Table 3.
Clustering of SNPs with low p-values.
| Rank | Chr | Start | End | Nsnps | Pmin | N <0.0001 |
N <0.001 |
N <0.01 |
Expressed in brain? |
Genes | Gene products |
SLEP ‡ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 7 | 30,928,587 | 30,931,521 | 3 | 1.25E-06 | 2 | 0 | 1 | Yes | ADCYAP1R1 | adenylate cyclase activating polypeptide 1 (pituitary) receptor type I |
Neuroactive ligand-receptor interaction |
| 2 | 7 | 82,041,576 | 82,208,167 | 10 | 1.50E-06 | 6 | 4 | 0 | Yes | PCLO | piccolo (presynaptic cytomatrix protein) |
|
| 4 | 6 | 14,388,932 | 14,399,068 | 2 | 9.09E-06 | 1 | 1 | 0 | ||||
| 5 | 2 | 20,177,820 | 20,183,313 | 2 | 1.18E-05 | 2 | 0 | 0 | Yes | LAPTM4A | lysosomal-associated protein transmembrane 4 alpha | |
| 6 | 15 | 46,979,618 | 46,980,083 | 2 | 1.36E-05 | 1 | 1 | 0 | Yes |
CRI1 EID1 RaLP SHC4 |
CREBBP/EP300 inhibitor 1/EP300 interacting inhibitor of differentiation 1/rai-like protein/SHC (Src homology 2 domain containing) family, member 4 |
|
| 9 | 2 | 201,794,446 | 201,880,818 | 2 | 2.44E-05 | 1 | 1 | 0 | Yes |
AJ487678 AJ487679 AK125394 AY690601 CASP10 CFLAR NDUFB3 |
Caspase 10./Caspase 10./PRO3098./Caspase 10 splice variant G./caspase 10, apoptosis-related cysteine peptidase/CASP8 and FADD-like apoptosis regulator/NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa |
CASP10 causes multiple neoplasms (OMIM 601762); CFLAR upregulated in MDD in post-mortem brain |
| 14 | 20 | 39,724,220 | 39,742,644 | 5 | 4.27E-05 | 5 | 0 | 0 | ||||
| 15 | 6 | 14,386,148 | 14,397,061 | 3 | 4.23E-05 | 1 | 1 | 1 | ||||
| 16 | 4 | 184,652,456 | 184,658,003 | 3 | 4.28E-05 | 1 | 0 | 2 | ||||
| 17 | 5 | 117,174,763 | 117,282,887 | 4 | 4.84E-05 | 1 | 1 | 2 | ||||
| 19 | 10 | 127,071,672 | 127,087,021 | 3 | 0.000046 | 1 | 2 | 0 | ||||
| 20 | 5 | 22,752,605 | 22,792,155 | 3 | 4.65E-05 | 1 | 0 | 2 | Yes | CDH12 | cadherin 12, type 2 (N-cadherin 2) |
|
| 22 | 15 | 88,130,196 | 88,136,792 | 2 | 5.52E-05 | 1 | 1 | 0 | Yes | ANPEP MESP2 | alanyl (membrane) aminopeptidase (aminopeptidase N, aminopeptidase M, microsomal aminopeptidase, CD13, p150)/mesoderm posterior 2 homolog (mouse) |
MESP2 causes spondylocostal dysostosis (OMIM 605195) |
| 23 | 8 | 54,098,247 | 54,102,064 | 2 | 4.83E-05 | 2 | 0 | 0 | ||||
| 24 | 4 | 145,875,183 | 145,878,794 | 2 | 5.47E-05 | 1 | 0 | 1 | ||||
| 27 | 11 | 32,242,721 | 32,244,520 | 2 | 4.25E-05 | 2 | 0 | 0 | ||||
| 28 | 8 | 27,249,840 | 27,379,524 | 6 | 5.38E-05 | 1 | 2 | 3 | Yes |
AK128371 CHRNA2 PTK2B |
Hypothetical protein FLJ46514./cholinergic receptor, nicotinic, alpha 2 (neuronal)/PTK2B protein tyrosine kinase 2 beta |
CHRNA2 causes nocturnal frontal lobe epilepsy (OMIM 118502) |
| 29 | 3 | 12,453,817 | 12,459,985 | 2 | 0.00005 | 1 | 1 | 0 | PPARG | peroxisome proliferator-activated receptor gamma | Type 2 diabetes mellitus risk gene | |
| 32 | 3 | 99,975,821 | 100,183,009 | 2 | 7.26E-05 | 1 | 0 | 1 | Yes | DCBLD2 ST3GAL6 | discoidin, CUB and LCCL domain containing 2/ST3 beta- galactoside alpha-2,3-sialyltransferase 6 |
|
| 34 | 3 | 70,451,852 | 70,476,913 | 2 | 8.22E-05 | 1 | 0 | 1 | ||||
| 38 | 2 | 7,424,098 | 7,440,754 | 3 | 8.95E-05 | 1 | 1 | 1 | ||||
| 41 | 5 | 54,352,635 | 54,363,712 | 3 | 0.000071 | 1 | 1 | 1 | Yes | GZMK | granzyme K (granzyme 3; tryptase II) |
|
| 43 | 13 | 111,889,281 | 111,902,203 | 2 | 7.87E-05 | 1 | 1 | 0 | ||||
| 44 | 1 | 211,470,329 | 211,508,991 | 4 | 0.000072 | 1 | 3 | 0 | ||||
| 46 | 8 | 24,784,576 | 24,825,085 | 2 | 0.000359 | 0 | 2 | 0 | NEF3 NEFM | neurofilament 3 (150kDa medium)/neurofilament, medium polypeptide 150kDa |
‡
SLEP=Sullivan Lab Evidence Project (http://slep.unc.edu) a compendium of genetic findings from the literature.