rs12993544

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

UGP2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0204 (6121/29976,GnomAD)
G=0146 (4276/29116,TOPMED)
G=0111 (555/5008,1000G)
G=0247 (951/3854,ALSPAC)
G=0254 (943/3708,TWINSUK)

Position: chr2:63878419 (GRCh38.p7) (2p15)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 223 Enhancers around

Promoter: 48 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.63878419A>G
GRCh37.p13 chr 2	NC_000002.11:g.64105553A>G

Gene: UGP2, UDP-glucose pyrophosphorylase 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UGP2 transcript variant 2	NM_001001521.1:c.	N/A	Intron Variant
UGP2 transcript variant 1	NM_006759.3:c.	N/A	Intron Variant
UGP2 transcript variant X2	XM_005264537.2:c.	N/A	Intron Variant
UGP2 transcript variant X1	XM_005264538.1:c.	N/A	Intron Variant
UGP2 transcript variant X4	XM_006712088.1:c.	N/A	Intron Variant
UGP2 transcript variant X12	XM_011533091.1:c.	N/A	Intron Variant
UGP2 transcript variant X3	XM_017004855.1:c.	N/A	Intron Variant
UGP2 transcript variant X6	XM_017004856.1:c.	N/A	Intron Variant
UGP2 transcript variant X6	XM_017004857.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.967	G=0.033
1000Genomes	American	Sub	694	A=0.790	G=0.210
1000Genomes	East Asian	Sub	1008	A=0.925	G=0.075
1000Genomes	Europe	Sub	1006	A=0.786	G=0.214
1000Genomes	Global	Study-wide	5008	A=0.889	G=0.111
1000Genomes	South Asian	Sub	978	A=0.920	G=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.753	G=0.247
The Genome Aggregation Database	African	Sub	8732	A=0.934	G=0.066
The Genome Aggregation Database	American	Sub	838	A=0.810	G=0.190
The Genome Aggregation Database	East Asian	Sub	1622	A=0.926	G=0.074
The Genome Aggregation Database	Europe	Sub	18484	A=0.717	G=0.282
The Genome Aggregation Database	Global	Study-wide	29976	A=0.795	G=0.204
The Genome Aggregation Database	Other	Sub	300	A=0.880	G=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29116	A=0.853	G=0.146
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.746	G=0.254

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs12993544	0.00067	alcohol dependence	20201924

eQTL of rs12993544 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 rs12993544 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.

