rs9834678

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SLC6A6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0119 (3584/29962,GnomAD)
C=0147 (4308/29118,TOPMED)
C=0162 (811/5008,1000G)
C=0058 (222/3854,ALSPAC)
C=0060 (221/3708,TWINSUK)

Position: chr3:14475607 (GRCh38.p7) (3p25.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 392 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.14475607T>C
GRCh37.p13 chr 3	NC_000003.11:g.14517115T>C

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

Molecule type	Change	Amino acid[Codon]	SO Term
SLC6A6 transcript variant 2	NM_001134367.3:c.	N/A	Intron Variant
SLC6A6 transcript variant 1	NM_003043.5:c.	N/A	Intron Variant
SLC6A6 transcript variant 3	NM_001134368.3:c.	N/A	Genic Downstream Transcript Variant
SLC6A6 transcript variant 4	NR_103507.2:n.	N/A	Intron Variant
SLC6A6 transcript variant X1	XM_006713307.2:c.	N/A	Intron Variant
SLC6A6 transcript variant X2	XM_011534030.2:c.	N/A	Intron Variant
SLC6A6 transcript variant X4	XM_011534031.2:c.	N/A	Intron Variant
SLC6A6 transcript variant X5	XR_427286.2:n.	N/A	Intron Variant
SLC6A6 transcript variant X3	XR_940495.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.700	C=0.300
1000Genomes	American	Sub	694	T=0.940	C=0.060
1000Genomes	East Asian	Sub	1008	T=0.836	C=0.164
1000Genomes	Europe	Sub	1006	T=0.942	C=0.058
1000Genomes	Global	Study-wide	5008	T=0.838	C=0.162
1000Genomes	South Asian	Sub	978	T=0.850	C=0.150
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.942	C=0.058
The Genome Aggregation Database	African	Sub	8710	T=0.736	C=0.264
The Genome Aggregation Database	American	Sub	838	T=0.930	C=0.070
The Genome Aggregation Database	East Asian	Sub	1620	T=0.853	C=0.147
The Genome Aggregation Database	Europe	Sub	18492	T=0.948	C=0.051
The Genome Aggregation Database	Global	Study-wide	29962	T=0.880	C=0.119
The Genome Aggregation Database	Other	Sub	302	T=0.920	C=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.852	C=0.147
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.940	C=0.060

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs9834678	0.000056	alcohol dependence	20201924
rs9834678	0.0000565	alcoholism	pha002893
rs9834678	0.00025	alcohol dependence(early age of onset)	20201924

eQTL of rs9834678 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 rs9834678 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 )
chr3	14472636	14475032	E067	-42083
chr3	14475200	14476695	E067	-40420
chr3	14476959	14477550	E067	-39565
chr3	14477722	14478031	E067	-39084
chr3	14478143	14478565	E067	-38550
chr3	14480420	14480478	E067	-36637
chr3	14480614	14480676	E067	-36439
chr3	14480757	14480851	E067	-36264
chr3	14480880	14481468	E067	-35647
chr3	14481738	14481949	E067	-35166
chr3	14482042	14482400	E067	-34715
chr3	14482519	14482866	E067	-34249
chr3	14483054	14483104	E067	-34011
chr3	14483164	14483347	E067	-33768
chr3	14483351	14483486	E067	-33629
chr3	14483547	14483698	E067	-33417
chr3	14483790	14483840	E067	-33275
chr3	14484088	14484138	E067	-32977
chr3	14484357	14484469	E067	-32646
chr3	14490318	14490456	E067	-26659
chr3	14490668	14490807	E067	-26308
chr3	14490869	14491069	E067	-26046
chr3	14493183	14493247	E067	-23868
chr3	14493276	14493453	E067	-23662
