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Table 4 Coding non-synonymous common population-specific SNPs and potential functional impact

From: Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance

Pop

SNP

Gene

SIFT

PolyPhen-2

LRT

Mutation Taster

IBS

rs34804805

MRPL35

T

B

N

N

JPT

rs3749130

ARHGAP25

D

P

N

N

 

rs2296151

ASIP

T

P

N

N

 

rs17846992

CCKAR

D

D

N

D

 

rs77945315

CSNK1E

D

B

D

D

 

rs76875855

KRT73

D

D

D

N

 

rs1800885

MTNR1A

T

P

U

D

 

rs41428447

NDUFS2

D

B

D

D

 

rs74548274

OR5D13

T

P

U

N

LWK

rs61749435

ABCA4

D

B

D

N

 

rs34018205

ATP8B1

T

B

D

D

 

rs34744783

C20orf26

D

B

N

N

 

rs34347250

EGLN3

T

B

D

D

 

rs6413484

GHR

D

B

N

N

 

rs34752664

KCNF1

T

B

D

N

 

rs35706839

MCCC1

T

NA

D

D

 

rs76085152

NLRP12

D

NA

N

N

 

rs104895564

NLRP12

T

D

N

N

 

rs35651739

NOXO1

D

D

N

N

 

rs3087400

REV1

T

B

N

N

 

rs34994431

SLC16A11

T

D

N

D

YRI

rs35755269

DIAPH1

NA

NA

N

P

 

rs34901743

HDAC3

T

D

D

P

 

rs1065759

HLCS

T

P

N

D

 

rs6299

HTR1D

D

P

N

P

 

rs8176804

PAWR

T

B

N

N

 

rs34781001

RPN1

T

P

D

D

 

rs2229464

TGM1

T

B

N

D

 

rs59896509

TRIM5

D

D

D

D

 

rs1799126

UPK3B

D

NA

NA

N

 

rs1799125

UPK3B

T

NA

U

N

 

rs34995077

ZNF565

T

P

N

N

  1. Functions were assessed using a set of four different tools [79–82]. The predictions D and T for SIFT mean Deleterious and Tolerable respectively. For Polyphen2, B = Benign; P = Possibly Damaging; D = Probably Damaging and NA refers to SNPs for which no information was found. Similarly for LRT; D = Deleterious Non-synonymous SNP; N = Neutral; U = Unknown and for MutationTaster; N = Polymorphism; D = Disease Causing; P = Polymorphism automatic.