Table 2.

Association Results for Genome-wide-Significant Low-Frequency Variants from Discovery 25OHD Meta-analysis before and after Conditioning on the Lead Common CYP2R1 SNP, rs10741657, and the Lead Low-Frequency CYP2R1 Variant, rs117913124

SNV	Chr	Position	EAa	EAFb	Candidate Gene	Function	Betac	p Value	Conditional on rs10741657		Conditional on rs117913124		n
									Betac	p Value	Betac	p Value
rs117913124	11	14900931	A	0.025	CYP2R1	exon 4 (synonymous codon)	−0.43	1.5 × 10−88	−0.39	2.4 × 10−78	NA	NA	41,336
rs116970203	11	14876718	A	0.025	CYP2R1d	intron 11 variant	−0.43	2.2 × 10−90	−0.40	3.3 × 10−80	NA	NA	41,138
rs117361591	11	14861957	T	0.014	CYP2R1d	intron 11 variant	−0.44	9.1 × 10−51	−0.40	2.2 × 10−44	−0.05	0.017	38,286
rs117621176	11	14861320	G	0.014	CYP2R1d	intron 11 variant	−0.44	8.7 × 10−51	−0.40	2.1 × 10−44	−0.05	0.016	38,273
rs142830933	11	14838760	C	0.014	CYP2R1d	intron 5 variant	−0.44	1.4 × 10−48	−0.40	1.7 × 10−42	−0.05	0.03	37,541
rs117672174	11	14746404	T	0.014	CYP2R1d	intron 1 variant	−0.43	2.8 × 10−45	−0.39	2.9 × 10−39	−0.04	0.062	37,209

Abbreviations are as follows: Chr, chromosome; EA, effect allele; EAF, effect allele frequency; NA, not applicable; SNV, single-nucleotide variant.

^aEffect allele is the 25OHD decreasing allele.

^bEffect allele frequency.

^cBeta values represent changes in standard deviations of the standardized log-transformed 25OHD levels.

^dNearest gene: PDE3B.