TABLE 2

SNPs marginally (independently) associated with iris pigmentation and SNPs associated only within the context of haplotypes and/or diplotypes

GeneHaplotype orderaSequenceFCA (minor)bHWE-PcColors PShade PBrown/blue PBrown/other PPigment history
AIM (MATP) 5p13.31rs353910.03-T,C 0.04 0.01* 0.02 <0.01* 0.02 None
2rs401320.02-GA0.32 0.02 0.01 <0.01 0.02 None
3rs267220.02-T,C0.290.08 0.04 0.01 0.08None
ASIP 20q11.2–q121rs24249870.12-GA0.130.360.510.840.50Brown irises, Kanetsky et al. (2002)
2rs24249840.13-C,T0.140.810.730.860.75None
3rs8191350.42-GA0.500.920.510.680.82None
CYP1A2 15q22–ter1AY3921360.45-G,C0.980.090.710.110.03*None
CYP1B1 2p211rs1625600.24-T,C 0.01 0.11*0.02*0.110.46None
2rs10568370.44-T,C0.130.840.500.460.71None
CYP2C8 10q231rs19267050.32-C,T 0.01 0.100.30 0.04 0.03*None
2rs13411640.30-GA0.700.450.210.140.11None
3AY3921320.12-GA0.800.150.910.950.84None
CYP2C9 10q241AY3921310.22-C,T0.700.130.07*0.110.05*None
DCT 13q321rs14079950.18-T,C0.17<0.01*0.350.640.14None
2rs13256110.18-C,T 0.05 <0.01*0.500.910.08None
3rs28926810.34-C,G0.420.370.440.560.75None
4rs10288060.20-GA0.940.450.370.660.40None
5rs20315270.21-T,C0.810.670.990.850.71None
6rs22964980.11-GA0.370.880.510.660.91None
GSTT2 22q11.231rs21401860.46-GA0.180.400.370.920.85None
2rs21401960.49-GA0.060.550.330.740.63None
MAOAXp11.4–11.31rs9796050.28-T,C<0.010.05*0.01* 0.04 0.27None
2rs20727430.33-A,G<0.010.24*0.05*0.090.28None
MC1R 16q24.31rs18050070.09-T,C0.140.180.310.670.29Red hair/blue irises, multiple authors
2rs18050080.07-T,C0.370.690.250.450.64Red hair/blue irises, multiple authors
3rs22284790.08-T,C<0.010.840.580.940.83Red hair/blue irises, multiple authors
MYO5A 15q211rs17246300.20-G,C0.760.02*0.05*0.220.74None
2rs17246310.24-T,G<0.010.05*0.320.550.41None
3rs22903320.13-G,A0.660.08*0.240.380.64None
4rs7528640.38-C,T0.800.22*0.080.110.45None
5rs17246390.38-T,C0.510.17*0.140.200.82None
6rs9358920.40-G,A0.540.250.490.400.87None
7rs16152350.22-A,G0.380.190.090.310.92None
8rs22420570.35-T,C0.780.280.130.290.85None
9rs28994880.16-T,C0.710.890.690.990.78None
10rs18691260.16-T,C0.650.930.530.700.79None
OCA2 15q11.2–q121rs7498460.15-T,G0.34<0.01*<0.01*<0.01*<0.01*None
2AY3921350.18-A,G0.08<0.01*<0.01*<0.01*<0.01*None
3AY3921340.28-G,A0.90<0.01*<0.01*<0.01*<0.01*None
4rs19007580.30-G,A0.81<0.01*<0.01*<0.01*<0.01*None
5rs10372080.18-CA0.13<0.01*<0.01*<0.01*<0.01*None
6rs18004110.27-C,T0.78<0.01*<0.01*<0.01*0.02*None
7rs18004040.21-G,A0.95<0.01*<0.01*<0.01*0.02*None
8AY3921330.04-C,G0.65 0.02 0.07 0.01*<0.01*None
9rs18004010.04-T,C0.63 0.03 0.02*<0.01*<0.01*Brown irises, Rebbeck et al. (2003)
10rs20446270.38-GA0.190.05*0.290.02*0.03*None
11rs14484830.04-GA<0.010.130.060.310.25None
12rs7370510.29-GA0.160.370.390.160.08None
13rs18004100.11-GA0.960.460.50.250.12None
POMC 2p231rs9347780.30-C,T0.110.870.770.910.67None
SILV 12q13–q141rs10522060.18-C,T0.080.430.680.220.18None
2rs10521650.29-T,C0.530.420.760.920.37None
TYR 11q14–q211rs18274300.45-G,A0.410.060.370.520.65None
2rs10426020.36-A,C0.060.640.550.720.45None
3rs18519920.42-G,A0.190.920.970.760.58None
TYRP1 9p231rs27338320.41-C,T0.450.02*<0.01*<0.01*<0.01*None
2rs20755080.06-C,T0.540.06<0.01* 0.04 0.08None
3rs6830.35-G,T0.19 0.01 <0.01*<0.01*<0.01*None
4rs27624640.35-A,T0.85 0.03 0.04*0.01*<0.01*None
5AY3957370.06-T,C0.890.390.090.130.17None
6AY3957360.06-T,G0.920.620.200.240.43None

Asterisks represent P values that remained significant after the correction for multiple tests and P values in italic are those that were statistically significant (P ≤ 0.05).

  • a Haplotype order refers to the order of the SNPs in the haplotypes shown in Table 4 and described in the text.

  • b Frequency of the minor allele and the major and minor allele nucleotide.

  • c Hardy-Weinberg equilibrium P value, where a value <0.05 indicates that the alleles are not in equilibrium.