chr3	14493460	14495149	E067	-21966
chr3	14495225	14495659	E067	-21456
chr3	14495735	14495789	E067	-21326
chr3	14495806	14496177	E067	-20938
chr3	14496229	14496396	E067	-20719
chr3	14496473	14496537	E067	-20578
chr3	14496574	14496646	E067	-20469
chr3	14496660	14496814	E067	-20301
chr3	14496866	14496937	E067	-20178
chr3	14497168	14497364	E067	-19751
chr3	14502148	14502555	E067	-14560
chr3	14503000	14503054	E067	-14061
chr3	14503107	14503267	E067	-13848
chr3	14503287	14503532	E067	-13583
chr3	14503601	14503701	E067	-13414
chr3	14467126	14467185	E068	-49930
chr3	14467385	14467966	E068	-49149
chr3	14468677	14468727	E068	-48388
chr3	14468733	14468845	E068	-48270
chr3	14468990	14469057	E068	-48058
chr3	14469334	14469411	E068	-47704
chr3	14469462	14469524	E068	-47591
chr3	14472350	14472454	E068	-44661
chr3	14472636	14475032	E068	-42083
chr3	14475200	14476695	E068	-40420
chr3	14476759	14476847	E068	-40268
chr3	14476959	14477550	E068	-39565
chr3	14477722	14478031	E068	-39084
chr3	14478143	14478565	E068	-38550
chr3	14480191	14480247	E068	-36868
chr3	14480303	14480366	E068	-36749
chr3	14480420	14480478	E068	-36637
chr3	14480614	14480676	E068	-36439
chr3	14480757	14480851	E068	-36264
chr3	14480880	14481468	E068	-35647
chr3	14481738	14481949	E068	-35166
chr3	14482042	14482400	E068	-34715
chr3	14482519	14482866	E068	-34249
chr3	14483054	14483104	E068	-34011
chr3	14483164	14483347	E068	-33768
chr3	14483351	14483486	E068	-33629
chr3	14483547	14483698	E068	-33417
chr3	14490318	14490456	E068	-26659
chr3	14490668	14490807	E068	-26308
chr3	14490869	14491069	E068	-26046
chr3	14492774	14493110	E068	-24005
chr3	14493183	14493247	E068	-23868
chr3	14493276	14493453	E068	-23662
chr3	14493460	14495149	E068	-21966
chr3	14495225	14495659	E068	-21456
chr3	14495735	14495789	E068	-21326
chr3	14495806	14496177	E068	-20938
chr3	14496229	14496396	E068	-20719
chr3	14496473	14496537	E068	-20578
chr3	14496574	14496646	E068	-20469
chr3	14496660	14496814	E068	-20301
chr3	14496866	14496937	E068	-20178
chr3	14497168	14497364	E068	-19751
chr3	14501625	14501711	E068	-15404
chr3	14501752	14502058	E068	-15057
chr3	14502148	14502555	E068	-14560
chr3	14503000	14503054	E068	-14061
chr3	14523439	14523499	E068	6324
chr3	14523538	14523603	E068	6423
chr3	14523651	14523828	E068	6536
chr3	14469662	14470158	E069	-46957
chr3	14470161	14470211	E069	-46904
chr3	14470302	14470402	E069	-46713
chr3	14470596	14470646	E069	-46469
chr3	14470816	14471083	E069	-46032
chr3	14471194	14471332	E069	-45783
chr3	14472350	14472454	E069	-44661
chr3	14472636	14475032	E069	-42083
chr3	14475200	14476695	E069	-40420
chr3	14476759	14476847	E069	-40268
chr3	14476959	14477550	E069	-39565
chr3	14477722	14478031	E069	-39084
chr3	14478143	14478565	E069	-38550
chr3	14480191	14480247	E069	-36868
chr3	14480303	14480366	E069	-36749
chr3	14480420	14480478	E069	-36637
chr3	14480614	14480676	E069	-36439
chr3	14480757	14480851	E069	-36264
chr3	14480880	14481468	E069	-35647
chr3	14481738	14481949	E069	-35166
chr3	14482042	14482400	E069	-34715
chr3	14482519	14482866	E069	-34249
chr3	14483054	14483104	E069	-34011
chr3	14483164	14483347	E069	-33768
chr3	14483351	14483486	E069	-33629
chr3	14483547	14483698	E069	-33417
chr3	14483790	14483840	E069	-33275
