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Table 2 Newly detected replicated and meta-analysis sets of significant SNPs located outside chromosome 19q13 region

From: Genome-wide analysis of genetic predisposition to Alzheimer’s disease and related sex disparities

Chromosome

Closest gene

SNP

Position

A1

Sig?

P min

Effects

Freq

OR (se)

P meta

P q

i 2

P abs

Proxy?

Gene?

Region?

Plan 1—males and females

 6p22.3

LOC101928519

rs62402815a

19,350,484

G

NYYN

1.94E–07

– – – –

0.941

0.690 (0.050)

1.80E–06

1.41E–04

0.853

1.80E–06

N

N

N

 7q22.1

TRIM56

rs10953322

101,103,377

G

YYNN

2.89E–03

– – – –

0.871

0.758 (0.043)

4.65E–06

7.84E–01

0

4.66E–06

N

N

Y

 9p22.3

C9orf92

rs4961664

16,161,235

T

YNNY

3.45E–03

– – – –

0.711

0.811 (0.035)

4.44E–06

8.14E–01

0

4.44E–06

N

N

N

 9p13.2

PAX5

rs2282079

37,036,250

G

Y?NN

6.49E–05

– ? – –

0.959

0.595 (0.06)

3.81E–06

4.48E–01

0

3.81E–06

N

N

N

 11p15.5

AP2A2

rs10794342

924,904

C

YNYY

2.46E–04

– – – –

0.456

0.824 (0.033)

4.45E–06

1.19E–01

0.488

4.42E–06

Y

Y

Y

 13q33.3

MYO16

rs9555561

109,152,426

C

YNNN

6.99E–05

+ + + +

0.727

1.249 (0.056)

2.53E–06

4.64E–01

0

2.54E–06

N

Y

Y

 13q33.3

MYO16

rs912322

109,155,938

A

YNNY

5.44E–05

+ + + +

0.733

1.260 (0.057)

1.29E–06

4.56E–01

0

1.29E–06

N

Y

Y

 17q12

LHX1

rs8070114

36,817,647

A

NNNY

6.07E–04

– – – –

0.949

0.675 (0.053)

3.58E–06

6.06E–01

0

3.58E–06

N

N

N

 17q12

LHX1

rs1497197

36,819,274

A

NNNY

7.69E–04

– – – –

0.949

0.668 (0.053)

2.96E–06

4.79E–01

0

2.98E–06

N

N

N

 18q12.1

MIR302F

rs35242772

30,214,382

C

YYNY

3.31E–03

+ + + +

0.356

1.231 (0.051)

1.31E–06

8.42E–01

0

1.31E–06

N

N

Y

 21q21.2

LINC00158

rs76252969

25,277,446

G

YYNN

1.12E–04

– – – –

0.971

0.594 (0.061)

4.86E–06

3.47E–01

0.092

4.86E–06

N

N

N

 21q21.3

LINC00515,MRPL39

rs2298369

25,583,969

C

YYYN

6.02E–06

– – – +

0.605

0.802 (0.033)

3.67E–07

1.81E–04

0.849

1.43E–10

N

N

Y

Plan 2—only males

 5q15

LNPEP

rs9918162a

96,987,845

T

YNYN

4.66E–06

+ – – –

0.966

0.958 (0.138)

8.00E–01

2.95E–08

0.921

2.27E–06

N

N

N

 8q24.22

ADCY8

rs726411a

130,734,543

G

NYNY

2.16E–06

– – + –

0.939

0.621 (0.071)

2.45E–04

5.65E–04

0.828

1.65E–05

N

Y

Y

 3p14.1

KBTBD8

rs9862849

66,855,351

C

YNNY

1.12E–03

– – – –

0.900

0.603 (0.059)

2.66E–06

7.53E–01

0

2.65E–06

N

N

Y

 23q21.31

KLHL4

rs5969117

87,181,248

C

YN?N

1.67E–05

+ + ? +

0.295

1.490 (0.114)

1.42E–06

8.61E–01

0

1.42E–06

N

N

Y

Plan 3—only females

 6p22.3

LOC101928519

rs62402815a,b

19,350,484

G

NYYN

1.20E–08

– – – –

0.941

0.610 (0.054)

4.29E–07

5.89E–04

0.827

4.31E–07

N

N

N

 2p13.3

ANTXR1

rs7561207

69,138,666

A

Y??N

7.35E–05

– ? ? –

0.055

0.470 (0.066)

4.08E–06

9.22E–01

0

4.08E–06

N

N

N

 4p16.2

STK32B

rs17675640

5,095,813

G

YYYN

7.90E–04

– – – –

0.667

0.769 (0.040)

1.89E–06

4.52E–01

0

1.89E–06

N

Y

Y

 4p16.2

STK32B

rs6838792

5,096,839

C

YYYN

7.04E–05

– – – –

0.617

0.772 (0.040)

1.61E–06

1.17E–01

0.491

1.61E–06

N

Y

Y

 4p16.2

STK32B

rs895681

5,099,404

T

YYYN

1.23E–04

– – – –

0.617

0.776 (0.040)