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	64072284	64072460	E067	-33093
chr2	64072478	64072747	E067	-32806
chr2	64072892	64073017	E067	-32536
chr2	64073108	64073328	E067	-32225
chr2	64076349	64077275	E067	-28278
chr2	64077357	64077407	E067	-28146
chr2	64077858	64078094	E067	-27459
chr2	64078885	64079168	E067	-26385
chr2	64080164	64080204	E067	-25349
chr2	64080516	64080702	E067	-24851
chr2	64080727	64080887	E067	-24666
chr2	64080896	64080975	E067	-24578
chr2	64081019	64081300	E067	-24253
chr2	64081399	64081580	E067	-23973
chr2	64081622	64081718	E067	-23835
chr2	64081786	64081902	E067	-23651
chr2	64081918	64081983	E067	-23570
chr2	64082014	64082140	E067	-23413
chr2	64082197	64082237	E067	-23316
chr2	64096942	64097025	E067	-8528
chr2	64101547	64101822	E067	-3731
chr2	64101951	64102964	E067	-2589
chr2	64103000	64103369	E067	-2184
chr2	64118923	64119039	E067	13370
chr2	64072284	64072460	E068	-33093
chr2	64072478	64072747	E068	-32806
chr2	64072892	64073017	E068	-32536
chr2	64073333	64073517	E068	-32036
chr2	64073567	64073719	E068	-31834
chr2	64073773	64073861	E068	-31692
chr2	64074586	64074681	E068	-30872
chr2	64074792	64074879	E068	-30674
chr2	64074940	64075311	E068	-30242
chr2	64075396	64075455	E068	-30098
chr2	64075782	64076232	E068	-29321
chr2	64076349	64077275	E068	-28278
chr2	64077357	64077407	E068	-28146
chr2	64077858	64078094	E068	-27459
chr2	64080516	64080702	E068	-24851
chr2	64080727	64080887	E068	-24666
chr2	64080896	64080975	E068	-24578
chr2	64081019	64081300	E068	-24253
chr2	64081399	64081580	E068	-23973
chr2	64081622	64081718	E068	-23835
chr2	64081786	64081902	E068	-23651
chr2	64081918	64081983	E068	-23570
chr2	64082014	64082140	E068	-23413
chr2	64082197	64082237	E068	-23316
chr2	64096942	64097025	E068	-8528
chr2	64097961	64098068	E068	-7485
chr2	64098298	64098481	E068	-7072
chr2	64098531	64098599	E068	-6954
chr2	64101547	64101822	E068	-3731
chr2	64101951	64102964	E068	-2589
chr2	64103000	64103369	E068	-2184
chr2	64103606	64103732	E068	-1821
chr2	64103778	64104022	E068	-1531
chr2	64107709	64108197	E068	2156
chr2	64108399	64108563	E068	2846
chr2	64118923	64119039	E068	13370
chr2	64072284	64072460	E069	-33093
chr2	64072478	64072747	E069	-32806
chr2	64072892	64073017	E069	-32536
chr2	64073108	64073328	E069	-32225
chr2	64073333	64073517	E069	-32036
chr2	64073567	64073719	E069	-31834
chr2	64073773	64073861	E069	-31692
chr2	64074586	64074681	E069	-30872
chr2	64077357	64077407	E069	-28146
chr2	64077858	64078094	E069	-27459
chr2	64079211	64079293	E069	-26260
chr2	64080516	64080702	E069	-24851
chr2	64080727	64080887	E069	-24666
chr2	64080896	64080975	E069	-24578
chr2	64081019	64081300	E069	-24253
chr2	64081399	64081580	E069	-23973
chr2	64081622	64081718	E069	-23835
chr2	64081786	64081902	E069	-23651
chr2	64081918	64081983	E069	-23570
chr2	64082014	64082140	E069	-23413
chr2	64082197	64082237	E069	-23316
chr2	64100349	64100399	E069	-5154
chr2	64101547	64101822	E069	-3731
chr2	64101951	64102964	E069	-2589
chr2	64103000	64103369	E069	-2184
chr2	64075782	64076232	E070	-29321
chr2	64076349	64077275	E070	-28278
chr2	64064272	64064600	E071	-40953
chr2	64072284	64072460	E071	-33093
chr2	64072478	64072747	E071	-32806
chr2	64072892	64073017	E071	-32536
chr2	64073108	64073328	E071	-32225
chr2	64073333	64073517	E071	-32036
chr2	64073567	64073719	E071	-31834
chr2	64073773	64073861	E071	-31692
chr2	64074586	64074681	E071	-30872
chr2	64074792	64074879	E071	-30674
chr2	64074940	64075311	E071	-30242
chr2	64075396	64075455	E071	-30098
chr2	64075782	64076232	E071	-29321
chr2	64077357	64077407	E071	-28146
chr2	64078885	64079168	E071	-26385
chr2	64079211	64079293	E071	-26260
chr2	64081019	64081300	E071	-24253
chr2	64081399	64081580	E071	-23973
chr2	64081622	64081718	E071	-23835
chr2	64081786	64081902	E071	-23651
chr2	64081918	64081983	E071	-23570
chr2	64082014	64082140	E071	-23413
chr2	64082197	64082237	E071	-23316
chr2	64082442	64082520	E071	-23033
chr2	64082567	64082640	E071	-22913
chr2	64082713	64082901	E071	-22652
chr2	64082922	64082973	E071	-22580
chr2	64088337	64088701	E071	-16852
chr2	64097961	64098068	E071	-7485
chr2	64098298	64098481	E071	-7072
chr2	64098531	64098599	E071	-6954
chr2	64098897	64098988	E071	-6565
chr2	64099188	64099330	E071	-6223
chr2	64101547	64101822	E071	-3731
chr2	64101951	64102964	E071	-2589
chr2	64103000	64103369	E071	-2184
chr2	64103606	64103732	E071	-1821
chr2	64108399	64108563	E071	2846
chr2	64115713	64115763	E071	10160
chr2	64115933	64116246	E071	10380
chr2	64118923	64119039	E071	13370
chr2	64064272	64064600	E072	-40953
chr2	64072284	64072460	E072	-33093
chr2	64072478	64072747	E072	-32806
chr2	64072892	64073017	E072	-32536
chr2	64080516	64080702	E072	-24851
chr2	64080727	64080887	E072	-24666
chr2	64080896	64080975	E072	-24578
chr2	64081019	64081300	E072	-24253
chr2	64081399	64081580	E072	-23973
chr2	64081622	64081718	E072	-23835
chr2	64081786	64081902	E072	-23651
chr2	64081918	64081983	E072	-23570
chr2	64082014	64082140	E072	-23413
chr2	64082197	64082237	E072	-23316
chr2	64082442	64082520	E072	-23033
chr2	64082567	64082640	E072	-22913
chr2	64082713	64082901	E072	-22652
chr2	64082922	64082973	E072	-22580
chr2	64096942	64097025	E072	-8528
chr2	64097129	64097179	E072	-8374
chr2	64097961	64098068	E072	-7485
chr2	64101211	64101303	E072	-4250
chr2	64101547	64101822	E072	-3731
chr2	64101951	64102964	E072	-2589
chr2	64103000	64103369	E072	-2184
chr2	64115388	64115469	E072	9835
chr2	64115713	64115763	E072	10160
chr2	64118923	64119039	E072	13370
chr2	64072284	64072460	E073	-33093
chr2	64072478	64072747	E073	-32806
chr2	64072892	64073017	E073	-32536
chr2	64073108	64073328	E073	-32225
chr2	64073333	64073517	E073	-32036
chr2	64076349	64077275	E073	-28278
chr2	64079211	64079293	E073	-26260
chr2	64088337	64088701	E073	-16852
chr2	64099979	64100163	E073	-5390
chr2	64101211	64101303	E073	-4250
chr2	64101547	64101822	E073	-3731
chr2	64101951	64102964	E073	-2589
chr2	64103000	64103369	E073	-2184
chr2	64115933	64116246	E073	10380
chr2	64072284	64072460	E074	-33093
chr2	64072478	64072747	E074	-32806
chr2	64072892	64073017	E074	-32536
chr2	64073108	64073328	E074	-32225
chr2	64073333	64073517	E074	-32036
chr2	64073567	64073719	E074	-31834
chr2	64073773	64073861	E074	-31692
chr2	64074586	64074681	E074	-30872
chr2	64074792	64074879	E074	-30674
chr2	64074940	64075311	E074	-30242
chr2	64075396	64075455	E074	-30098
chr2	64075782	64076232	E074	-29321
chr2	64076349	64077275	E074	-28278
chr2	64077357	64077407	E074	-28146
chr2	64077858	64078094	E074	-27459
chr2	64078885	64079168	E074	-26385
chr2	64079211	64079293	E074	-26260
chr2	64080164	64080204	E074	-25349
chr2	64080516	64080702	E074	-24851
chr2	64080727	64080887	E074	-24666
chr2	64080896	64080975	E074	-24578
chr2	64081019	64081300	E074	-24253
chr2	64081399	64081580	E074	-23973
chr2	64081622	64081718	E074	-23835
chr2	64081786	64081902	E074	-23651
chr2	64081918	64081983	E074	-23570
chr2	64082014	64082140	E074	-23413
chr2	64082197	64082237	E074	-23316
chr2	64082442	64082520	E074	-23033
chr2	64082567	64082640	E074	-22913
chr2	64082713	64082901	E074	-22652
chr2	64082922	64082973	E074	-22580
chr2	64096942	64097025	E074	-8528
chr2	64097129	64097179	E074	-8374
chr2	64099979	64100163	E074	-5390
chr2	64101547	64101822	E074	-3731
chr2	64101951	64102964	E074	-2589
chr2	64103000	64103369	E074	-2184
chr2	64103606	64103732	E074	-1821
chr2	64103778	64104022	E074	-1531
chr2	64115713	64115763	E074	10160
chr2	64118923	64119039	E074	13370
chr2	64076349	64077275	E081	-28278
chr2	64101547	64101822	E081	-3731
chr2	64101951	64102964	E081	-2589
chr2	64103000	64103369	E081	-2184
chr2	64103606	64103732	E081	-1821
chr2	64103778	64104022	E081	-1531
chr2	64076349	64077275	E082	-28278
chr2	64077357	64077407	E082	-28146
chr2	64101547	64101822	E082	-3731
chr2	64101951	64102964	E082	-2589
chr2	64103000	64103369	E082	-2184

