Table 1. Genome-wide significant associations with Y chromosome loss.
| SNP | Location | Alleles1 | UK Biobank (N=67,034) |
EPIC Norfolk (N=9,793) |
deCODE (N=8,715) |
Replication P | Overall P | Gene4 | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Effect2 | P | Effect2 | P | Effect3 | P | ||||||
| rs17758695 | 18q21.33 | C/T/0.97 | -0.01 | 6.4x10-21 | -0.014 | 3.7x10-04 | -0.020 | 9.1x10-13 | 2.7x10-17 | 1.3x10-33 | BCL2 [NC] |
| rs1122138 | 14q32.13 | C/A/0.84 | -0.005 | 3.6x10-23 | -0.006 | 4.3x10-04 | -0.007 | 1.5x10-04 | 8.0x10-10 | 6.3x10-31 | TCL1A [NEC] |
| rs78378222 | 17p13.1 | G/T/0.01 | -0.013 | 1.3x10-15 | -0.032 | 1.8x10-06 | -0.026 | 3.8x10-10 | 7.3x10-18 | 3.4x10-28 | TP53 [CN] |
| rs59633341 | 3q25.1 | A/AT/0.16 | -0.004 | 2.6x10-18 | -0.009 | 7.5x10-07 | -0.007 | 1.1x10-05 | 8.5x10-14 | 4.1x10-28 | TSC22D2 [N] |
| rs2736609 | 1q22 | T/C/0.36 | -0.003 | 1.9x10-12 | -0.003 | 4.9x10-02 | -0.006 | 2.5x10-07 | 2.4x10-10 | 2.0x10-19 | PMF1 [CFN], SEMA4A [CE] |
| rs13191948 | 6q21 | C/T/0.54 | -0.002 | 1.2x10-11 | -0.006 | 5.4x10-06 | -0.005 | 3.8x10-05 | 4.5x10-12 | 2.2x10-19 | SMPD2 [E], CCDC162P [NE] |
| rs60084722 | 20q11.21 | CT/C/0.79 | -0.003 | 6.6x10-13 | -0.002 | 2.5x10-01 | -0.006 | 9.4x10-05 | 1.5x10-6 | 1.6x10-17 | TPX2 [NEC], BCL2L1 [C], HM13 [E] |
| rs381500 | 6q26 | C/A/0.55 | -0.002 | 5.7x10-11 | -0.002 | 1.9x10-01 | -0.005 | 1.1x10-07 | 1.8x10-7 | 5.0x10-16 | QKI [N] |
| rs56084922 | 5q22.1 | G/A/0.08 | -0.005 | 2.9x10-13 | -0.004 | 1.2x10-01 | -0.005 | 1.6x10-03 | 2.8x10-3 | 3.0x10-15 | NREP [N] |
| rs137952017 | 14q32.2 | C/CT/0.85 | -0.003 | 1.2x10-09 | -0.01 | 1.3x10-07 | -0.004 | 4.0x10-04 | 2.4x10-8 | 4.0x10-15 | DLK1 [N] |
| rs4721217 | 7p22.3 | T/C/0.4 | -0.002 | 6.5x10-10 | -0.005 | 2.8x10-04 | -0.003 | 1.1x10-05 | 1.7x10-6 | 3.5x10-14 | MAD1L1 [NFC] |
| rs35091702 | 8p12 | C/CAAAAAAG/0.74 | -0.002 | 4.2x10-10 | -0.004 | 6.0x10-03 | -0.002 | 3.9x10-02 | 6.5x10-3 | 9.5x10-12 | RBPMS [N] |
| rs4754301 | 11q22.3 | A/G/0.55 | -0.002 | 1.3x10-09 | -0.001 | 5.4x10-01 | -0.002 | 2.8x10-02 | 1.5x10-2 | 6.5x10-11 | NPAT [NF], ATM [C], ACAT1 [E] |
| rs12448368 | 16q23.2 | C/T/0.13 | -0.003 | 9.8x10-10 | -0.002 | 2.5x10-01 | -0.003 | 2.4x10-02 | 2.2x10-2 | 7.1x10-11 | CENPN [NEC], ATMIN [CE] |
| rs11082396 | 18q12.3 | C/T/0.13 | -0.003 | 3.3x10-09 | -0.004 | 6.7x10-02 | -0.003 | 1.2x10-01 | 1.1x10-2 | 1.2x10-10 | SETBP1 [N] |
| rs13088318 | 3q12.3 | G/A/0.34 | -0.002 | 4.1x10-09 | -0.0004 | 7.7x10-01 | -0.003 | 1.7x10-02 | 2.1x10-2 | 2.7x10-10 | SENP7 [E] |
| rs77522818 | 17q21.33 | A/T/0.96 | -0.005 | 1.3x10-09 | -0.004 | 3.0x10-01 | -0.002 | 2.4x10-01 | 1.6x10-1 | 8.8x10-10 | FAM117A (N) |
| rs10687116 | 13q14.11 | AGATG/A/0.8 | -0.002 | 2.6x10-08 | -0.001 | 5.8x10-01 | -0.003 | 5.8x10-02 | 1.0x10-2 | 8.8x10-10 | WBP4 [N] |
| rs115854006 | 3p21.31 | C/T/0.96 | -0.006 | 3.7x10-08 | -0.007 | 5.4x10-02 | 0.002 | 9.3x10-01 | 3.4x10-1 | 4.5x10-08 | TREX1 [C], PLXNB1 [C] |
1
mLRR-Y lowering allele / increasing allele / lowering allele frequency
2
Effect estimates in per-allele decreases in raw mean intensity log-R ratio units
3
Effect estimate per allele for copy number transformed log2(chrY copy-number)
4
Labelled gene where preceding nomenclature refers to [N] nearest (default), [C] biological candidate, [E] expression mediated by mLRR-Y associated SNPs, [F] non-synonymous variant in gene.