chr3	14484088	14484138	E069	-32977
chr3	14490318	14490456	E069	-26659
chr3	14490668	14490807	E069	-26308
chr3	14490869	14491069	E069	-26046
chr3	14493276	14493453	E069	-23662
chr3	14493460	14495149	E069	-21966
chr3	14495225	14495659	E069	-21456
chr3	14495735	14495789	E069	-21326
chr3	14495806	14496177	E069	-20938
chr3	14496229	14496396	E069	-20719
chr3	14496473	14496537	E069	-20578
chr3	14496574	14496646	E069	-20469
chr3	14496660	14496814	E069	-20301
chr3	14496866	14496937	E069	-20178
chr3	14502148	14502555	E069	-14560
chr3	14503000	14503054	E069	-14061
chr3	14503107	14503267	E069	-13848
chr3	14503287	14503532	E069	-13583
chr3	14503601	14503701	E069	-13414
chr3	14550360	14550939	E069	33245
chr3	14550960	14551052	E069	33845
chr3	14480191	14480247	E070	-36868
chr3	14480303	14480366	E070	-36749
chr3	14480420	14480478	E070	-36637
chr3	14480614	14480676	E070	-36439
chr3	14480757	14480851	E070	-36264
chr3	14480880	14481468	E070	-35647
chr3	14481738	14481949	E070	-35166
chr3	14482519	14482866	E070	-34249
chr3	14483054	14483104	E070	-34011
chr3	14483164	14483347	E070	-33768
chr3	14493276	14493453	E070	-23662
chr3	14493460	14495149	E070	-21966
chr3	14497168	14497364	E070	-19751
chr3	14550960	14551052	E070	33845
chr3	14552846	14552896	E070	35731
chr3	14553255	14553436	E070	36140
chr3	14553558	14553608	E070	36443
chr3	14468733	14468845	E071	-48270
chr3	14468990	14469057	E071	-48058
chr3	14469334	14469411	E071	-47704
chr3	14469462	14469524	E071	-47591
chr3	14469662	14470158	E071	-46957
chr3	14470161	14470211	E071	-46904
chr3	14470302	14470402	E071	-46713
chr3	14470596	14470646	E071	-46469
chr3	14470816	14471083	E071	-46032
chr3	14471194	14471332	E071	-45783
chr3	14471360	14471434	E071	-45681
chr3	14472350	14472454	E071	-44661
chr3	14472636	14475032	E071	-42083
chr3	14475200	14476695	E071	-40420
chr3	14477722	14478031	E071	-39084
chr3	14478143	14478565	E071	-38550
chr3	14480191	14480247	E071	-36868
chr3	14480303	14480366	E071	-36749
chr3	14480420	14480478	E071	-36637
chr3	14480614	14480676	E071	-36439
chr3	14480757	14480851	E071	-36264
chr3	14480880	14481468	E071	-35647
chr3	14481738	14481949	E071	-35166
chr3	14482042	14482400	E071	-34715
chr3	14482519	14482866	E071	-34249
chr3	14483054	14483104	E071	-34011
chr3	14483164	14483347	E071	-33768
chr3	14483351	14483486	E071	-33629
chr3	14483547	14483698	E071	-33417
chr3	14490318	14490456	E071	-26659
chr3	14490668	14490807	E071	-26308
chr3	14490869	14491069	E071	-26046
chr3	14493276	14493453	E071	-23662
chr3	14493460	14495149	E071	-21966
chr3	14495225	14495659	E071	-21456
chr3	14495735	14495789	E071	-21326
chr3	14495806	14496177	E071	-20938
chr3	14496229	14496396	E071	-20719
chr3	14496473	14496537	E071	-20578
chr3	14496574	14496646	E071	-20469
chr3	14496660	14496814	E071	-20301
chr3	14496866	14496937	E071	-20178
chr3	14497168	14497364	E071	-19751
chr3	14497505	14497574	E071	-19541
chr3	14501752	14502058	E071	-15057
chr3	14502148	14502555	E071	-14560
chr3	14503000	14503054	E071	-14061
chr3	14503107	14503267	E071	-13848
chr3	14503287	14503532	E071	-13583
chr3	14503601	14503701	E071	-13414
chr3	14470596	14470646	E072	-46469
chr3	14470816	14471083	E072	-46032
chr3	14472350	14472454	E072	-44661
chr3	14472636	14475032	E072	-42083
