SNP Detail Info-rs11150542

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

CDH13 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0413 (12293/29752,GnomAD)
A=0359 (10480/29118,TOPMED)
A=0381 (1907/5008,1000G)
G==0496 (1912/3854,ALSPAC)
G==0477 (1769/3708,TWINSUK)

Position: chr16:83123514 (GRCh38.p7) (16q23.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 40 Enhancers around

Promoter: 9 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 16	NC_000016.10:g.83123514G>A
GRCh37.p13 chr 16	NC_000016.9:g.83157119G>A

Molecule type	Change	Amino acid[Codon]	SO Term
CDH13 transcript variant 2	NM_001220488.1:c.	N/A	Intron Variant
CDH13 transcript variant 3	NM_001220489.1:c.	N/A	Intron Variant
CDH13 transcript variant 4	NM_001220490.1:c.	N/A	Intron Variant
CDH13 transcript variant 5	NM_001220491.1:c.	N/A	Intron Variant
CDH13 transcript variant 6	NM_001220492.1:c.	N/A	Intron Variant
CDH13 transcript variant 1	NM_001257.4:c.	N/A	Intron Variant
CDH13 transcript variant X1	XM_011522804.2:c.	N/A	Intron Variant
CDH13 transcript variant X2	XM_017022848.1:c.	N/A	Intron Variant
CDH13 transcript variant X3	XM_017022849.1:c.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.840	A=0.160
1000Genomes	American	Sub	694	G=0.450	A=0.550
1000Genomes	East Asian	Sub	1008	G=0.601	A=0.399
1000Genomes	Europe	Sub	1006	G=0.481	A=0.519
1000Genomes	Global	Study-wide	5008	G=0.619	A=0.381
1000Genomes	South Asian	Sub	978	G=0.600	A=0.400
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.496	A=0.504
The Genome Aggregation Database	African	Sub	8682	G=0.807	A=0.193
The Genome Aggregation Database	American	Sub	828	G=0.390	A=0.610
The Genome Aggregation Database	East Asian	Sub	1602	G=0.571	A=0.429
The Genome Aggregation Database	Europe	Sub	18338	G=0.491	A=0.508
The Genome Aggregation Database	Global	Study-wide	29752	G=0.586	A=0.413
The Genome Aggregation Database	Other	Sub	302	G=0.680	A=0.320
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.640	A=0.359
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.477	A=0.523

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

SNP ID	p-value	Traits	Study
rs11150542	2.21E-05	alcohol consumption	23743675

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr16	83147514	83147727	E068	-9392
chr16	83172325	83172440	E068	15206
chr16	83172585	83172635	E068	15466
chr16	83179665	83179715	E068	22546
chr16	83179934	83179978	E068	22815
chr16	83180103	83180174	E068	22984
chr16	83147022	83147275	E069	-9844
chr16	83147514	83147727	E069	-9392
chr16	83148409	83148685	E069	-8434
chr16	83168460	83168510	E069	11341
chr16	83170459	83170699	E069	13340
chr16	83177330	83177916	E069	20211
chr16	83147022	83147275	E071	-9844
chr16	83168696	83168785	E071	11577
chr16	83170459	83170699	E071	13340
chr16	83177330	83177916	E071	20211
chr16	83179665	83179715	E071	22546
chr16	83179934	83179978	E071	22815
chr16	83180103	83180174	E071	22984
chr16	83147022	83147275	E072	-9844
chr16	83147514	83147727	E072	-9392
chr16	83170459	83170699	E072	13340
chr16	83172325	83172440	E072	15206
chr16	83179665	83179715	E072	22546
chr16	83179934	83179978	E072	22815
chr16	83180103	83180174	E072	22984
chr16	83147022	83147275	E074	-9844
chr16	83168460	83168510	E074	11341
chr16	83168696	83168785	E074	11577
chr16	83177330	83177916	E074	20211
chr16	83179934	83179978	E074	22815
chr16	83180103	83180174	E074	22984
chr16	83108271	83108371	E081	-48748
chr16	83108642	83108692	E081	-48427
chr16	83109065	83109305	E081	-47814
chr16	83109344	83110439	E081	-46680
chr16	83116655	83116748	E081	-40371
chr16	83116816	83117356	E081	-39763
chr16	83109065	83109305	E082	-47814
chr16	83116655	83116748	E082	-40371

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr16	83170734	83171415	E067	13615
chr16	83170734	83171415	E068	13615
chr16	83170734	83171415	E069	13615
chr16	83170734	83171415	E071	13615
chr16	83171449	83171780	E071	14330
chr16	83170734	83171415	E072	13615
chr16	83171449	83171780	E072	14330
chr16	83170734	83171415	E074	13615
chr16	83171449	83171780	E074	14330

rs11150542