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	64067290	64070236	E067	-35317
chr2	64070283	64070351	E067	-35202
chr2	64070406	64070537	E067	-35016
chr2	64070555	64070609	E067	-34944
chr2	64067290	64070236	E068	-35317
chr2	64070283	64070351	E068	-35202
chr2	64070406	64070537	E068	-35016
chr2	64070555	64070609	E068	-34944
chr2	64067290	64070236	E069	-35317
chr2	64070283	64070351	E069	-35202
chr2	64070406	64070537	E069	-35016
chr2	64070555	64070609	E069	-34944
chr2	64070669	64070754	E069	-34799
chr2	64070879	64071000	E069	-34553
chr2	64067290	64070236	E070	-35317
chr2	64070283	64070351	E070	-35202
chr2	64070406	64070537	E070	-35016
chr2	64070555	64070609	E070	-34944
chr2	64070669	64070754	E070	-34799
chr2	64070879	64071000	E070	-34553
chr2	64067290	64070236	E071	-35317
chr2	64070283	64070351	E071	-35202
chr2	64070406	64070537	E071	-35016
chr2	64070555	64070609	E071	-34944
chr2	64070669	64070754	E071	-34799
chr2	64067290	64070236	E072	-35317
chr2	64070283	64070351	E072	-35202
chr2	64070406	64070537	E072	-35016
chr2	64070555	64070609	E072	-34944
chr2	64070669	64070754	E072	-34799
chr2	64067290	64070236	E073	-35317
chr2	64070283	64070351	E073	-35202
chr2	64070406	64070537	E073	-35016
chr2	64070555	64070609	E073	-34944
chr2	64070669	64070754	E073	-34799
chr2	64067290	64070236	E074	-35317
chr2	64070283	64070351	E074	-35202
chr2	64070406	64070537	E074	-35016
chr2	64070555	64070609	E074	-34944
chr2	64067290	64070236	E081	-35317
chr2	64070283	64070351	E081	-35202
chr2	64070406	64070537	E081	-35016
chr2	64070555	64070609	E081	-34944
chr2	64067290	64070236	E082	-35317
chr2	64070283	64070351	E082	-35202
chr2	64070406	64070537	E082	-35016
chr2	64070555	64070609	E082	-34944
chr2	64070669	64070754	E082	-34799