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Table 1 HIV MTCT association results for SNPs, selected by P-value

From: A whole genome association study of mother-to-child transmission of HIV in Malawi

CHR

SNPtype

A1

A2

MAF

Unadjusted OR (95% CI)

P

Adjusted OR (95% CI)

P

Nearest gene

17

rs12306a

A

G

0.23

0.33 (0.20, 0.55)

2.02E-05

0.34 (0.20, 0.57)

3.92E-05

WD repeat and SOCS box-containing 1 (WSB1)

8

rs476321a

T

C

0.27

2.55 (1.65, 3.92)

2.15E-05

2.50 (1.62, 3.87)

3.42E-05

Protein coding, protein info: transcription factor CP2-like 3, deafness, autosomal dominant 28, grainyhead-like 2 (Drosophila) (GRHL2)

6

rs2268993a

C

G

0.27

2.71 (1.71, 4.28)

2.20E-05

2.70 (1.70, 4.28)

2.65E-05

Solute carrier family 35 (CMP-sialic acid transporter), member A1 (SLC35A1)

18

rs8084223b

T

C

0.15

0.26 (0.14, 0.49)

3.41E-05

0.26 (0.14, 0.50)

4.21E-05

AC104961.7

23

rs5934013a

G

A

0.15

4.18 (2.12, 8.24)

3.61E-05

4.09 (2.08, 8.06)

4.68E-05

FERM and PDZ domain containing 4 (FRMPD4)

8

rs9314565b

G

C

0.47

0.42 (0.27, 0.63)

4.13E-05

0.41 (0.27, 0.63)

3.64E-05

AC019176.4

3

rs4234621b

C

T

0.28

0.39 (0.25, 0.61)

5.03E-05

0.38 (0.24, 0.60)

4.58E-05

Pyrin domain containing 2 (PYDC2)

14

rs2287652a

C

A

0.2

0.32 (0.19, 0.56)

5.15E-05

0.33 (0.19, 0.57)

7.12E-05

aarF domain containing kinase 1 (ADCK1)

9

rs1889055b

C

N/A

0.24

2.52 (1.61, 3.93)

5.21E-05

2.48 (1.59, 3.87)

6.32E-05

RP11-48L13.1

7

rs216743a

A

G

0.1

4.22 (2.09, 8.53)

6.16E-05

4.23 (2.08, 8.61)

6.89E-05

cAMP responsive element binding protein 5 (CREB5)

7

rs216744a

G

G

0.1

4.22 (2.09, 8.53)

6.16E-05

4.23 (2.08, 8.61)

6.89E-05

cAMP responsive element binding protein 5 (CREB5)

22

rs131817a

T

G

0.23

0.37 (0.22, 0.60)

6.68E-05

0.36 (0.22, 0.59)

6.62E-05

Non-SMC condensin II complex, subunit H2 (NCAPH2)

7

rs4722999a

C

C

0.32

2.46 (1.58, 3.84)

7.07E-05

2.38 (1.52, 3.72)

1.49E-04

Corticotropin releasing hormone receptor 2 (CRHR2)

17

rs8069770a

T

G

0.14

0.27 (0.14, 0.51)

7.17E-05

0.25 (0.13, 0.49)

3.79E-05

Heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1 (HS3ST3A1)

5

rs6884962c

G

A

0.49

2.18 (1.48, 3.21)

7.31E-05

2.15 (1.46, 3.17)

1.07E-04

AC008412.8

12

rs12579934a

T

A

0.46

2.24 (1.49, 3.36)

9.59E-05

2.48 (1.63, 3.78)

2.45E-05

Branched chain aminotransferase 1, cytosolic (BCAT1)

9

rs12376718b

T

A

0.15

3.07 (1.75, 5.39)

9.79E-05

2.97 (1.69, 5.20)

1.47E-04

RP11-48L13.1

16

rs6540013b

G

C

0.39

0.45 (0.30, 0.68)

1.16E-04

0.44 (0.29, 0.66)

8.99E-05

AC010531.8

16

rs12598821a

T

T

0.48

0.45 (0.30, 0.68)

1.20E-04

0.43 (0.28, 0.65)

6.65E-05

AC010333.7

1

rs3861824b

A

G

0.11

0.23 (0.11, 0.50)

1.98E-04

0.20 (0.09, 0.44)

6.29E-05

Disabled homolog 1 (Drosophila) (DAB1)

  1. Top 20 most significant SNPs based on P-values from crude and/or adjusted by maternal HIV viral load analyses, sorted by unadjusted P-value. CHR, chromosome; SNPtype, SNP and type, where type refers to the position of the SNP relative to the closest gene (aintronic, bintergenic, cupstream); A1, risk allele designated by PLINK; A2, major allele; MAF, minor allele frequency; OR, odds ratio; 95% CI, 95% confidence interval of the OR; Adjusted OR, OR from analyses adjusted by maternal HIV viral load.
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Genome Medicine

ISSN: 1756-994X

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