rs6708498

Homo sapiens
C>T
LOC105373612 : Non Coding Transcript Variant
LOC151121 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
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)
chr2:129244613 (GRCh38.p7) (2q21.1)
AD
GWASdb2
1   publication(s)
See rs on genome
20 Enhancers around
0 Promoter around

Genomic Coordinates

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

Gene: LOC151121, uncharacterized LOC151121(minus strand)

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

Gene: LOC105373612, uncharacterized LOC105373612(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC105373612 transcriptXR_001739709.1:n....XR_001739709.1:n.251C>TC>TNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.960T=0.040
1000GenomesAmericanSub694C=0.710T=0.290
1000GenomesEast AsianSub1008C=0.836T=0.164
1000GenomesEuropeSub1006C=0.493T=0.507
1000GenomesGlobalStudy-wide5008C=0.759T=0.241
1000GenomesSouth AsianSub978C=0.710T=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.504T=0.496
The Genome Aggregation DatabaseAfricanSub8702C=0.901T=0.099
The Genome Aggregation DatabaseAmericanSub836C=0.710T=0.290
The Genome Aggregation DatabaseEast AsianSub1618C=0.865T=0.135
The Genome Aggregation DatabaseEuropeSub18442C=0.507T=0.492
The Genome Aggregation DatabaseGlobalStudy-wide29898C=0.646T=0.353
The Genome Aggregation DatabaseOtherSub300C=0.440T=0.560
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.696T=0.303
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.516T=0.484
PMID Title Author Journal
24962325Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.Kapoor MDrug Alcohol Depend

P-Value

SNP ID p-value Traits Study
rs67084985.97E-06alcohol dependence (age at onset)24962325

eQTL of rs6708498 in Brain tissues (GTEx Analysis Release V7)

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

meQTL of rs6708498 in Fetal Brain

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

Genomic View

Chromatin Interaction

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

Enhancer Annotation (GRCh37.p13)

Chromosome Start End Region Distance ( -/+ : Up/Downstream )
chr2129990903129991022E070-11164
chr2129991443129991904E070-10282
chr2129990903129991022E081-11164
chr2129991443129991904E081-10282
chr2129996773129997036E081-5150
chr2130010223130010353E0818037
chr2130010398130011293E0818212
chr2130038915130039052E08136729
chr2130039472130039687E08137286
chr2130039843130039996E08137657
chr2130050579130050658E08148393
chr2130050695130050812E08148509
chr2129996773129997036E082-5150
chr2130010223130010353E0828037
chr2130038591130038845E08236405
chr2130038915130039052E08236729
chr2130039472130039687E08237286
chr2130039843130039996E08237657
chr2130050579130050658E08248393
chr2130050695130050812E08248509