Table 1.
Summary of significantly associated genetic clusters with the vulnerable ‘last in, first out’ brain network
| Significant variants |
N | P-value | beta | Chr | Position | a1 | a2 | af | Gene | eQTL, tissue | Reproduction P-value | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 |
rs6540873 rs1452628 |
2 | 1.71E−08 | 0.06 | 1 | 215,137,222 | A | C | 0.38 | intergenic, ~40 kb from KCNK2 (TREK1) |
KCNK2 (TREK1) Non-brain |
3.92E−04 |
| 2 |
rs13107325 rs13135092 rs35518360 rs35225200 rs13105682 rs6855246 rs1813006 |
7 | 2.82E−13 | 0.14 | 4 | 103,188,709 | C | T | 0.07 | exon (missense), SLC39A8 (ZIP8) |
UBE2D3 Non-brain |
1.18E−03 |
| 3 | rs35187443 (6:45442860_TA_T) | 1 | 9.03E−09 | 0.06 | 6 | 45,442,860 | TA | T | 0.38 | intron of RUNX2 |
in high LD (R2 = 0.86) with rs2677109, eQTL of RUNX2 Brain |
3.05E−03 |
| 4 | rs12146713 | 1 | 1.26E−09 | −0.10 | 12 | 106,476,805 | T | C | 0.09 | intron of NUAK1 (ARK5) |
RP11-114F10.2 Non-brain |
5.64E−03 |
| 5 | rs2532395 (highest hit after tri-allelic rs2693333)a | 3,906 | 3.56E−15 | −0.09 | 17 | 44,307,193 | C | T | 0.21 | intergenic, in MAPT region, <10 kb from KANSL1 |
multiple genes, including MAPT, KANSL1, CRHR1, SPPL2C, ARL17A Non-brain |
1.97E−02 |
| 6 |
rs312238 rs312241 rs312245 rs312250 rs113075535 rs312257 rs312255 rs312256 |
8 | 1.77E−10 | −0.05 |
X Y |
2,669,044 2,619,044 |
G | T | 0.15 | intergenic, ~1 kb from XG, ~10 kb from CD99 |
CD99 Non-brain |
1.12E−06 |
| 7 |
rs2857316 rs2109378 rs2534628 rs2534630 rs2534629 rs311155 rs28620378 rs28758440 rs2534635 |
9 | 2.27E−29 | −0.08 |
X Y |
2,698,954 2,648,954 |
G | A | 0.32 |
intron of XG intron of XGPY2 |
XG Non-brain |
3.87E−19 |
Lead variant in bold. Due to formatting constraints, this is an abbreviated version without e.g., the association with nIDPs; the full table is available as Supplementary Data 1. P-values are derived from a two-sided linear association test.
aFull list of significant hits in cluster in Supplementary Data 4.