rs6516643

Homo sapiens
T>C
LOC339622 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0236 (7082/29936,GnomAD)
C=0241 (7044/29118,TOPMED)
C=0311 (1557/5008,1000G)
C=0234 (903/3854,ALSPAC)
C=0222 (825/3708,TWINSUK)
chr21:24850084 (GRCh38.p7) (21q21.2)
AD
GWASdb2
1   publication(s)
See rs on genome
4 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 21NC_000021.9:g.24850084T>C
GRCh37.p13 chr 21NC_000021.8:g.26222398T>C

Gene: LOC339622, uncharacterized LOC339622(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LINC01692 transcriptNR_046198.3:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.822C=0.178
1000GenomesAmericanSub694T=0.540C=0.460
1000GenomesEast AsianSub1008T=0.510C=0.490
1000GenomesEuropeSub1006T=0.780C=0.220
1000GenomesGlobalStudy-wide5008T=0.689C=0.311
1000GenomesSouth AsianSub978T=0.710C=0.290
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.766C=0.234
The Genome Aggregation DatabaseAfricanSub8702T=0.798C=0.202
The Genome Aggregation DatabaseAmericanSub838T=0.520C=0.480
The Genome Aggregation DatabaseEast AsianSub1618T=0.493C=0.507
The Genome Aggregation DatabaseEuropeSub18476T=0.781C=0.219
The Genome Aggregation DatabaseGlobalStudy-wide29936T=0.763C=0.236
The Genome Aggregation DatabaseOtherSub302T=0.820C=0.180
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.758C=0.241
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.778C=0.222
PMID Title Author Journal
20201924Genome-wide association study of alcohol dependence implicates a region on chromosome 11.Edenberg HJAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs65166430.00034alcohol dependence20201924

eQTL of rs6516643 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 rs6516643 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 )
chr212626858726269137E07046189
chr212626946426269514E07047066
chr212626957126269708E07047173
chr212626983926269927E07047441