rs3897230

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC102723490 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0225 (6735/29932,GnomAD)
T=0190 (5550/29116,TOPMED)
T=0141 (708/5008,1000G)
T=0281 (1084/3854,ALSPAC)
T=0279 (1036/3708,TWINSUK)

Position: chr13:36773840 (GRCh38.p7) (13q13.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 39 Enhancers around

Promoter: 9 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 13	NC_000013.11:g.36773840C>T
GRCh37.p13 chr 13	NC_000013.10:g.37347977C>T

Molecule type	Change	Amino acid[Codon]	SO Term
LOC102723490 transcript variant X2	XR_001749823.1:n.	N/A	Intron Variant
LOC102723490 transcript variant X2	XR_001749824.1:n.	N/A	Intron Variant
LOC102723490 transcript variant X5	XR_001749825.1:n.	N/A	Intron Variant
LOC102723490 transcript variant X9	XR_001749828.1:n.	N/A	Intron Variant
LOC102723490 transcript variant X7	XR_001749829.1:n.	N/A	Intron Variant
LOC102723490 transcript variant X8	XR_001749830.1:n.	N/A	Intron Variant
LOC102723490 transcript variant X11	XR_001749832.1:n.	N/A	Intron Variant
LOC102723490 transcript variant X1	XR_941857.2:n.	N/A	Intron Variant
LOC102723490 transcript variant X5	XR_001749826.1:n.	N/A	Genic Upstream Transcript Variant
LOC102723490 transcript variant X9	XR_001749831.1:n.	N/A	Genic Upstream Transcript Variant
LOC102723490 transcript variant X10	XR_941872.2:n.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.900	T=0.100
1000Genomes	American	Sub	694	C=0.740	T=0.260
1000Genomes	East Asian	Sub	1008	C=0.969	T=0.031
1000Genomes	Europe	Sub	1006	C=0.724	T=0.276
1000Genomes	Global	Study-wide	5008	C=0.859	T=0.141
1000Genomes	South Asian	Sub	978	C=0.910	T=0.090
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.719	T=0.281
The Genome Aggregation Database	African	Sub	8722	C=0.874	T=0.126
The Genome Aggregation Database	American	Sub	834	C=0.710	T=0.290
The Genome Aggregation Database	East Asian	Sub	1616	C=0.975	T=0.025
The Genome Aggregation Database	Europe	Sub	18458	C=0.712	T=0.288
The Genome Aggregation Database	Global	Study-wide	29932	C=0.775	T=0.225
The Genome Aggregation Database	Other	Sub	302	C=0.870	T=0.130
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.809	T=0.190
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.721	T=0.279

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

SNP ID	p-value	Traits	Study
rs3897230	0.00071	alcohol dependence	20201924

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

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

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr13	37395262	37395319	E067	47285
chr13	37395486	37395537	E067	47509
chr13	37395573	37395721	E067	47596
chr13	37397002	37397132	E067	49025
chr13	37397144	37397184	E067	49167
chr13	37397212	37397301	E067	49235
chr13	37378349	37378435	E068	30372
chr13	37395262	37395319	E068	47285
chr13	37395486	37395537	E068	47509
chr13	37395573	37395721	E068	47596
chr13	37395915	37395979	E070	47938
chr13	37396077	37396179	E070	48100
chr13	37396618	37396668	E070	48641
chr13	37397474	37397514	E070	49497
chr13	37397890	37397940	E070	49913
chr13	37392303	37392495	E071	44326
chr13	37395262	37395319	E071	47285
chr13	37395486	37395537	E071	47509
chr13	37395573	37395721	E071	47596
chr13	37395915	37395979	E071	47938
chr13	37397002	37397132	E071	49025
chr13	37397144	37397184	E071	49167
chr13	37397212	37397301	E071	49235
chr13	37392303	37392495	E074	44326
chr13	37395262	37395319	E074	47285
chr13	37395262	37395319	E081	47285
chr13	37395486	37395537	E081	47509
chr13	37395573	37395721	E081	47596
chr13	37395915	37395979	E081	47938
chr13	37396077	37396179	E081	48100
chr13	37396618	37396668	E081	48641
chr13	37397002	37397132	E081	49025
chr13	37397144	37397184	E081	49167
chr13	37397212	37397301	E081	49235
chr13	37395915	37395979	E082	47938
chr13	37397002	37397132	E082	49025
chr13	37397144	37397184	E082	49167
chr13	37397212	37397301	E082	49235
chr13	37397474	37397514	E082	49497

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr13	37392528	37394597	E067	44551
chr13	37392528	37394597	E068	44551
chr13	37392528	37394597	E069	44551
chr13	37392528	37394597	E070	44551
chr13	37392528	37394597	E071	44551
chr13	37392528	37394597	E072	44551
chr13	37392528	37394597	E073	44551
chr13	37392528	37394597	E074	44551
chr13	37392528	37394597	E082	44551