chr3	14475200	14476695	E072	-40420
chr3	14476759	14476847	E072	-40268
chr3	14476959	14477550	E072	-39565
chr3	14477722	14478031	E072	-39084
chr3	14478143	14478565	E072	-38550
chr3	14480191	14480247	E072	-36868
chr3	14480303	14480366	E072	-36749
chr3	14480420	14480478	E072	-36637
chr3	14480614	14480676	E072	-36439
chr3	14480757	14480851	E072	-36264
chr3	14480880	14481468	E072	-35647
chr3	14481738	14481949	E072	-35166
chr3	14482042	14482400	E072	-34715
chr3	14482519	14482866	E072	-34249
chr3	14483054	14483104	E072	-34011
chr3	14483164	14483347	E072	-33768
chr3	14483351	14483486	E072	-33629
chr3	14483547	14483698	E072	-33417
chr3	14483790	14483840	E072	-33275
chr3	14484088	14484138	E072	-32977
chr3	14490318	14490456	E072	-26659
chr3	14490668	14490807	E072	-26308
chr3	14490869	14491069	E072	-26046
chr3	14492655	14492740	E072	-24375
chr3	14492774	14493110	E072	-24005
chr3	14493183	14493247	E072	-23868
chr3	14493276	14493453	E072	-23662
chr3	14493460	14495149	E072	-21966
chr3	14495225	14495659	E072	-21456
chr3	14495735	14495789	E072	-21326
chr3	14495806	14496177	E072	-20938
chr3	14496229	14496396	E072	-20719
chr3	14496574	14496646	E072	-20469
chr3	14496660	14496814	E072	-20301
chr3	14496866	14496937	E072	-20178
chr3	14497168	14497364	E072	-19751
chr3	14501752	14502058	E072	-15057
chr3	14502148	14502555	E072	-14560
chr3	14503000	14503054	E072	-14061
chr3	14503107	14503267	E072	-13848
chr3	14503287	14503532	E072	-13583
chr3	14510255	14510305	E072	-6810
chr3	14470302	14470402	E073	-46713
chr3	14472636	14475032	E073	-42083
chr3	14475200	14476695	E073	-40420
chr3	14476759	14476847	E073	-40268
chr3	14476959	14477550	E073	-39565
chr3	14478143	14478565	E073	-38550
chr3	14480191	14480247	E073	-36868
chr3	14480303	14480366	E073	-36749
chr3	14480420	14480478	E073	-36637
chr3	14480614	14480676	E073	-36439
chr3	14480757	14480851	E073	-36264
chr3	14480880	14481468	E073	-35647
chr3	14481738	14481949	E073	-35166
chr3	14482042	14482400	E073	-34715
chr3	14482519	14482866	E073	-34249
chr3	14483054	14483104	E073	-34011
chr3	14483164	14483347	E073	-33768
chr3	14483351	14483486	E073	-33629
chr3	14483547	14483698	E073	-33417
chr3	14490318	14490456	E073	-26659
chr3	14493460	14495149	E073	-21966
chr3	14495225	14495659	E073	-21456
chr3	14495735	14495789	E073	-21326
chr3	14495806	14496177	E073	-20938
chr3	14496229	14496396	E073	-20719
chr3	14496473	14496537	E073	-20578
chr3	14496574	14496646	E073	-20469
chr3	14502148	14502555	E073	-14560
chr3	14503000	14503054	E073	-14061
chr3	14503107	14503267	E073	-13848
chr3	14503287	14503532	E073	-13583
chr3	14503601	14503701	E073	-13414
chr3	14529478	14529525	E073	12363
chr3	14550360	14550939	E073	33245
chr3	14550960	14551052	E073	33845
chr3	14469334	14469411	E074	-47704
chr3	14469462	14469524	E074	-47591
chr3	14469662	14470158	E074	-46957
chr3	14470161	14470211	E074	-46904
chr3	14470302	14470402	E074	-46713
chr3	14470596	14470646	E074	-46469
chr3	14470816	14471083	E074	-46032
chr3	14471194	14471332	E074	-45783
chr3	14471360	14471434	E074	-45681
chr3	14471548	14471708	E074	-45407
chr3	14471755	14471903	E074	-45212
chr3	14472350	14472454	E074	-44661
chr3	14472636	14475032	E074	-42083
chr3	14475200	14476695	E074	-40420
chr3	14476759	14476847	E074	-40268
