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. 2021 May 19;11:296. doi: 10.1038/s41398-021-01412-9

Table 3.

List of novel candidate variants significantly associated with customized genotyping AD chip application set (P value < 0.005).

Chromosome SNP Positionb Assigned genesc Functional refGene Minor/major allele Our results Known resultsa
Groups MAF in cases MAF in controls P valued OR (CI, 95%) Non-effect/effect alleles Beta (SE)e P value East Asian frequencyf European frequency (non-Finnish)f
1 rs12063304 25071668 CLIC4 Upstream G/A WGS 0.041 0.086 3.07.E−03 0.45 (0.26–0.78) A/G −0.023 (0.049) 0.64 0.063 0.029
cAD chip 0.032 0.055 4.98.E−03 0.57 (0.38–0.84)
Combined 0.036 0.060 4.31.E−04 0.57 (0.42–0.78)
7 rs80020083 158283748 PTPRN2 Intronic A/G WGS 0.038 0.077 8.67.E−03 0.47 (0.27–0.83) NA NA NA 0.039 <0.001
cAD chip 0.035 0.060 2.60.E−03 0.57 (0.39–0.83)
Combined 0.036 0.063 1.49.E−04 0.56 (0.41–0.76)
8 rs967326 18547261 PSD3 Intronic A/G WGS 0.334 0.219 1.08.E−04 1.79 (1.32–2.42) G/A 0 (0.034) 1.00 0.37 0.049
cAD chip 0.338 0.287 4.35.E−03 1.27 (1.08–1.49)
Combined 0.336 0.276 4.90.E−05 1.33 (1.16–1.53)
10 rs144835823 109002092 SORCS1,LINC01435 Intergenic A/T WGS 0.011 0.038 2.61.E−03 0.27 (0.11–0.68) NA NA NA 0.022 0
cAD chip 0.008 0.026 8.40.E−04 0.32 (0.15–0.65)
Combined 0.009 0.028 2.42.E−05 0.32 (0.19–0.56)
10 rs78442236 109033178 SORCS1,LINC01435 Intergenic A/G WGS 0.008 0.036 1.10.E−03 0.21 (0.07–0.59) NA NA NA 0.020 0
cAD chip 0.004 0.022 9.57.E−05 0.17 (0.06–0.47)
Combined 0.005 0.024 1.99.E−06 0.21 (0.10–0.43)
11 rs74352072 119792009 LOC102724301,TRIM29 Intergenic G/C WGS 0.245 0.166 4.95.E−03 1.63 (1.17–2.29) NA NA NA 0.25 <0.001
cAD chip 0.251 0.198 1.02.E−03 1.36 (1.13–1.62)
Combined 0.248 0.193 3.74.E−05 1.39 (1.19–1.61)
15 rs79919241 93434633 LINC01578 ncRNA_intronic T/C WGS 0.172 0.104 6.17.E−03 1.80 (1.20–2.70) C/T 0.049 (0.039) 0.21 0.066 0.043
cAD chip 0.176 0.132 1.57.E−03 1.40 (1.13–1.73)
Combined 0.174 0.127 6.11.E−05 1.45 (1.21–1.73)
17 rs201351606 1082940 ABR Intronic A/G WGS 0.005 0.030 1.97.E−03 0.15 (0.04–0.55) NA NA NA 0.026 <0.001
cAD chip 0.005 0.018 1.80.E−03 0.25 (0.10–0.64)
Combined 0.005 0.020 3.37.E−05 0.23 (0.11–0.48)
17 rs117665140 58280925 USP32 Intronic T/C WGS 0.100 0.038 9.28.E−04 2.77 (1.50–5.09) NA NA NA 0.049 0
cAD chip 0.099 0.063 8.17.E−04 1.62 (1.23–2.13)
Combined 0.099 0.059 7.73.E−06 1.74 (1.37–2.21)

In the WGS, n = 500; cAD chip n = 1437; combined n = 1937.

AD Alzheimer’s disease, MAF minor allele frequency, OR odds ratio, CI confidence interval, SNP single nucleotide polymorphism, NA not available.

aNon-effect/effect alleles, Beta and P values in the International Genomics of Alzheimer’s Project (IGAP).

bPhysical position based on human reference genome build hg19 (GRCh37).

cThe nearest gene to each SNP is underlined.

dP-values were calculated using Cochran-Armitage trend test.

eOverall estimated effect size and standard error for the effect allele.

fPopulation frequency based on gnomAD database (http://gnomad.broadinstitute.org/).