Table 2:

D4Z4 methylation gradient analysis using a linear mixed-effects model to estimate intercept and slope.

			% Methylated CpG RU1		Change in % methylated CpG per RUa
Subject ID	Chromosome	Length D4Z4	Intercept	90% CI	Slope	90% CI
FSHD1
P6	chr4qA-S	3U	14.2	10.6 – 17.7	0	−2.1 – 2.1
P1	chr4qA-S	6U	10.3	7.3 – 13.2	2.8	2.3 – 3.4
P2	chr4qA-S	6U	15.3	12.0 – 18.5	2.1	1.5 – 2.8
P3	chr4qA-S	6U	11.5	8.6 – 14.5	2.3	1.8 – 2.8
P4	chr4qA-S	6U	10.4	7.2 – 13.7	2.9	2.3 – 3.5
P5	chr4qA-S	9U	10.1	5.6 – 14.5	2	1.3 – 2.7
P5	chr4qA-L	9U	18	12.8 – 23.2	2.3	1.4 – 3.1
P3	chr10q	9U	24.9	21.5 – 28.3	2.3	1.7 – 2.8
P1	chr10q	11U	17.4	15.1 – 19.7	2.2	1.9 – 2.6
P1	chr10q	13U	25.4	22.0 – 28.8	1.9	1.3 – 2.4
P1, P2, P3, P4, P5, P6	chr4qA-S	>10U, centromeric	46.6	42.5 – 50.7	6.1	5.3 – 6.8
P1, P2, P3, P4, P5, P6	chr4qA-S	>10U, telomeric	76.2	72.1 – 80.3	−1	−1.6 – −0.3
FSHD2
P7	chr10q	8U	9.5	6.5 – 12.5	1.2	0.7 – 1.7
P8	chr10q	10U	11.9	8.6 – 15.2	0.7	0.2 – 1.3
P7	chr10q	12U	11.8	8.4 – 15.3	0.8	0.2 – 1.3
P8	chr4qA-S	16U	13.3	8.4 – 18.2	0.5	−0.3 – 1.2
P7	chr4qA-S	19U	14.4	7.0 – 21.8	0.6	−0.5 – 1.7
Unaffected Control
C4	chr4qB	16U, prox 6U	33.7	30.4 – 37.0	6.2	5.6 – 6.8
C4	chr4qB	16U, distal 6U	64.1	60.7 – 67.4	−1.3	−1.9 – −0.7
C4	chr10q	20U, prox 6U	29.4	25.9 – 33.0	5.7	5.1 – 6.4
C4	chr10q	20U, distal 6U	71.4	67.9 – 74.9	−0.5	−1.2 – 0.1
C4	chr10q	21U, prox 6U	34.5	31.0 – 37.9	5.7	5.1 – 6.4
C4	chr10q	21U, distal 6U	77.1	73.5 – 80.6	−0.9	−1.6 – −0.2
C4	chr4qA-L	42U, prox 6U	42.5	38.4 – 46.6	7.1	6.3 – 7.9
C4	chr4qA-L	42U, distal 6U	89.8	86.3 – 93.4	−1	−1.6 – −0.4

^aRU-repeat unit