Table 2.
SNP information and quality criteria in African-American and European-American samples.
SNP | Positiona | Function | African-Americans | European-Americans | ||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
| ||||||||||||
Alleles (Major/Minor) | Call rate (%) | MAFb (%) | MAFc (%) | HWE | Alleles (Major/Minor) | Call rate (%) | MAFb (%) | MAFd (%) | HWE | |||
rs2236196 | 61448000 | 3’-UTR | G/A | 97.1 | 30.9 | 34.1 | 0.64 | A/G | 98.5 | 27.6 | 29.2 | 1 |
rs3787138 | 61449668 | Intron 5 | A/G | 96.9 | 49.8 | 49.2 | 1 | A/G | 97 | 14.4 | 9.2 | 0.62 |
rs1044396 | 61451578 | Exon 5 (Synonymous) | G/A | 98 | 7.7 | 2.5 | 0.37 | A/G | 97.8 | 47.7 | 40.5 | 0.94 |
rs1044394 | 61452529 | Exon 5 (Synonymous) | G/A | 97.7 | 41.3 | 33.9 | 0.42 | G/A | 97.1 | 8.3 | 6.9 | 1 |
rs6010918 | 61459945 | Intron 2 | G/A | 95.8 | 39.1 | 35.0 | 0.33 | G/A | 97 | 6.6 | 5.8 | 1 |
Abbreviation: UTR, untranslated region; MAF, minor allele frequency; HWE, p-value for Hardy-Weinberg equilibrium. MAFb and HWE were calculated from the controls without a DSM-IV diagnosis of ND and dichotomized FTND cases.
coordinate based on Genome Build 36.3;
MAF from our study samples.
MAF from Hapmap YRI samples (except rs2236196 for which the MAF was from African American sample in dbSNP);
MAF from Hapmap CEU samples (except rs2236196 for which the MAF was from pilot 1 CEU sample in dbSNP).
We note that our observed allele frequency for rs1044396 differs from the HapMap frequency by about 7%; our observation however is very close to that reported in an article with a much larger sample (Breitling, 2009)