Table 3

List of SNPs that are known to be associated with different levels of HbF and results of the analysis based on pooled DNA samples.
Number
 SNP
 Band
 Gene
 Validated
 Distance
 D'
 BF
 P_H
 P_L
 OR
1
 rs1143637
 2q13
 IL1B
 rs12469600
 16976
 NA
 1.39
 0.13
 0.04
 3.08
2
 rs31481
 5q23.3
 IL3
 rs40401
 724
 1.00
 2.32
 0.48
 0.65
 0.48
3
 rs271158
 6q23.2
rs271156
 641
 1.00
 22.86
 0.53
 0.77
 0.35
4
 rs454877
 6q23.2
 EYA4
 rs211433
 475
 NA
 2.43
 0.49
 0.32
 2.09
5
 rs212770
 6q23.2
 EYA4
 rs11154727
 4274
 NA
 1.25
 0.12
 0.04
 3.03
6
 rs2295199
 6q23.2
rs2295199
 0
0.51
 0.83
 0.89
 0.58
7
 rs210948
 6q23.2
 MYB
 rs210798
 17242
 NA
 2.17
 0.78
 0.90
 0.38
8
 rs509342
 6q23.2
 PDE7B
 rs560713
 23645
 0.95
 1.47
 1.00
 0.95
 17.80
9
 rs2076192
 6q23.3
 MAP7
 rs2076193
 44438
 0.97
 1.30
 0.52
 0.37
 1.88
10
 rs997139
 6q23.3
 MAP7
 rs3799419
 2100
 1.00
 1.35
 0.06
 0.14
 0.36
11
 rs3778314
 6q23.3
 MAP7
 rs2181096
 25746
 0.89
 57.04
 0.61
 0.85
 0.28
12
 rs2237262
 6q23.3
 MAP3K5
 rs3799472
 18405
 0.98
 1.03
 0.62
 0.76
 0.53
13
 rs2012700
 6q23.3
 PEX7
 rs2012700
 0
 0
 1.50
 0.34
 0.50
 0.52
14
 rs717088
 6q23.3
 PEX7
 rs717088
 0
0.47
 0.37
 0.47
 0.65
15
 rs3799476
 6q23.3
 PEX7
 rs3799479
 44021
 NA
 1.98
 0.12
 0.25
 0.42
16
 rs1342645
 6q23.3
 PEX7
 rs1342645
 0
0.67
 0.77
 0.86
 0.55
17
 rs1342641
 6q23.3
rs1342642
 22583
 0.06
 6.12
 0.96
 0.84
 4.98
18
 rs1322393
 6q23.3
 IL20RA
 rs1322394
 661
 1.00
 3.00
 0.23
 0.40
 0.44
19
 rs44450
 6q23.3
rs276568
 3229
 1.00
 47.32
 0.37
 0.64
 0.34
20
 rs1349115
 8q12.1
 TOX
 rs1349115
 0
0.69
 0.29
 0.41
 0.59
21
 rs10504269
 8q12.1
 TOX
 rs10504269
 0
0.61
 0.72
 0.82
 0.58
22
 rs6997859
 8q12.1
 TOX
 rs6997859
 0
0.37
 0.23
 0.17
 1.45
23
 rs12155519
 8q12.1
 TOX
 rs12155519
 0
0.94
 0.58
 0.44
 1.77
24
 rs1947178
 8q12.1
 TOX
 rs1947178
 0
21.86
 0.10
 0.29
 0.28
25
 rs746867
 8q12.1
 TOX
 rs746867
 0
0.29
 0.29
 0.35
 0.76
26
 rs389349
 8q12.1
 TOX
 rs389349
 0
0.42
 0.95
 0.93
 1.43
27
 rs851800
 8q12.1
 TOX
 rs396720
 23622
 0.15
 9.20
 0.28
 0.11
 3.24
28
 rs380620
 8q12.1
 TOX
 rs2561145
 300069
 0.58
 10.67
 0.08
 0.24
 0.26
29
 rs2043190
 9q34.11
 ASS
 rs540140
 609
 NA
 19.56
 0.99
 0.88
 24.90
30
 rs7482144
 11p15.4
 HBG2
 rs3813727
 20257
 NA
 2.52
 0.17
 0.32
 0.43
31
 rs723623
 15q13.3
 C15orf16
 rs6493688
 8825
 0.51
 1.31
 0.93
 0.84
 2.66
32
 rs1867380
 15q22.31
 AQP9
 rs1867380
 0
0.28
 0.82
 0.84
 0.85
33
 rs4489951
 15q22.31
 MAP2K1
 rs4489951
 0
17.66
 0.36
 0.60
 0.38
34
 rs1440372
 15q22.31
 SMAD6
 rs2469141
 65753
 0.03
 2181.00
 0.68
 0.33
 4.24
35
 rs8038623
 15q22.31
 SMAD3
 rs6494633
 16831
 NA
 87.23
 0.88
 0.65
 4.09
36
 rs2227319
 17q21.1
 CSF3
 rs2071369
 1460
 1.00
 3.42
 0.90
 0.77
 2.88

Column 1: row number; Column 2: SNP ID; Column 3: Cytogenic band; Column 4: Genes tagged by the SNP; Column 5: SNP in the Illumina array that was used to compare the association. If the SNP to be validated was not in the array, we searched for the closest SNP within 100 kb from that to be validated with a positive Bayes Factor; Column 6: distance between the two SNPs; Column 7: Bayes D' between the two SNPs, an NA means that the SNPs originally reported as associated with HbF is not in the HapMap data. Column 8: Bayes Factor; Column 9–10: estimates of allele frequencies in the pools of DNA from patients with high HbF and low HbF; Column 11: Odds ratio. The SNPs 6, 13, 14, 16, 20–26, 32 and 33 are in the array and SNPs 13, 24 and 33 were found associated with different levels of HbF. Highlighted in bold are the associations confirmed by our analysis.

Sebastiani et al. BMC Genetics 2008 9:6   doi:10.1186/1471-2156-9-6