Table 1 This table includes the 10 most significant SNPs and 13 other significant SNPs that have a RegulomeDB score less than 3, are non-synonymous, a splicing variant, or are located in untranslated regions (UTRs). All 23 SNPs are located in or near the ACPP gene on chromosome 3, which codes for PAP. There were no significant non-synonymous SNPs. The table includes SNP ids, reference and alternate alleles, minor allele frequency, predicted SNP function, and its directions in the Knight ADRC and ADNI data sets. Also included are the p-values from ADNI and Knight ADRC alone, their meta-analysis p-value and their RegulomeDB score, where available
From: Variants in ACPP are associated with cerebrospinal fluid Prostatic Acid Phosphatase levels
SNP | Minor Allele | Major Allele | MAF | Predicted Function | Direction | ADNI p-value | Knight ADRC p-value | Meta-analysis p-value | RegulomeDB score |
|---|---|---|---|---|---|---|---|---|---|
rs3844501 | T | G | 0.1458 | Intergenic | ++ | 1.972e-13 | 7.974e-09 | 1.743e-20 | 6 |
rs3762671 | T | C | 0.1060 | Intergenic | ++ | 3.815e-13 | 3.245e-08 | 1.515e-19 | 6 |
rs11716607 | G | A | 0.0923 | Intronic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | No Data |
rs56158166 | T | G | 0.0921 | Intronic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | No Data |
rs73213842 | A | T | 0.0923 | Intergenic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | No Data |
rs11706024 | A | G | 0.0921 | Intergenic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | 5 |
rs113143077 | A | G | 0.0923 | Intergenic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | 6 |
rs17344445 | A | G | 0.0923 | Intergenic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | 6 |
rs2887519 | A | G | 0.0923 | Intergenic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | 6 |
rs56073503 | A | T | 0.0921 | Intronic | ++ | 1.708e-12 | 3.615e-08 | 6.397e-19 | 6 |
rs3889987 | T | G | 0.0913 | Intergenic | ++ | 2.15E-13 | 4.08E-07 | 1.77E-18 | 2a |
rs56030168 | G | A | 0.1769 | 5upstream | ++ | 2.94E-11 | 1.34E-06 | 4.65E-16 | 2b |
rs11714139 | A | G | 0.1232 | Intergenic | ++ | 1.25E-07 | 4.81E-04 | 5.41E-10 | 2b |
rs56226080 | C | G | 0.1228 | Intergenic | ++ | 1.25E-07 | 4.81E-04 | 5.41E-10 | 2b |
rs73211958 | A | C | 0.1218 | Intergenic | ++ | 1.25E-07 | 5.11E-4 | 5.82E-10 | 2b |
rs16839055 | T | C | 0.3081 | Intergenic | ++ | 2.49E-05 | 2.52E-04 | 2.55E-08 | 1f |
rs1804136 | T | G | 0.3962 | UTR3 | ++ | 4.80E-05 | 1.39E-04 | 2.57E-08 | No Data |
rs14192 | C | T | 0.3964 | UTR3 | ++ | 4.80E-05 | 1.39E-04 | 2.57E-08 | 5 |
rs1042330 | A | G | 0.3962 | UTR3 | ++ | 6.49E-05 | 1.39E-04 | 3.43E-08 | No Data |
rs17182812 | T | C | 0.3962 | Intronic | ++ | 6.49E-05 | 1.39E-04 | 3.43E-08 | 1f |
rs4257547 | G | C | 0.4113 | Intronic | ++ | 5.19E-05 | 1.94E-04 | 3.87E-08 | 2b |
rs11928839 | A | C | 0.3954 | Intronic | ++ | 6.49E-05 | 1.60E-04 | 3.93E-08 | 2b |
rs11917521 | C | T | 0.3954 | Intronic | ++ | 6.49E-05 | 1.60E-04 | 3.93E-08 | 2b |