Table 1.

New SNP associations with dyslexia, including gene-based results, eQTL status, expression in brain and validation in three independent cohorts (GenLang Consortium, CRS and NeuroDys)

Cytoband	SNP	Effect allele	Frequency	Odds Ratio	GWAS P	Gene(s)	Most probable gene	Validation cohort (P uncorrected for multiple testing)
chr1q21.3	rs4845687	A	0.56	1.044	1.1 × 10−9	KCNN3, PMVK	PMVKab	GenLang (0.02)
chr2q22.3	rs497418	A	0.38	1.043	3.0 × 10−9	ACVR2A	AC062032.1c	GenLang (0.009)
chr2q33.1	rs72916919	G	0.51	1.049	4.1 × 10−12	RFTN2	MARS2a	NeuroDys (0.02), GenLang (0.02)
chr3p12.1	rs10511073	A	0.37	1.046	4.6 × 10−10	CADM2	CADM2a	GenLang (0.02)
chr3q22.3	rs13082684	A	0.24	1.069	1.0 × 10−16	PPP2R3A	PPP2R3A (intron)a	GenLang (0.0004); not in CRS
chr6p22.3	rs2876430	T	0.34	1.041	3.7 × 10−8	ATXN1, STMND1	STMND1	GenLang (0.04)
chr7p14.1	rs62453457	G	0.48	1.039	3.3 × 10−8	POU6F2	POU6F2	CRS (0.04)
chr7q11.22	rs3735260	G	0.08	1.075	4.7 × 10−8	AUTS2	AUTS2	GenLang (0.02)
chr7q11.22	rs77059784	G	0.97	1.123	3.0 × 10−8	CALN1	CALN1	GenLang (0.02); not in CRS
chr9q34.11	rs9696811	C	0.69	1.069	1.1 × 10−16	PPP2R3A	AL158151.4abc	GenLang (0.03)
chr11q23.1	rs138127836	A	0.65	1.056	1.7 × 10−13	PPP2R1B	PPP2R1B (intron)ab	GenLang (0.02)
chr17q23.3	rs72841395c	C	0.77	1.049	5.4 × 10−9	TANC2	TANC2a	GenLang (0.005)
chrXq27.3	rs5904158	GTA	0.65	1.037	3.3 × 10−8	TMEM257, CXorf51Bb	AL109653.3c	GenLang (0.02); not in NeuroDys/CRS
chr2q12.1	rs367982014	CAAT	0.29	1.045	1.8 × 10−8	TMEM182	MFSD9a	Not available
chr3p24.3	rs373178590	G	0.51	1.046	1.3 × 10−9	TBC1D5	TBC1D5 (intron)a	Not available
chr10q24.33	rs34732054	C	0.57	1.045	3.7 × 10−9	PCGF6	USMG5a	Not available
chr13q12.13	rs375018025	CA	0.57	1.044	5.6 × 10−9	CDK8, WASF3	WASF3	Not available
chr1p32.1	rs12737449	G	0.85	1.070	1.4 × 10−11	C1orf87	C1orf87 (missense)a	Not significant
chr2p23.2	rs1969131	T	0.17	1.053	3.0 × 10−8	BABAM2	BABAM2	Not significant
chr3q26.33	rs7625418	C	0.21	1.056	4.3 × 10−9	PEX5L, TTC14	TTC14a	Not significant
chr3p13	rs13097431	G	0.58	1.044	1.3 × 10−9	MITF	MITFa	Not significant
chr5q33.3	rs867009	G	0.36	1.041	2.3 × 10−9	SGCD	SGCDa	Not significant
chr9p22.3	rs3122702	T	0.5	1.041	8.3 × 10−9	CCDC171	CCDC171ab	Not significant
chr10q24.2	rs10786387	C	0.68	1.049	1.1 × 10−10	CRTAC1, R3HCC1L	R3HCC1La	Not significant
chr11p14.1	rs676217	G	0.37	1.050	1.1 × 10−11	KCNA4, FSHB	ARL14EPab	Not significant
chr19q13.2	rs60963584	A	0.89	1.065	2.7 × 10−8	GMFG, SAMD4B	SAMD4Ba	Not significant
chr20q11.21	rs4911257	C	0.39	1.055	7.5 × 10−14	DNMT3B	DNMT3B (intron)ab	Not significant

Statistics for each variant are from the 23andMe GWAS (see Supplementary Table 1 for all 42 significant variants). Genes that are significant in gene-based tests are set in bold. Multi-allelic effect alleles represent insertions. The most probable gene is that most likely to be causal based on genetic and functional genomic data tied to the tag SNP (https://platform.opentargets.org/).

^aeQTL.

^beQTL linked to brain expression.

^cNot available in gene-based results.