rs16930625

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

CYP2R1 : 5 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0119 (3593/29980,GnomAD)
G=0129 (3760/29118,TOPMED)
G=0152 (760/5008,1000G)
G=0086 (332/3854,ALSPAC)
G=0093 (344/3708,TWINSUK)

Position: chr11:14896762 (GRCh38.p7) (11p15.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 0 Enhancer around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 11	NC_000011.10:g.14896762A>G
GRCh37.p13 chr 11 fix patch HG873_PATCH	NW_003871082.1:g.123100T>C
CYP2R1 RefSeqGene	NG_007936.1:g.444T>C
GRCh37.p13 chr 11	NC_000011.9:g.14918308A>G

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

Molecule type	Change	Amino acid[Codon]	SO Term
CYP2R1 transcript	NM_024514.4:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X9	XM_011519898.2:c.	N/A	5 Prime UTR Variant
CYP2R1 transcript variant X1	XM_005252788.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X2	XM_005252789.2:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X4	XM_011519895.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X3	XM_017017190.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X5	XM_017017191.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X6	XM_017017192.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X7	XM_017017193.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X8	XM_017017194.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X11	XM_017017195.1:c.	N/A	Genic Upstream Transcript Variant
CYP2R1 transcript variant X10	XR_242777.2:n.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.808	G=0.192
1000Genomes	American	Sub	694	A=0.710	G=0.290
1000Genomes	East Asian	Sub	1008	A=0.872	G=0.128
1000Genomes	Europe	Sub	1006	A=0.917	G=0.083
1000Genomes	Global	Study-wide	5008	A=0.848	G=0.152
1000Genomes	South Asian	Sub	978	A=0.910	G=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.914	G=0.086
The Genome Aggregation Database	African	Sub	8724	A=0.840	G=0.160
The Genome Aggregation Database	American	Sub	838	A=0.760	G=0.240
The Genome Aggregation Database	East Asian	Sub	1618	A=0.881	G=0.119
The Genome Aggregation Database	Europe	Sub	18498	A=0.905	G=0.094
The Genome Aggregation Database	Global	Study-wide	29980	A=0.880	G=0.119
The Genome Aggregation Database	Other	Sub	302	A=0.820	G=0.180
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.870	G=0.129
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.907	G=0.093

PMID	Title	Author	Journal
24277619	ALDH2 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 EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs16930625	0.000454	alcohol dependence	24277619

eQTL of rs16930625 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs16930625 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.