SNP Detail Info-rs6756671

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

LOC105373612 : Intron Variant
LOC151121 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0389 (11665/29930,GnomAD)
A=0360 (10485/29118,TOPMED)
A=0286 (1432/5008,1000G)
A=0496 (1911/3854,ALSPAC)
A=0485 (1798/3708,TWINSUK)

Position: chr2:129249602 (GRCh38.p7) (2q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 29 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.129249602G>A
GRCh37.p13 chr 2	NC_000002.11:g.130007175G>A

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01854 transcript variant 1	NR_122040.1:n.	N/A	Intron Variant
LINC01854 transcript variant 2	NR_122041.1:n.	N/A	Intron Variant
LINC01854 transcript variant 3	NR_122042.1:n.	N/A	Intron Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373612 transcript	XR_001739709.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.812	A=0.188
1000Genomes	American	Sub	694	G=0.700	A=0.300
1000Genomes	East Asian	Sub	1008	G=0.843	A=0.157
1000Genomes	Europe	Sub	1006	G=0.495	A=0.505
1000Genomes	Global	Study-wide	5008	G=0.714	A=0.286
1000Genomes	South Asian	Sub	978	G=0.690	A=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.504	A=0.496
The Genome Aggregation Database	African	Sub	8710	G=0.778	A=0.222
The Genome Aggregation Database	American	Sub	834	G=0.700	A=0.300
The Genome Aggregation Database	East Asian	Sub	1620	G=0.863	A=0.137
The Genome Aggregation Database	Europe	Sub	18466	G=0.507	A=0.492
The Genome Aggregation Database	Global	Study-wide	29930	G=0.610	A=0.389
The Genome Aggregation Database	Other	Sub	300	G=0.450	A=0.550
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.639	A=0.360
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.515	A=0.485

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

SNP ID	p-value	Traits	Study
rs6756671	9.7E-06	alcohol dependence (age at onset)	24962325

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 )
chr2	129990903	129991022	E070	-16153
chr2	129991443	129991904	E070	-15271
chr2	130054088	130054995	E073	46913
chr2	130055135	130055241	E073	47960
chr2	130055547	130055759	E073	48372
chr2	129990903	129991022	E081	-16153
chr2	129991443	129991904	E081	-15271
chr2	129996773	129997036	E081	-10139
chr2	130010223	130010353	E081	3048
chr2	130010398	130011293	E081	3223
chr2	130038915	130039052	E081	31740
chr2	130039472	130039687	E081	32297
chr2	130039843	130039996	E081	32668
chr2	130050579	130050658	E081	43404
chr2	130050695	130050812	E081	43520
chr2	130054088	130054995	E081	46913
chr2	130055135	130055241	E081	47960
chr2	130055547	130055759	E081	48372
chr2	129996773	129997036	E082	-10139
chr2	130010223	130010353	E082	3048
chr2	130038591	130038845	E082	31416
chr2	130038915	130039052	E082	31740
chr2	130039472	130039687	E082	32297
chr2	130039843	130039996	E082	32668
chr2	130050579	130050658	E082	43404
chr2	130050695	130050812	E082	43520
chr2	130054088	130054995	E082	46913
chr2	130055135	130055241	E082	47960
chr2	130055547	130055759	E082	48372

rs6756671