rs12321570

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SLC35E3 : 3 Prime UTR Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0109 (3269/29930,GnomAD)
C=0149 (4338/29118,TOPMED)
C=0109 (545/5008,1000G)
C=0040 (153/3854,ALSPAC)
C=0049 (181/3708,TWINSUK)

Position: chr12:68768463 (GRCh38.p7) (12q15)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 81 Enhancers around

Promoter: 32 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.68768463T>C
GRCh37.p13 chr 12	NC_000012.11:g.69162243T>C

Gene: SLC35E3, solute carrier family 35 member E3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC35E3 transcript	NM_018656.2:c.	N/A	Genic Downstream Transcript Variant
SLC35E3 transcript variant X1	XM_017019584.1:c.	N/A	3 Prime UTR Variant
SLC35E3 transcript variant X2	XM_005269006.3:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.695	C=0.305
1000Genomes	American	Sub	694	T=0.920	C=0.080
1000Genomes	East Asian	Sub	1008	T=0.984	C=0.016
1000Genomes	Europe	Sub	1006	T=0.938	C=0.062
1000Genomes	Global	Study-wide	5008	T=0.891	C=0.109
1000Genomes	South Asian	Sub	978	T=0.990	C=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.960	C=0.040
The Genome Aggregation Database	African	Sub	8698	T=0.741	C=0.259
The Genome Aggregation Database	American	Sub	838	T=0.940	C=0.060
The Genome Aggregation Database	East Asian	Sub	1620	T=0.984	C=0.016
The Genome Aggregation Database	Europe	Sub	18472	T=0.951	C=0.048
The Genome Aggregation Database	Global	Study-wide	29930	T=0.890	C=0.109
The Genome Aggregation Database	Other	Sub	302	T=0.880	C=0.120
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.851	C=0.149
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.951	C=0.049

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
rs12321570	0.00086	alcohol dependence	20201924

eQTL of rs12321570 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 rs12321570 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 )
chr12	69142039	69142089	E067	-20154
chr12	69142646	69142686	E067	-19557
chr12	69143296	69143379	E067	-18864
chr12	69143478	69143549	E067	-18694
chr12	69143625	69143697	E067	-18546
chr12	69144185	69144606	E067	-17637
chr12	69144629	69144709	E067	-17534
chr12	69204656	69204767	E067	42413
chr12	69204929	69205026	E067	42686
chr12	69142646	69142686	E068	-19557
chr12	69143296	69143379	E068	-18864
chr12	69143478	69143549	E068	-18694
chr12	69143625	69143697	E068	-18546
chr12	69144185	69144606	E068	-17637
chr12	69174876	69175553	E068	12633
chr12	69206435	69206990	E068	44192
chr12	69206997	69207390	E068	44754
chr12	69141798	69141855	E069	-20388
chr12	69141898	69142003	E069	-20240
chr12	69142039	69142089	E069	-20154
chr12	69142646	69142686	E069	-19557
chr12	69143296	69143379	E069	-18864
chr12	69143478	69143549	E069	-18694
chr12	69143625	69143697	E069	-18546
chr12	69144185	69144606	E069	-17637
chr12	69144629	69144709	E069	-17534
chr12	69142646	69142686	E070	-19557
chr12	69141798	69141855	E071	-20388
chr12	69141898	69142003	E071	-20240
chr12	69142039	69142089	E071	-20154
chr12	69142646	69142686	E071	-19557
chr12	69143296	69143379	E071	-18864
chr12	69143478	69143549	E071	-18694
chr12	69143625	69143697	E071	-18546
chr12	69144629	69144709	E071	-17534
chr12	69174542	69174849	E071	12299
chr12	69174876	69175553	E071	12633
chr12	69206435	69206990	E071	44192
chr12	69208807	69208871	E071	46564
chr12	69141798	69141855	E072	-20388
chr12	69141898	69142003	E072	-20240
chr12	69142039	69142089	E072	-20154
chr12	69142646	69142686	E072	-19557
chr12	69143296	69143379	E072	-18864
chr12	69143478	69143549	E072	-18694
chr12	69143625	69143697	E072	-18546
chr12	69144629	69144709	E072	-17534
chr12	69174542	69174849	E072	12299
chr12	69174876	69175553	E072	12633
chr12	69179078	69179794	E072	16835
chr12	69206435	69206990	E072	44192
chr12	69206997	69207390	E072	44754
chr12	69208496	69208540	E072	46253
chr12	69208583	69208623	E072	46340
chr12	69208807	69208871	E072	46564
chr12	69208951	69209001	E072	46708
chr12	69141798	69141855	E073	-20388
chr12	69141898	69142003	E073	-20240
chr12	69143296	69143379	E073	-18864
chr12	69143478	69143549	E073	-18694
chr12	69143625	69143697	E073	-18546
chr12	69144185	69144606	E073	-17637
chr12	69206435	69206990	E073	44192
chr12	69141798	69141855	E074	-20388
chr12	69141898	69142003	E074	-20240
chr12	69142039	69142089	E074	-20154
chr12	69142646	69142686	E074	-19557
chr12	69143296	69143379	E074	-18864
chr12	69143478	69143549	E074	-18694
chr12	69144629	69144709	E074	-17534
chr12	69146149	69146231	E074	-16012
chr12	69174542	69174849	E074	12299
chr12	69174876	69175553	E074	12633
chr12	69180846	69181729	E074	18603
chr12	69206435	69206990	E074	44192
chr12	69141798	69141855	E081	-20388
chr12	69141898	69142003	E081	-20240
chr12	69142039	69142089	E081	-20154
chr12	69143296	69143379	E082	-18864
chr12	69143478	69143549	E082	-18694
chr12	69143625	69143697	E082	-18546

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr12	69138900	69141033	E067	-21210
chr12	69200855	69201058	E067	38612
chr12	69201152	69203363	E067	38909
chr12	69203467	69203640	E067	41224
chr12	69203737	69203787	E067	41494
chr12	69138900	69141033	E068	-21210
chr12	69200855	69201058	E068	38612
chr12	69201152	69203363	E068	38909
chr12	69138900	69141033	E069	-21210
chr12	69201152	69203363	E069	38909
chr12	69138900	69141033	E070	-21210
chr12	69200855	69201058	E070	38612
chr12	69201152	69203363	E070	38909
chr12	69138900	69141033	E071	-21210
chr12	69200855	69201058	E071	38612
chr12	69201152	69203363	E071	38909
chr12	69138900	69141033	E072	-21210
chr12	69200855	69201058	E072	38612
chr12	69201152	69203363	E072	38909
chr12	69203467	69203640	E072	41224
chr12	69203737	69203787	E072	41494
chr12	69138900	69141033	E073	-21210
chr12	69200855	69201058	E073	38612
chr12	69201152	69203363	E073	38909
chr12	69138900	69141033	E074	-21210
chr12	69200855	69201058	E074	38612
chr12	69201152	69203363	E074	38909
chr12	69138900	69141033	E081	-21210
chr12	69201152	69203363	E081	38909
chr12	69138900	69141033	E082	-21210
chr12	69200855	69201058	E082	38612
chr12	69201152	69203363	E082	38909