rs1562902

Homo sapiens
C>T
CYP2R1 : 5 Prime UTR Variant
Check p-value
SNV (Single Nucleotide Variation)
C==0460 (13765/29878,GnomAD)
C==0462 (13460/29118,TOPMED)
C==0422 (2112/5008,1000G)
C==0457 (1760/3854,ALSPAC)
C==0443 (1643/3708,TWINSUK)
chr11:14896670 (GRCh38.p7) (11p15.2)
AD
GWASdb2
7   publication(s)
See rs on genome
0 Enhancer around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 11NC_000011.10:g.14896670C>T
GRCh37.p13 chr 11 fix patch HG873_PATCHNW_003871082.1:g.123192G>A
CYP2R1 RefSeqGeneNG_007936.1:g.536G>A
GRCh37.p13 chr 11NC_000011.9:g.14918216C>T

Gene: CYP2R1, cytochrome P450 family 2 subfamily R member 1(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CYP2R1 transcriptNM_024514.4:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X9XM_011519898.2:c.N/A5 Prime UTR Variant
CYP2R1 transcript variant X1XM_005252788.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X2XM_005252789.2:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X4XM_011519895.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X3XM_017017190.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X5XM_017017191.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X6XM_017017192.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X7XM_017017193.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X8XM_017017194.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X11XM_017017195.1:c.N/AGenic Upstream Transcript Variant
CYP2R1 transcript variant X10XR_242777.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.477T=0.523
1000GenomesAmericanSub694C=0.330T=0.670
1000GenomesEast AsianSub1008C=0.379T=0.621
1000GenomesEuropeSub1006C=0.441T=0.559
1000GenomesGlobalStudy-wide5008C=0.422T=0.578
1000GenomesSouth AsianSub978C=0.430T=0.570
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.457T=0.543
The Genome Aggregation DatabaseAfricanSub8696C=0.486T=0.514
The Genome Aggregation DatabaseAmericanSub836C=0.460T=0.540
The Genome Aggregation DatabaseEast AsianSub1610C=0.391T=0.609
The Genome Aggregation DatabaseEuropeSub18436C=0.456T=0.543
The Genome Aggregation DatabaseGlobalStudy-wide29878C=0.460T=0.539
The Genome Aggregation DatabaseOtherSub300C=0.340T=0.660
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.462T=0.537
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.443T=0.557
PMID Title Author Journal
22205958Common variation in vitamin D pathway genes predicts circulating 25-hydroxyvitamin D Levels among African Americans.Signorello LBPLoS One
19852851Asthma and genes encoding components of the vitamin D pathway.Bosse YRespir Res
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet
22801813The GC, CYP2R1 and DHCR7 genes are associated with vitamin D levels in northeastern Han Chinese children.Zhang YSwiss Med Wkly
27473187CYP2R1 polymorphisms are important modulators of circulating 25-hydroxyvitamin D levels in elderly females with vitamin insufficiency, but not of the response to vitamin D supplementation.Arabi AOsteoporos Int
22649517Polymorphisms related to the serum 25-hydroxyvitamin D level and risk of myocardial infarction, diabetes, cancer and mortality. The Tromso Study.Jorde RPLoS One
16600026Asthma families show transmission disequilibrium of gene variants in the vitamin D metabolism and signalling pathway.Wjst MRespir Res

P-Value

SNP ID p-value Traits Study
rs15629020.000736alcohol dependence24277619

eQTL of rs1562902 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr11:14918216CALCBENSG00000175868.9C>T6.8080e-4-8327Cerebellum
Chr11:14918216CALCBENSG00000175868.9C>T3.0467e-5-8327Cerebellar_Hemisphere

meQTL of rs1562902 in Fetal Brain

Probe ID Position Gene beta p-value
There is no meQTL annotation for this SNP

Genomic View

Chromatin Interaction

There is no significant Hi-C chromatin interaction data for this SNP.