Table 3.

Single nucleotide polymorphisms in one-carbon metabolism genes assessed in study.

Gene	SNP	LD block	Type	Cases (n)	Controls (n)	Ref. allele	Risk allele	Risk allele freq, cases	Risk allele freq, controls	Risk allele freq, BEBa
AS3MT	rs10748835	1	Intron	666	617	A	G	0.53	0.54	0.47
AS3MT	rs3740393	1	Intron	690	630	G	C	0.21	0.21	0.25
BHMT	rs3733890	2	Missense mutation (R239Q)	688	624	G	A	0.28	0.29	0.28
FOLR1	rs1540087	3	5 prime UTR	684	625	C	T	0.07	0.08	0.05
FOLR1	rs2071010	3	Intron	690	631	G	A	0.16	0.15	0.22
FOLR1	rs7109250	3	Intron/5 prime UTR	688	629	C	T	0.07	0.09	0.05
FOLR2	rs2298444	4	Intron	692	631	A	G	0.40	0.40	0.44
FOLR2	rs514933	5	Intron	674	615	G	A	0.62	0.59	0.65
FOLR2	rs651646	5	Intron	691	627	A	T	0.46	0.45	0.42
FOLR2	rs651933	5	Upstream	674	617	A	G	0.45	0.44	0.41
MTHFD1	rs11627387	6	Intron	679	621	G	A	0.28	0.26	0.24
MTHFD1	rs2236224	6	Intron	674	616	C	T	0.40	0.41	0.49
MTHFD1	rs2236225	6	Missense mutation (R653Q)	685	630	C	T	0.45	0.48	0.52
MTHFD1	rs1950902	7	Missense mutation (K134R)	693	633	C	T	0.13	0.10	0.12
MTHFR	rs1476413	8	Intron	690	631	G	A	0.43	0.42	0.48
MTHFR	rs1801131	8	Missense mutation (E429A)	669	615	A	C	0.38	0.38	0.41
MTHFR	rs1801133	8	Missense mutation (A222V)	691	631	C	T	0.12	0.13	0.12
MTR	rs1805087	9	Missense mutation (D919G)	690	631	A	G	0.27	0.27	0.33
MTRR	rs1801394	10	Missense mutation (I49M)	686	631	A	G	0.50	0.54	0.54
SHMT1	rs1979277	11	Missense mutation (L474F)	675	625	G	A	0.17	0.17	0.16
SLC19A1	rs1888530	12	Intron	688	624	T	C	0.49	0.50	0.46
SLC46A1	rs1128162	13	3 prime UTR	666	614	T	G	0.50	0.50	0.46
TCN2	rs1801198	14	Missense mutation (R259P)	686	632	G	C	0.39	0.38	0.45
TYMS	rs1001761	15	Intron	685	625	C	T	0.54	0.53	0.62
TYMS	rs2847149	15	Intron	693	627	G	A	0.53	0.52	0.60
TYMS	rs502396	15	Intron	689	629	T	C	0.54	0.54	0.55

^aAllele frequencies for the Bengali in Bangladesh (BEB) population in the 1000 Genomes Project database