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Table 1 Details on SIM2 and ETS2 functional SNPs explored in this study

From: Potential contribution of SIM2 and ETS2 functional polymorphisms in Down syndrome associated malignancies

Gene

SNP ID

Position and typea

Alleles (A1/A2)b

Probable functionc

MAF (A2) in other populations (CEU, HCB, JPT and YRI)d

SIM2

rs2269188

Intronic, regulatory

G/C

AhR binding site

0.305, 0.567, 0.534, 0.092

 

rs2070650

Intronic

C/A

C-Myc binding site

0.358,0.578, 0.456, 0.500

 

rs79727992

Intronic

G/A

NK

0.014 (CEU)

 

rs16994404

Syn, Cod

C/T

SR protein mediated splicing regulation

100% C (all populations)

 

rs77335240

Intronic

A/C

NK

No population data

 

rs78455239

Intronic

C/A

NK

No population data

 

rs79022672

Intronic

G/A

NK

0.020 (YRI)

ETS2

rs34373350

NS, cod

C/T

Damaging

0.006 (CEU), 0.025 (YRI)

 

rs11700777

Syn, Cod

A/G

SR protein mediated splicing regulation

No population data

 

rs114481523

NS, cod

A/G

NK

0.005 (YRI)

 

rs73450556

Intronic

G/T

AML-1a banding site

0.500 (YRI)

 

rs77688599

Intronic

G/A

NK

0.056 (CEU)

 

rs60277131

Intronic

A/G

NK

0.180 (YRI)

 

rs78391361

NS, cod

C/T

NK

0.042 (CEU)

 

rs1803557

NS, cod

A/T

Damaging

No population data

 

rs34472454

FS, Cod

-/C

NK

No population data

 

rs113798497

Syn, Cod

A/G

NK

No population data

 

rs374575

Intronic

C/T

Transcriptional regulation

0.290, 0.140, 0.041, 0.005

 

rs2070529

 

C/T

Cf1, AML-1a binding site

0.168, 0.523, 0.610, 0.270

 

rs2070530

 

G/C

V-Myb binding site

0.168, 0.523, 0.610, 0.290

 

rs2070531

 

C/T

NIT2 binding site change

0.398, 0.221, 0.227, 0.288

 

rs434421

 

C/T

Nkx-2, USF binding

No population data

 

rs8128227

 

C/A

NK

0.014 (CEU)

 

rs6517481

 

A/G

Ttk 69 binding site

0.361, 0.318 (HCB + JPT), 0.300

 

rs79863249

 

C/G

NK

0.011 (HCB + JPT)

 

rs60538921

 

A/G

Lyf-1 banding site

No population data

 

rs7276961

 

A/G

HSF binding site change

0.347, 0.466 (HCB + JPT), 0.300

 

rs1051475

3′UTR

T/C

Transcriptional regulation

0.347, 0.227 (HCB + JPT), 0.200

 

rs1051476

 

C/G

SR protein mediated Splicing regulation

0.420, 0.239, 0.209, 0.246

 

rs72094783

 

-/GA

NK

No population data

 

rs116542090

 

G/A

NK

0.008 (YRI)

 

rs74551083

 

A/G

NK

No population data

 

rs11540409

 

A/G

NK

No population data

 

rs11254

 

C/T

Alteration of miRNA target site

0.432, 0.233, 0.200, 0.250

 

rs711

 

G/A

Affects SR protein mediated ESE activity

0.425, 0.200 (HCB + JPT), 0.441

  1. a NS = Nonsynonymous, Syn = Synonymous, Cod = Coding, FS = Frame shift.
  2. b A1 = Major allele, A2 = Minor allele, allele mentioned in bold letter is the ancestral allele.
  3. c NK = Not known.
  4. d CEU: Caucasians from Utah with ancestry from western and northern Europe; YRI: Yoruba from Ibadan, Nigeria; HCB: Han Chinese from Beijing, China and JPT: Japanese from Tokyo, Japan.
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BMC Medical Genetics

ISSN: 1471-2350

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