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Table 4 PCA correction for ancestry using ESAIMs.

From: European Population Genetic Substructure: Further Definition of Ancestry Informative Markers for Distinguishing among Diverse European Ethnic Groups

 

SNP

Chr

Mb

P valuea

270,000b

EUROset1c

EUROset2

North

South

Ran 3,000

Ran 6,000

Ran 12,000

ASH/OSOUTHd

rs6587597

1

150

8.2E−11 e

2.5E−01

6.5E−01

2.9E−01

1.5E−02

5.8E−01

2.2E−01

3.2E−01

1.7E−01

ASH/OSOUTH

rs1400452f

2

18

3.0E−11

1.3E−03

1.8E−03

9.1E−04

2.5E−06

1.1E−04

8.6E−03

4.3E−04

2.1E−02

ASH/OSOUTH

rs4859259

3

184

2.2E−10

5.3E−01

7.5E−01

7.5E−01

4.4E−01

3.7E−01

2.8E−02

1.1E−01

5.8E−01

ASH/OSOUTH

rs7456425

7

81

4.7E−09

7.5E−01

7.5E−01

6.5E−01

6.1E−02

8.3E−02

5.1E−02

5.3E−01

6.5E−01

ASH/OSOUTH

rs7139066

12

26

1.3E−10

6.9E−02

3.4E−01

2.5E−01

1.4E−02

4.0E−02

2.5E−01

1.6E−02

2.9E−01

OSOUTH/FRENCH

rs6723108

2

135

5.2E−11

6.5E−01

2.5E−01

4.6E−02

5.1E−02

7.8E−02

4.4E−03

1.1E−01

2.4E−01

OSOUTH/FRENCH

rs1584930

3

95

1.3E−07

3.4E−01

7.7E−03

2.4E−02

6.1E−02

4.5E−04

1.6E−02

1.3E−03

4.7E−03

OSOUTH/FRENCH

rs10515893

5

165

2.9E−08

2.4E−01

5.1E−02

1.7E−01

4.8E−02

8.2E−03

3.1E−04

1.4E−02

3.6E−02

OSOUTH/FRENCH

rs2072633

6

32

2.9E−08

1.3E−01

4.2E−03

6.2E−03

1.1E−03

1.1E−02

5.6E−04

7.8E−02

8.9E−02

OSOUTH/FRENCH

rs11663558

18

19

5.9E−08

1.0E + 00

1.6E−01

1.8E−01

6.5E−02

1.6E−02

8.9E−02

8.9E−02

1.7E−01

FRENCH/SCAN

rs4954564

2

137

<E−12

3.2E−01

3.7E−04

5.8E−01

4.8E−01

4.9E−07

1.6E−04

5.0E−04

1.0E−02

FRENCH/SCAN

rs2856718

6

33

3.5E−12

3.7E−01

2.2E−03

2.3E−02

1.4E−02

4.6E−06

1.5E−05

7.7E−03

1.5E−02

FRENCH/SCAN

rs11038910

11

47

4.7E−09

1.1E−01

4.1E−04

5.2E−03

6.2E−03

2.3E−04

9.7E−05

1.9E−02

1.0E + 00

FRENCH/SCAN

rs1146904

13

76

2.2E−08

6.5E−02

1.7E−02

4.9E−03

2.2E−03

4.1E−04

7.4E−07

2.3E−02

2.1E−02

FRENCH/SCAN

rs11631323f

15

96

1.7E−09

1.0E + 00

3.8E−03

2.1E−02

9.6E−03

8.7E−05

2.2E−03

1.1E−01

1.8E−01

SCAN/IRISHUK

rs10517522

4

39

3.9E−08

1.3E−02

3.0E−02

3.2E−02

9.1E−03

5.7E−07

1.3E−05

4.8E−04

6.5E−02

SCAN/IRISHUK

rs1265048

6

31

6.9E−08

1.8E−02

3.0E−03

2.5E−02

5.8E−03

1.8E−06

8.3E−05

1.8E−02

6.9E−03

SCAN/IRISHUK

rs511512

13

76

8.3E−10

2.7E−02

4.7E−03

6.5E−03

8.2E−03

3.3E−08

2.7E−08

1.9E−08

3.3E−04

SCAN/IRISHUK

rs255052

16

67

1.5E−08

1.7E−01

1.1E−01

4.4E−01

9.4E−02

1.3E−07

5.0E−04

1.8E−01

5.4E−02

SCAN/IRISHUK

rs9303363

17

50

1.0E−08

1.8E−01

3.4E−02

6.9E−03

3.4E−03

1.5E−07

6.9E−03

6.5E−03

4.8E−02

FRENCH/IRISHUK

rs6723108

2

135

2.2E−10

5.6E−04

8.9E−08

4.8E−01

6.5E−01

4.2E−10

4.0E−10

5.1E−06

8.2E−04

FRENCH/IRISHUK

rs1965299f

4

117

1.2E−07

2.8E−04

9.2E−05

1.1E−04

1.8E−05

5.4E−07

3.4E−07

6.3E−05

1.7E−03

FRENCH/IRISHUK

rs12498670

4

178

4.9E−07

1.5E−03

2.9E−05

3.9E−05

3.7E−05

3.2E−07

8.7E−07

7.4E−05

5.6E−04

FRENCH/IRISHUK

rs3135029

6

33

7.4E−07

7.4E−02

1.5E−03

1.4E−02

2.6E−03

1.6E−04

4.1E−06

9.2E−05

1.9E−03

FRENCH/IRISHUK

rs11645416

16

50

6.5E−08

3.5E−04

2.9E−05

1.5E−03

2.0E−04

1.9E−07

8.9E−08

1.5E−05

9.1E−04

  1. aThe P value was determined by the Armitage χ2 test using the first population group as “case” and the second group as “control.”
  2. bThe adjusted P value based on correction for PCA using EIGENSTRAT software is shown for 270,000 SNPs and each of the AIMs and random marker sets. The EUROset1 and EUROset2 are as defined in Table 2 and Supplemental Table 3.
  3. cThe EUROset1 contains 1,037 of 1,212 ESAIMs previously reported (12) and an additional 1,757 SNPs (see Materials and Methods).
  4. dThe five different population groups were defined by PCA (see Materials and Methods): Ashkenazi (ASH), 88 individuals; Other South (OSOUTH), 210 individuals; French, 444 individuals; and Irish United Kingdom (IRISHUK), 328 individuals.
  5. eBold P values highlight P values <10−4.
  6. fThese SNPs were isolated significant values. For each of the other SNPs chosen, multiple closely linked SNPs (within 50 Kb) showed similar P values.
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Molecular Medicine

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