rs11961117

Homo sapiens
G>A
TDRD6 : 2KB Upstream Variant
LOC101926934 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0074 (2178/29118,TOPMED)
A=0101 (2906/28766,GnomAD)
A=0092 (461/5008,1000G)
A=0141 (543/3854,ALSPAC)
A=0139 (516/3708,TWINSUK)
chr6:46686509 (GRCh38.p7) (6p12.3)
AD
GWASdb2
1   publication(s)
See rs on genome
14 Enhancers around
50 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 6NC_000006.12:g.46686509G>A
GRCh37.p13 chr 6NC_000006.11:g.46654246G>A

Gene: TDRD6, tudor domain containing 6(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
TDRD6 transcript variant 1NM_001010870.2:c.N/AUpstream Transcript Variant
TDRD6 transcript variant 2NM_001168359.1:c.N/AUpstream Transcript Variant

Gene: LOC101926934, uncharacterized LOC101926934(minus strand)

Molecule type Change Amino acid[Codon] SO Term
LOC101926934 transcript variant 1NR_134642.1:n.N/AIntron Variant
LOC101926934 transcript variant 2NR_134643.1:n.N/AIntron Variant
LOC101926934 transcript variant 3NR_134644.1:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.995A=0.005
1000GenomesAmericanSub694G=0.900A=0.100
1000GenomesEast AsianSub1008G=0.887A=0.113
1000GenomesEuropeSub1006G=0.873A=0.127
1000GenomesGlobalStudy-wide5008G=0.908A=0.092
1000GenomesSouth AsianSub978G=0.850A=0.150
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.859A=0.141
The Genome Aggregation DatabaseAfricanSub8558G=0.975A=0.025
The Genome Aggregation DatabaseAmericanSub716G=0.910A=0.090
The Genome Aggregation DatabaseEast AsianSub1610G=0.899A=0.101
The Genome Aggregation DatabaseEuropeSub17582G=0.864A=0.136
The Genome Aggregation DatabaseGlobalStudy-wide28766G=0.899A=0.101
The Genome Aggregation DatabaseOtherSub300G=0.760A=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.925A=0.074
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.861A=0.139
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
rs119611170.00084alcohol dependence20201924

eQTL of rs11961117 in Brain tissues (GTEx Analysis Release V7)

Position (v37) eGene GeneID Variant p-value TSS Tissue
Chr6:46654246SLC25A27ENSG00000153291.11G>A2.7425e-2133568Cerebellum
Chr6:46654246TDRD6ENSG00000180113.11G>A5.8864e-22-1366Cerebellum
Chr6:46654246SLC25A27ENSG00000153291.11G>A7.8680e-2533568Cortex
Chr6:46654246SLC25A27ENSG00000153291.11G>A7.8290e-2133568Caudate_basal_ganglia

meQTL of rs11961117 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 )
chr64662921446629520E068-24726
chr64667245646672670E06818210
chr64668691646687132E06832670
chr64664197046642744E069-11502
chr64664480846644913E070-9333
chr64664491546645010E070-9236
chr64664506646645253E070-8993
chr64664144146641555E071-12691
chr64664197046642744E071-11502
chr64667245646672670E07318210
chr64664197046642744E074-11502
chr64660490446605279E081-48967
chr64664480846644913E082-9333
chr64664491546645010E082-9236








Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr64661939746621871E067-32375
chr64662211146622173E067-32073
chr64670167946702160E06747433
chr64670221046702345E06747964
chr64670237046702461E06748124
chr64670249646703621E06748250
chr64661939746621871E068-32375
chr64662211146622173E068-32073
chr64662292846622978E068-31268
chr64670221046702345E06847964
chr64670237046702461E06848124
chr64670249646703621E06848250
chr64661939746621871E069-32375
chr64670221046702345E06947964
chr64670237046702461E06948124
chr64670249646703621E06948250
chr64661939746621871E070-32375
chr64670221046702345E07047964
chr64670237046702461E07048124
chr64670249646703621E07048250
chr64661939746621871E071-32375
chr64662211146622173E071-32073
chr64670167946702160E07147433
chr64670221046702345E07147964
chr64670237046702461E07148124
chr64670249646703621E07148250
chr64661939746621871E072-32375
chr64662211146622173E072-32073
chr64662292846622978E072-31268
chr64670221046702345E07247964
chr64670237046702461E07248124
chr64670249646703621E07248250
chr64661939746621871E073-32375
chr64662211146622173E073-32073
chr64662292846622978E073-31268
chr64670221046702345E07347964
chr64670237046702461E07348124
chr64670249646703621E07348250
chr64661939746621871E074-32375
chr64670221046702345E07447964
chr64670237046702461E07448124
chr64670249646703621E07448250
chr64661878146619076E081-35170
chr64661919846619260E081-34986
chr64661939746621871E081-32375
chr64661939746621871E082-32375
chr64662211146622173E082-32073
chr64670221046702345E08247964
chr64670237046702461E08248124
chr64670249646703621E08248250