BR | 8.62E-06 | additive |
| rs680730 | 11 | 116,980,443 | DSCAML1 | intron | — | T: 12/58/50 | 0.34 | 1.68E-02 | 3.60E-02 | BR | 2.45E-05 | additive |
| rs4538394 | 3 | 21,774,713 | ZNF385D | intron | — | A: 14/40/58 | 0.30 | 3.45E-01 | 2.59E-01 | BR | 3.67E-05 | recessive |
| rs13265504 | 8 | 3,532,499 | CSMD1 | intron | — | C: 35/48/38 | 0.49 | 7.41E-01 | 9.11E-01 | BR | 4.43E-05 | additive |
| rs1484095 | 18 | 33,971,576 | BRUNOL4 | upst. | 571.8 | T: 10/46/65 | 0.27 | 1.25E-01 | 5.78E-02 | BR | 5.37E-05 | additive |
| rs11236909 | 11 | 76,116,716 | TSKU, LRRC32 | upst. | 55.2, 58.0 | C: 8/43/70 | 0.24 | 4.42E-01 | 3.99E-01 | BR | 6.11E-05 | additive |
| rs768343 | 18 | 37,686,676 | PIK3C3 | upst. | 102.5 | A: 15/58/44 | 0.38 | 7.53E-01 | 8.97E-01 | BR | 6.60E-05 | additive |
| rs2035804 | 10 | 133,884,369 | STK32C | intron | — | T: 3/31/88 | 0.15 | 4.74E-01 | 5.20E-01 | BR | 7.55E-05 | additive |
| rs4128691 | 3 | 72,432,553 | RYBP | dwnst. | 73.9 | T: 18/45/53 | 0.35 | 5.76E-01 | 6.49E-01 | BR | 8.40E-05 | additive |
| rs10488786 | 11 | 100,245,404 | ARHGAP42 | intron | — | T: 0/11/106 | 0.05 | 3.66E-01 | 6.01E-01 | BR | 8.70E-05 | additive |
| rs79110092 | 10 | 49,808,465 | LRRC18, WDFY4 | intron | — | T: 1/20/101 | 0.09 | 5.92E-01 | 8.23E-01 | BR | 9.49E-05 | additive |
| rs724078 | 6 | 29,597,027 | MAS1L, UBD | upst. | 33.7, 34.4 | T: 26/59/34 | 0.47 | 1.84E-01 | 7.12E-02 | BR | 9.99E-05 | recessive |
In the Chicago validation sample, P-values from 10,000 permutations are shown. Bolded P-values show the significant associations in the Chicago validation sample