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Table 1 SNPs found within validated MRESSs.

From: A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS

Rs#

Coordinates

Maj

Min

MAF

Site type

Pos in MRE

miR

Gene

pubmed id

rs3783620

1: 101204463

G

A

.005 (YRI.P1)

8-mer

7th

hsa-miR-126

VCAM1

18227515

rs1059479

1: 113243892

T

G

.01 (CEPH)

8-mer

1st

hsa-miR-138

RHOC

20232393

rs12392

2: 198351529

G

A

NA

7-8mer

2nd

hsa-miR-1

HSPD1

17715156

rs5186*

3: 148459988

A

C

.306 (CEU.P1)

7-8mer

4th

hsa-miR-155

AGTR1

16675453

rs56109847*

3: 183824557

G

A

.992 (CEU.P1-LC)

8-mer

4th

hsa-miR-510

HTR3E

18614545

rs3731563

3: 48199695

T

C

.017 (GIH)

8-mer

8th

hsa-miR-21

CDC25A

19826040

rs1434536*

4: 96075965

C

T

.545 (TSC-CSHL)

7-8mer

1st

hsa-miR-125b

BMPR1B

19738052

rs6875894

5: 112179965

C

T

.027 (YRI)

7-8mer

4th

hsa-miR-135b

APC

18632633

rs6875894

5: 112179965

C

T

.027 (YRI)

7-8mer

5th

hsa-miR-135a

APC

18632633

rs79468771

6: 135539805

T

A

NA

8-mer

7th

hsa-miR-15a

MYB

18818396

rs33986155

6: 152420685

C

G

.083 (CEU.P1)

7-8mer

8th

hsa-miR-206

ESR1

17312270

rs11551509

6: 34505633

C

A

NA

8-mer

8th

hsa-miR-510

SPDEF

18922924

rs8829

7: 148504618

A

C

1 (CEPH)

8-mer

2nd

hsa-miR-101

EZH2

20478051

rs78899540

7: 27181092

A

C

.04 (YRI.P1)

7-mer-A1

2nd

hsa-miR-130a

HOXA5

17957028

rs117556949

7: 27194074

T

C

.992 (CEU.P1-LC)

8-mer

8th

hsa-miR-196a

HOXA7

15105502

rs12720208*

8: 16850399

G

A

.125 (CEU.P1)

8-mer

6th

hsa-miR-433

FGF20

18252210

rs78202059

8: 26228382

G

T

.144 (YRI.P1-LC)

7-mer-A1

8th

hsa-miR-222

PPP2R2A

20103675

rs1058153

2: 46987391

C

T

NA

8-mer

2nd

hsa-miR-21

SOCS5

17991735

rs72808106

10: 74035161

A

G

NA

7-mer-A1

4th

hsa-miR-221

DDIT4

20018759

rs16917496*

12: 123893830

C

T

.22 (CEPH)

7-mer-A1

2nd

hsa-miR-502-5p

SET8

19789321

rs111842797*

12: 123893831

A

G

NA

7-mer-A1

8th

hsa-miR-502-5p

SET8

19789321

rs76290581

12: 6760093

T

C

.051 (YRI.P1-LC)

8-mer

1st

hsa-miR-650

ING4

20381459

rs77080081

15: 40382144

A

G

.014 (CEU.P1)

7-8mer

1st

hsa-miR-125b

BMF

19471102

rs28521337*

15: 88521280

C

G

.467 (CEU.P1)

8-mer

8th

hsa-miR-485-3p

NTRK3

19370765

rs72481816

15: 88521572

G

C

NA

8-mer

8th

hsa-miR-765

NTRK3

19370765

rs72481814

15: 88522372

T

C

NA

7-8mer

4th

hsa-miR-509-3p

NTRK3

19370765

rs28574753

16: 28109760

G

A

.076 (YRI-P1)

7-8mer

2nd

hsa-miR-122

XPO6

19296470

rs75817141

17: 12044581

C

T

.02 (YRI.P1)

7-8mer

1st

hsa-miR-15b

MKK4

19861690

rs62062994

17: 48261978

G

T

NA

8-mer

3rd

hsa-miR-29c

COL1A1

18390668

rs3218074

19: 30315176

A

G

.01 (PDR90)

8-mer

8th

hsa-miR-15b

CCNE1

18701644

rs3218074

19: 30315176

A

G

.01 (PDR90)

8-mer

8th

hsa-miR-16

CCNE1

18701644

rs6094029

20: 43356176

C

T

0

7-8mer

7th

hsa-miR-449a

WISP2

19351815

rs78301106

20: 62522710

C

G

.045 (CHB+JPT.P1)

8-mer

7th

hsa-miR-122

TPD52L2

19296470

  1. A list comprising 31 validated MREs (with perfect complimentarity in the MRE seed site -positions 2-7) in which a SNP has been identified. The Coordinates column provides the chromosomal number and position coordinates for each SNPs - all genomic coordinates correspond to Hg19. The MAF column reports the allele frequency of the minor allele from the population where it was highest, where NA indicates a SNP with unknown allele frequency. The Pos in MRE column refers to the position within the MRE to which the SNP maps. * SNPs reported to have shown association with disease phenotypes.
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BMC Genomics

ISSN: 1471-2164

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