2.72E–06

1.41E–01

0.450

2.72E–06

N

Y

Y

 6p21.33

TNXB

rs11969759

32,053,353

C

NNYY

3.65E–04

– – – –

0.942

0.616 (0.057)

2.10E–06

3.86E–01

0.012

2.10E–06

N

N

Y

 6p21.33

TNXB

rs10947230

32,056,618

C

NNYY

3.19E–04

– – – –

0.941

0.619 (0.057)

2.33E–06

4.36E–01

0

2.34E–06

N

N

Y

 6p21.33

TNXB

rs7774197

32,078,498

A

NNYY

3.68E–04

– – – –

0.941

0.627 (0.058)

4.17E–06

3.47E–01

0.092

4.20E–06

N

N

Y

 9q22.2

SYK

rs1172922

90,726,252

A

NYNY

5.27E–04

+ + + +

0.118

1.408 (0.098)

4.56E–06

1.14E–01

0.495

4.46E–06

N

N

N

 12q24.33

SFSWAP

rs73156187

131,542,412

G

YNYN

1.35E–04

– – – –

0.894

0.695 (0.051)

4.47E–06

2.08E–01

0.341

4.45E–06

N

N

Y

 12q24.33

SFSWAP

rs7963314

131,573,284

G

YNYN

6.65E–04

– – – –

0.881

0.700 (0.049)

2.72E–06

4.06E–01

0

2.73E–06

N

N

Y

 21q21.3

MIR155HG

rs12386284b

25,517,756

T

YYN?

3.61E–03

+ + + ?

0.249

1.367 (0.087)

4.55E–06

9.24E–01

0

4.54E–06

N

N

Y

 21q21.3

MIR155HG

rs1783012

25,547,104

T

YYN?

2.11E–03

– – – ?

0.748

0.732 (0.047)

4.59E–06

9.40E–01

0

4.59E–06

N

N

Y

 21q21.3

MIR155HG

rs1783013

25,547,257

T

YYN?

2.11E–03

– – – ?

0.748

0.733 (0.047)

4.65E–06

9.49E–01

0

4.65E–06

N

N

Y

 21q21.3

MIR155HG

rs926963

25,547,744

T

YYN?

2.11E–03

– – – ?

0.748

0.732 (0.047)

4.75E–06

9.49E–01

0

4.75E–06

N

N

Y

 21q21.3

MIR155HG

rs1893650

25,568,503

T

YYNN

2.32E–03

+ + + +

0.247

1.320 (0.075)

3.94E–06

5.41E–01

0

3.99E–06

N

N

Y

 21q21.3

MIR155HG

rs2226326

25,569,648

A

YYNN

2.57E–03

+ + + +

0.245

1.319 (0.075)

4.38E–06

6.34E–01

0

4.38E–06

N

N

Y

 21q21.3

MIR155HG

rs2829803b

25,575,998

G

YYNN

2.39E–03

+ + + +

0.247

1.319 (0.075)

4.09E–06

5.40E–01

0

4.10E–06

N

N

Y

 21q21.3

LINC00515,MRPL39

rs2298369b

25,583,969

C

YNYN

6.79E–05

– – – +

0.606

0.754 (0.039)

3.11E–07

1.77E–02

0.703

2.21E–07

N

N

Y

 21q21.3

MRPL39

rs2829823

25,599,076

A

YYNN

2.37E–03

+ + + +

0.245

1.320 (0.075)

4.06E–06

5.96E–01

0

4.07E–06

N

N

Y

 21q21.3

MRPL39

rs2829832

25,601,939

T

YYNN

2.47E–03

+ + + +

0.245

1.318 (0.075)

4.68E–06

6.04E–01

0

4.65E–06

N

N

Y

  1. SNP single-nucleotide polymorphism, Chromosome chromosomal region based on cytogenetic bands, Position position of SNP based on Human Genome version 38 (hg38), A1 effect allele, Sig? if SNP had p < 0.0167 in LOADFS, FHS, CHS, and HRS datasets, respectively (Yes, No, Missing), Pmin minimum p value detected for SNP in aforementioned datasets, Effects direction of SNP’s effects in aforementioned datasets (Positive, Negative, Missing), Freq frequency of effect allele based on meta-analysis, OR (se) odds ratio and its standard error based on meta-analysis, Pmeta p value of SNP in meta-analysis, Pq p value of Q-statistics (Cochran’s heterogeneity test), i2, inconsistency metric, Pabs p value of SNP in meta-analysis on absolute values of effect sizes (i.e., β coefficients), Proxy? if SNP is in linkage disequilibrium with any previously detected AD-associated loci whose p value is less than that detected in this study (Yes, No), Gene? if previous studies have detected AD-associated SNPs with p < 5E–06 in closest gene to detected SNP (Yes, No), Region? if previous studies have detected AD-associated SNPs with p < 5E–06 in chromosomal region in which detected SNP is located (Yes, No), Y yes, N no, AD Alzheimer’s disease
  2. aReplicated SNPs
  3. bSNP did not have significant sex-specific effects. All SNPs that were significant only in males or females also had significant sex-specific effects except rs62402815, rs12386284, rs2829803, and rs2298369
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Alzheimer's Research & Therapy

ISSN: 1758-9193