Markers typed in genome-wide analysis identify regions showing deviation from Hardy-Weinberg equilibrium

BMC Research Notes

Table 1 Region of 1q31-41 with summed heterozygosity score exceeding 50.

Marker or gene	Position		Marker genotype counts Observed Expected			Heterozygosity scores for single, two and three marker analysis			Gene description
			AA	AB	BB	1	2	3
CAMSAP1L1	198975309	Start							calmodulin regulated spectrin-associated protein 1-like 1
CAMSAP1L1	199096455	End
GPR25	199108789	Start							G protein-coupled receptor 25
GPR25	199109874	End
C1orf106	199127292	Start							chromosome 1 open reading frame 106
rs2792810	199146603		1468	0	12	-6.1	-6.1	-0.9
			1456.1	23.8	0.1
rs3767424	199148779		1480	0	0	0	-0.1	13.4
			1480	0	0
C1orf106	199151486	End
C1orf81	199151855	Start							chromosome 1 open reading frame 81
rs805909	199160517		1143	312	25	-0.1	13.4	3.9
			1140.1	317.7	22.1
rs1819043	199163659		345	940	195	26.4	9	8.8
			448.8	732.4	298.8
rs3767421	199163817		382	753	345	0.3	0.3	8.7
			388.7	739.5	351.7
rs805911	199172076		1463	17	0	0	24.7	8.8
			1463	16.9	0
rs705736	199173739		361	933	186	25.4	9	8.2
			462.7	729.7	287.7
C1orf81	199202415	End
KIF21B	199205143	Start							kinesin family member 21B
rs7522991	199223808		383	754	343	0.3	0.2	8.3
			390.3	739.5	350.3
rs6696611	199225346		395	742	343	0.1	8	7.9
			396.5	739.1	344.5
rs705747	199236940		366	936	178	26.5	26	8.7
			470	728.1	282
rs697455	199243733		1468	12	0	0	0.3	0.3
			1468	12	0
rs3767406	199243903		383	754	343	0.3	0.3	0
			390.3	739.5	350.3
rs497824	199256967		1468	12	0	0	0	0
			1468	12	0
KIF21B	199259451	End

The table shows markers and genes in a region of 1q31-41 showing increased heterozygosity using a threshold for the summed heterozygosity scores (ignoring the highest-scoring marker) exceeeding 50. Observed counts are shown for each marker genotype with the expected counts in the row below. Heterozygosity scores, defined as -log(p) for increased heterozygosity and log(p) for increased homozygosity, are shown for individual markers and for two and three marker haplotypes.

ISSN: 1756-0500