Table 1.

Average percent methylation as determined by pyrosequencing at promoter, intragenic and intergenic regions across the X chromosome in blood and placenta for high (HC), intermediate (IC) and low (LC) CpG density

Location and CpG density	Number of assaysa	Male blood (Xa)b, %	Female blood (XaXi), %	BloodXic, %	BloodXa:Xi ratiod	Male placenta (Xa)b, %	Female placenta (XaXi)	PlacentaXic, %	PlacentaXa:Xi ratiod	Blood–Placenta
										ΔXae, %	ΔXie, %
Promoter	9	23	44	64	0.35*	20	24	29	0.68	−3	−35**
HC	5	8	38	68	0.12	12	24	35	0.35	4	−33
ICf	1	12	37	62	0.20	3	8	13	0.19	−10	−49
LC	3	50	55	59	0.85	38	31	25	1.52	−13	−34
Intragenic	8	89	86	83	1.08*	82	73	63	1.30**	−7	−19**
HCg	1	91	90	90	1.01	65	62	60	1.09	−26	−30
ICg	2	92	91	90	1.03	88	81	73	1.21	−4	−16
LC	5	88	83	78	1.12	83	71	60	1.39	−5	−19
Intergenic	10	58	62	65	0.88	43	38	33	1.29*	−15	−32***
HC	3	29	42	56	0.52	11	18	25	0.43	−18	−31
IC	2	46	59	71	0.65	32	36	41	0.77	−15	−30
LC	5	79	74	69	1.15	66	50	34	1.92	−13	−34

^aNumber of independent regions assessed as shown on Figure 3, excluding the genes noted below (NDP, ARHGAP6 and BHLHB9) and discussed in the text.

^bMethylation in males was used as Xa methylation level.

^cXi methylation calculated assuming that Xa in female is equivalent to Xa in males.

^dXa and Xi were compared to determine if they differed in blood and placenta. Significance calculated using Mann–Whitney test with significance shown as P = 0.01 to 0.05 (*) and P = 0.001 to 0.01 (**).

^eBlood and placenta were compared to determine if the Xa and Xi differed in their tissue specific methylation levels. Significance calculated using Mann–Whitney test with significance shown as P = 0.001 to 0.01 (**) and P < 0.001 (***).

^fNDP removed from the average as it showed low methylation in all samples.

^gARHGAP6 and BHLHB9 removed from the average as both appeared to be an alternative promoter for an isoform of their respective genes.