SNP Detail Info-rs1177825

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC107985340 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0233 (6946/29794,GnomAD)
T=0221 (6460/29118,TOPMED)
T=0174 (871/5008,1000G)
T=0267 (1028/3854,ALSPAC)
T=0260 (964/3708,TWINSUK)

Position: chr19:49235225 (GRCh38.p7) (19q13.33)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 12 Enhancers around

Promoter: 12 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 19	NC_000019.10:g.49235225C>T
GRCh37.p13 chr 19	NC_000019.9:g.49738482C>T

Molecule type	Change	Amino acid[Codon]	SO Term
LOC107985340 transcript	XR_001753971.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.815	T=0.185
1000Genomes	American	Sub	694	C=0.800	T=0.200
1000Genomes	East Asian	Sub	1008	C=0.931	T=0.069
1000Genomes	Europe	Sub	1006	C=0.726	T=0.274
1000Genomes	Global	Study-wide	5008	C=0.826	T=0.174
1000Genomes	South Asian	Sub	978	C=0.860	T=0.140
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.733	T=0.267
The Genome Aggregation Database	African	Sub	8672	C=0.793	T=0.207
The Genome Aggregation Database	American	Sub	836	C=0.800	T=0.200
The Genome Aggregation Database	East Asian	Sub	1606	C=0.922	T=0.078
The Genome Aggregation Database	Europe	Sub	18378	C=0.738	T=0.261
The Genome Aggregation Database	Global	Study-wide	29794	C=0.766	T=0.233
The Genome Aggregation Database	Other	Sub	302	C=0.830	T=0.170
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.778	T=0.221
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.740	T=0.260

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
rs1177825	0.000485	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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr19	49700257	49700366	E069	-38116
chr19	49729167	49729214	E069	-9268
chr19	49729251	49729717	E069	-8765
chr19	49714881	49714939	E070	-23543
chr19	49699869	49700156	E071	-38326
chr19	49699869	49700156	E073	-38326
chr19	49700257	49700366	E073	-38116
chr19	49787516	49787566	E074	49034
chr19	49714881	49714939	E081	-23543
chr19	49714969	49715827	E081	-22655
chr19	49714881	49714939	E082	-23543
chr19	49714969	49715827	E082	-22655

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr19	49711007	49711567	E067	-26915
chr19	49711590	49711864	E067	-26618
chr19	49711590	49711864	E068	-26618
chr19	49711590	49711864	E069	-26618
chr19	49713247	49714444	E070	-24038
chr19	49711590	49711864	E071	-26618
chr19	49711007	49711567	E072	-26915
chr19	49711590	49711864	E072	-26618
chr19	49711590	49711864	E073	-26618
chr19	49711007	49711567	E074	-26915
chr19	49711590	49711864	E074	-26618
chr19	49713247	49714444	E074	-24038

rs1177825