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Table 2 Selected putatively adaptive genetic variants in SHP

From: Differentiated demographic histories and local adaptations between Sherpas and Tibetans

Chrom

Position

rsID

Ref

Alt

Ances

DAFSHPseq

DAFTBNseq

DAFHANseq

DAFTBN*

DAFSHP*

DAFSHPseq2

DAFESA

DAFSAS

DAFAFR

DAFEUR

DAFAMR

CADD

GERP

Gene

P value

8

107691513

rs28921397

A

G

A

0.5

0.0000

0.0000

0.0172

0.0789

0.0000

0.0029

0.0000

0.0000

0.0000

0.0000

31

5.96

OXR1

0.003

8

108264111

NeA

G

A

G

0.5

0.0152

0.0000

0.0086

0.0724

0.0000

-

-

-

-

-

31

5.9

ANGPT1

0.0

17

19645417

NA

T

A

T

0.4

0.0000

0.0000

0.0000

0.0987

0.0000

-

-

-

-

-

31

4.49

ALDH3A1

0.0

3

196921405

rs527829647

A

G

A

0.3

0.0000

0.0000

0.0129

0.0789

0.0000

0.0011

0.0000

0.0000

0.0000

0.0000

22.3

5.17

DLG1

0.0

12

117768315

rs549340789

G

A

G

0.3

0.0000

0.0000

0.0086

0.0855

0.0000

0.0022

0.0000

0.0000

0.0000

0.0000

17.79

4.74

NOS1

0.0

10

45956828

rs3764990

G

A

G

0.4

0.0303

0.0256

0.0905

0.1974

0.2500

0.0528

0.0226

0.0143

0.0787

0.0293

18.84

5.65

MARCH8

0.001

7

21948010

rs200891942

A

G

A

0.3

0.0152

0.0000

0.0129

0.1053

0.0000

0.0010

0.0000

0.0000

0.0000

0.0000

21.1

5.95

CDCA7L

0.0

2

37232879

rs2302657

A

C

A

0.3

0.0152

0.0128

0.0086

0.1067

0.2500

0.0325

0.0023

0.0000

0.0000

0.0000

16.87

5.63

HEATR5B

0.0

2

109545691

rs61761321

T

C

T

0.3

0.0152

0.1795

0.0345

0.1447

0.0000

0.0910

0.0023

0.0012

0.0000

0.0000

10.27

4.09

EDAR

0.0

1

91405998

rs149597385

C

T

C

0.3

0.0152

0.0000

0.0259

0.1184

0.0000

0.0100

0.0012

0.0000

0.0000

0.0000

32

4.63

ZNF644

0.001

1

156551628

rs116035113

G

T

G

0.3

0.0152

0.0000

0.0474

0.1250

0.0000

0.0030

0.0010

0.0475

0.0125

0.0124

23.9

4.83

TTC24

0.002

2

46707674

rs116983452

C

T

C

0.4

0.2121

0.0256

0.7241

0.6389

1.0000

0.0207

0.0035

0.0000

0.0000

0.0000

11.18

2.97

TMEM247

-

1

231557623

rs186996510

G

C

G

0.1

0.5910

0.0385

0.5500

0.4800

0.25

0.0100

0.0020

0.0000

0.0000

0.0020

14.73

3.51

EGLN1

-

  1. Among these adaptive genetic variants (AGVs), ten (top 10) showed differences between SHP and TBN, and two (rs116983452 in TMEM247 near the EPAS1 region and rs186996510 in EGLN1) had similar derived allele frequencies (DAFs), suggesting that both distinct and shared genetic adaptations occurred between TBN and SHP. Conservation scores with CADD >15 and GERP >2 are highlighted in bold. NA denotes that the variant is novel and has no current rsID. The physical position of each site follows GRCh37. The p value for each candidate was estimated by simulation based on the demographic history of SHP.Zhangmu estimated by MSMC. Chrom chromosome, Ref reference, Alt alteration, Ances ancestral, ESA East Asians, SAS South Asians, AFR Africans, EUR Europeans, and AMR Americans