chr3	14476959	14477550	E074	-39565
chr3	14477722	14478031	E074	-39084
chr3	14478143	14478565	E074	-38550
chr3	14480191	14480247	E074	-36868
chr3	14480303	14480366	E074	-36749
chr3	14480420	14480478	E074	-36637
chr3	14480614	14480676	E074	-36439
chr3	14480757	14480851	E074	-36264
chr3	14480880	14481468	E074	-35647
chr3	14481738	14481949	E074	-35166
chr3	14482042	14482400	E074	-34715
chr3	14482519	14482866	E074	-34249
chr3	14483054	14483104	E074	-34011
chr3	14483164	14483347	E074	-33768
chr3	14483351	14483486	E074	-33629
chr3	14483547	14483698	E074	-33417
chr3	14483790	14483840	E074	-33275
chr3	14490318	14490456	E074	-26659
chr3	14490668	14490807	E074	-26308
chr3	14490869	14491069	E074	-26046
chr3	14493183	14493247	E074	-23868
chr3	14493276	14493453	E074	-23662
chr3	14493460	14495149	E074	-21966
chr3	14495225	14495659	E074	-21456
chr3	14495735	14495789	E074	-21326
chr3	14495806	14496177	E074	-20938
chr3	14496229	14496396	E074	-20719
chr3	14496473	14496537	E074	-20578
chr3	14496574	14496646	E074	-20469
chr3	14496660	14496814	E074	-20301
chr3	14496866	14496937	E074	-20178
chr3	14497168	14497364	E074	-19751
chr3	14501752	14502058	E074	-15057
chr3	14502148	14502555	E074	-14560
chr3	14503000	14503054	E074	-14061
chr3	14503107	14503267	E074	-13848
chr3	14503287	14503532	E074	-13583
chr3	14503601	14503701	E074	-13414
chr3	14509507	14509817	E074	-7298
chr3	14475200	14476695	E081	-40420
chr3	14476759	14476847	E081	-40268
chr3	14480191	14480247	E081	-36868
chr3	14480303	14480366	E081	-36749
chr3	14480420	14480478	E081	-36637
chr3	14480614	14480676	E081	-36439
chr3	14480757	14480851	E081	-36264
chr3	14480880	14481468	E081	-35647
chr3	14481738	14481949	E081	-35166
chr3	14482042	14482400	E081	-34715
chr3	14482519	14482866	E081	-34249
chr3	14483054	14483104	E081	-34011
chr3	14483164	14483347	E081	-33768
chr3	14493276	14493453	E081	-23662
chr3	14493460	14495149	E081	-21966
chr3	14495225	14495659	E081	-21456
chr3	14495735	14495789	E081	-21326
chr3	14495806	14496177	E081	-20938
chr3	14496229	14496396	E081	-20719
chr3	14496473	14496537	E081	-20578
chr3	14496574	14496646	E081	-20469
chr3	14496660	14496814	E081	-20301
chr3	14496866	14496937	E081	-20178
chr3	14497168	14497364	E081	-19751
chr3	14502148	14502555	E081	-14560
chr3	14528303	14528427	E081	11188
chr3	14528779	14528823	E081	11664
chr3	14528917	14529037	E081	11802
chr3	14529039	14529100	E081	11924
chr3	14529147	14529227	E081	12032
chr3	14529336	14529380	E081	12221
chr3	14529478	14529525	E081	12363
chr3	14529693	14529751	E081	12578
chr3	14529798	14529886	E081	12683
chr3	14530004	14530121	E081	12889
chr3	14530190	14530691	E081	13075
chr3	14531005	14531143	E081	13890
chr3	14531371	14531441	E081	14256
chr3	14475200	14476695	E082	-40420
chr3	14480191	14480247	E082	-36868
chr3	14480303	14480366	E082	-36749
chr3	14480420	14480478	E082	-36637
chr3	14480614	14480676	E082	-36439
chr3	14480757	14480851	E082	-36264
chr3	14480880	14481468	E082	-35647
chr3	14482519	14482866	E082	-34249
chr3	14493460	14495149	E082	-21966
chr3	14495225	14495659	E082	-21456
chr3	14495735	14495789	E082	-21326
chr3	14495806	14496177	E082	-20938
chr3	14496229	14496396	E082	-20719
chr3	14496473	14496537	E082	-20578
chr3	14496574	14496646	E082	-20469