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Table 4 Regions of CNV overlap showing the most significant associations with PC1/IQadjPC1 in the GWAS meta-analysis with CNV state (PLINK QFAM)

From: Investigating the effects of copy number variants on reading and language performance

Chr

Start (bp)

Stop (bp)

Kb

SNPs

p value (PC1)

p value (IQadjPC1)

Effecta

Frequency (%)b

Genec

3

2,663,757

2,675,189

11

13

[0.096; 0.245]

[0.003; 0.014]

+

0.4–0.6

CNTN4

6

168,336,080

168,597,552

261

130

[0.005; 0.176]

[0.001; 0.035]

−

1.7–3.4

MLLT4, KIF25, KIF25-AS1, HGC6.3, FRMD1

10

68,221,549

68,242,672

21

10

[0.015; 0.022]

[0.004; 0.007]

−

0.4

CTNNA3

11

55,241,556

55,362,955

121

28

[0.005; 0.013]

[0.002; 0.005]

−

0.4

OR4C15, OR4C16

  1. All the regions of overlap of two or more CNVs, showing at least two consecutive probes with association p < 0.005 and two or more contiguous probes with association p < 0.05, are reported. The results of this meta-analysis on an individual probe basis are reported in detail in Additional file 3: Table S3a, b. All the positions are expressed in hg19 coordinates
  2. aEffect of the CNV+ state, irrespective of the copy number, on PC1 and IQadjPC1
  3. bFrequency (%) of the CNV+ state in the CLDRC dataset
  4. cRefseq genes overlapped/encompassed by the region reported. None of these regions annotated to potentially regulatory elements in the genome, such as transcription factor binding sites, digital DNase I hypersensitivity clusters, and H3K27Ac histone marks, as collected in ENCODE tracks. Similarly, no annotation was detected to the most conserved genomic regions in the primate clade (PhastCons 46-way elements), nor to the most positively selected regions since Homo Sapiens-Neanderthal split (i.e., regions showing S scores from Selective Sweep Scan track in the lower 5 %). All the tracks used here are available for download from the UCSC table browser (http://genome.ucsc.edu/cgi-bin/hgTables)