Table 3.
Sample sizes, covariates and top hits for the 11 phenotypes
| Phenotype | n | Covariatesa | Top hit | rs Number | Closest gene | Type of variant | Notes |
|---|---|---|---|---|---|---|---|
| PAL total errors 6 patterns | 764 | Siteb | 1.01E−07 | rs5934953 | HCCS | 81 kb upstream | Fifth from top at P = 3 × 10−6 is a 3′-UTR SNP in GRIP2, a gene involved in synaptic plasticity (83) |
| PAL total errors 8 patterns | 718 | Education | 1.16E−07 | rs11856323 | COR2B | Intronic | |
| SWM between for 8 box stage | 784 | ESL, site, battery | 2.86E−07 | r s2326017 | AC103702.3 | 11 kb upstream | Fifteenth from top is an intronic SNP in NRXN1, P = 1.3 × 10−5. Rare NRXN1 deletions have been associated with schizophrenia (6,62,64) and autism (61,65) |
| SWM strategy | 721 | ESL, education, siteb, battery | 6.30E−06 | rs4472969 | FXYD2 | 1.5 kb upstream | Fourth from top was an intronic SNP in SHANK3, P = 1.9 × 105. Rare genetic variants affecting SHANK3 have been associated with autism (61,84,85) and possibly epilepsy (61) |
| IED EDS errors | 743 | ESL, site | 1.69E−06 | rs6592284 | c11orf73 | Intronic | Top hit is also close to ME3 which shows expression changes in a rat model of schizophrenia (86). Third from top at P = 1.9 × 10−5 was an intronic GRIN2B SNP. Overexpression of GRIN2B in mice enhances cognition (87) |
| RVP probability of a hit | 782 | ESL, site, battery | 2.17E−06 | rs6056209 | PLCB1 | intronic | PLCB1 knockout mice are used as schizophrenia models (88) |
| PRM percent correct | 740 | Education, siteb, battery | 3.23E−07 | rs2203512 | AC092725.3 | 88 kb downstream | |
| SSP span length | 714 | Education, siteb, battery | 1.00E−06 | rs7729273 | AC091951.3 | 71 kb downstream | |
| SRM percent correct | 1227 | Siteb, battery, length | 5.89E−07 | rs2229741 | NRIP1 | synonymous coding | Second strongest hit is intronic hit in GABRB3, P = 1.9 × 10−6. GABRB3 knockout mice have seizures, cognitive deficits and behavioral problems (89) |
| VRM free recall | 1235 | Education, battery | 3.94E−06 | rs4258076 | SLC24a2 | Intronic | Fifth from top is intronic hit in GRM7, 1.3 × 10−5. GRM7 knockout and transgenic mice show memory deficits (90–96) |
| PC1 | 707 | Education, site, battery | 2.76E−06 | rs4082514 | AC009117.8 | 108 kb upstream | Sixteenth from top is intronic SNP in NRXN1, rs4971648, P = 3 × 10−5 (see above) |
aSex and age were included as covariates in all analyses.
bLondon only, NC State and Duke scores did not differ; ESL: English learned as a second language, battery: whether the subject performed the original or the modified CANTAB battery, length: whether the subject performed the complete battery or just SRM and VRM.