SNP Detail Info-rs6708498

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

LOC105373612 : Non Coding Transcript Variant
LOC151121 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0353 (10575/29898,GnomAD)
T=0303 (8831/29118,TOPMED)
T=0241 (1208/5008,1000G)
T=0496 (1912/3854,ALSPAC)
T=0484 (1795/3708,TWINSUK)

Position: chr2:129244613 (GRCh38.p7) (2q21.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 20 Enhancers around

Promoter: 0 Promoter around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.129244613C>T
GRCh37.p13 chr 2	NC_000002.11:g.130002186C>T

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....XR_001739709.1:n.251C>T	C>T	Non Coding Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.960	T=0.040
1000Genomes	American	Sub	694	C=0.710	T=0.290
1000Genomes	East Asian	Sub	1008	C=0.836	T=0.164
1000Genomes	Europe	Sub	1006	C=0.493	T=0.507
1000Genomes	Global	Study-wide	5008	C=0.759	T=0.241
1000Genomes	South Asian	Sub	978	C=0.710	T=0.290
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.504	T=0.496
The Genome Aggregation Database	African	Sub	8702	C=0.901	T=0.099
The Genome Aggregation Database	American	Sub	836	C=0.710	T=0.290
The Genome Aggregation Database	East Asian	Sub	1618	C=0.865	T=0.135
The Genome Aggregation Database	Europe	Sub	18442	C=0.507	T=0.492
The Genome Aggregation Database	Global	Study-wide	29898	C=0.646	T=0.353
The Genome Aggregation Database	Other	Sub	300	C=0.440	T=0.560
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.696	T=0.303
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.516	T=0.484

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
rs6708498	5.97E-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	-11164
chr2	129991443	129991904	E070	-10282
chr2	129990903	129991022	E081	-11164
chr2	129991443	129991904	E081	-10282
chr2	129996773	129997036	E081	-5150
chr2	130010223	130010353	E081	8037
chr2	130010398	130011293	E081	8212
chr2	130038915	130039052	E081	36729
chr2	130039472	130039687	E081	37286
chr2	130039843	130039996	E081	37657
chr2	130050579	130050658	E081	48393
chr2	130050695	130050812	E081	48509
chr2	129996773	129997036	E082	-5150
chr2	130010223	130010353	E082	8037
chr2	130038591	130038845	E082	36405
chr2	130038915	130039052	E082	36729
chr2	130039472	130039687	E082	37286
chr2	130039843	130039996	E082	37657
chr2	130050579	130050658	E082	48393
chr2	130050695	130050812	E082	48509

rs6708498