rs2289128

Homo sapiens
G>A / G>C
SLC6A6 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0061 (1851/29936,GnomAD)
A=0063 (1859/29118,TOPMED)
G==0064 (843/13006,GO-ESP)
A=0104 (522/5008,1000G)
A=0054 (210/3854,ALSPAC)
A=0055 (205/3708,TWINSUK)
chr3:14472187 (GRCh38.p7) (3p25.1)
AD
GWASdb2
1   publication(s)
See rs on genome
109 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.14472187G>A
GRCh38.p7 chr 3NC_000003.12:g.14472187G>C
GRCh37.p13 chr 3NC_000003.11:g.14513695G>A
GRCh37.p13 chr 3NC_000003.11:g.14513695G>C

Gene: SLC6A6, solute carrier family 6 member 6(plus strand)

Molecule type Change Amino acid[Codon] SO Term
SLC6A6 transcript variant 2NM_001134367.3:c.N/AIntron Variant
SLC6A6 transcript variant 1NM_003043.5:c.N/AIntron Variant
SLC6A6 transcript variant 3NM_001134368.3:c.N/AGenic Downstream Transcript Variant
SLC6A6 transcript variant 4NR_103507.2:n.N/AIntron Variant
SLC6A6 transcript variant X1XM_006713307.2:c.N/AIntron Variant
SLC6A6 transcript variant X2XM_011534030.2:c.N/AIntron Variant
SLC6A6 transcript variant X4XM_011534031.2:c.N/AIntron Variant
SLC6A6 transcript variant X5XR_427286.2:n.N/AIntron Variant
SLC6A6 transcript variant X3XR_940495.2:n.N/AIntron Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322G=0.908A=0.092
1000GenomesAmericanSub694G=0.960A=0.040
1000GenomesEast AsianSub1008G=0.839A=0.161
1000GenomesEuropeSub1006G=0.951A=0.049
1000GenomesGlobalStudy-wide5008G=0.896A=0.104
1000GenomesSouth AsianSub978G=0.840A=0.160
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854G=0.946A=0.054
The Genome Aggregation DatabaseAfricanSub8704G=0.919A=0.081
The Genome Aggregation DatabaseAmericanSub838G=0.940A=0.060
The Genome Aggregation DatabaseEast AsianSub1616G=0.849A=0.151
The Genome Aggregation DatabaseEuropeSub18476G=0.955A=0.044
The Genome Aggregation DatabaseGlobalStudy-wide29936G=0.938A=0.061
The Genome Aggregation DatabaseOtherSub302G=0.920A=0.080
Trans-Omics for Precision MedicineGlobalStudy-wide29118G=0.936A=0.063
UK 10K study - TwinsTWIN COHORTStudy-wide3708G=0.945A=0.055
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
rs22891280.00022alcohol dependence(early age of onset)20201924
rs22891280.0004alcohol dependence20201924

eQTL of rs2289128 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 rs2289128 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 )
chr3104810105451E067-29932
chr3114174114280E067-21103
chr3114437114799E067-20584
chr3141018141128E0675635
chr3114174114280E068-21103
chr3114437114799E068-20584
chr3114802115003E068-20380
chr3115137115254E068-20129
chr3115361115440E068-19943
chr3139390139586E0684007
chr3139704139834E0684321
chr3141018141128E0685635
chr3141277141526E0685894
chr3104810105451E069-29932
chr3105525105633E069-29750
chr3114174114280E069-21103
chr3114437114799E069-20584
chr3114802115003E069-20380
chr3115137115254E069-20129
chr3115361115440E069-19943
chr3141018141128E0695635
chr3114174114280E070-21103
chr3114437114799E070-20584
chr3114802115003E070-20380
chr3115137115254E070-20129
chr3115361115440E070-19943
chr3116283116363E070-19020
chr3116414116901E070-18482
chr3117032117204E070-18179
chr3117319117416E070-17967
chr3117466117544E070-17839
chr3123630123786E070-11597
chr3123847123912E070-11471
chr3124839125153E070-10230
chr3139183139333E0703800
chr3139390139586E0704007
chr3139704139834E0704321
chr3142138142206E0706755
chr3144310144411E0708927
chr3145812145986E07010429
chr3152159152209E07016776
chr3152592152664E07017209
chr3152974153132E07017591
chr3153343153416E07017960
chr3173051173150E07037668
chr3173301173444E07037918
chr3104810105451E071-29932
chr3105525105633E071-29750
chr3114174114280E071-21103
chr3114437114799E071-20584
chr3114802115003E071-20380
chr3115137115254E071-20129
chr3141018141128E0715635
chr3141277141526E0715894
chr3105525105633E072-29750
chr3114174114280E072-21103
chr3114437114799E072-20584
chr3114802115003E072-20380
chr3115137115254E072-20129
chr3115361115440E072-19943
chr3141018141128E0725635
chr3141018141128E0735635
chr3141277141526E0735894
chr3142138142206E0736755
chr3111467111643E074-23740
chr3114437114799E074-20584
chr3114802115003E074-20380
chr3115137115254E074-20129
chr3115361115440E074-19943
chr3141018141128E0745635
chr3141277141526E0745894
chr38610586168E081-49215
chr3104810105451E081-29932
chr3105525105633E081-29750
chr3114437114799E081-20584
chr3114802115003E081-20380
chr3115137115254E081-20129
chr3115361115440E081-19943
chr3123630123786E081-11597
chr3139183139333E0813800
chr3139390139586E0814007
chr3139704139834E0814321
chr3141018141128E0815635
chr3141277141526E0815894
chr3164584164709E08129201
chr3173051173150E08137668
chr3173301173444E08137918
chr3104810105451E082-29932
chr3105525105633E082-29750
chr3114437114799E082-20584
chr3114802115003E082-20380
chr3115137115254E082-20129
chr3115361115440E082-19943
chr3117032117204E082-18179
chr3117319117416E082-17967
chr3117466117544E082-17839
chr3139183139333E0823800
chr3139390139586E0824007
chr3139704139834E0824321
chr3141018141128E0825635
chr3141277141526E0825894
chr3142138142206E0826755
chr3152974153132E08217591
chr3153343153416E08217960
chr3164433164483E08229050
chr3164584164709E08229201
chr3173051173150E08237668
chr3173301173444E08237918
chr3182518182753E08247135