rs12489456

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SLC6A6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0142 (4261/29886,GnomAD)
A=0117 (3414/29118,TOPMED)
A=0206 (1030/5008,1000G)
A=0179 (690/3854,ALSPAC)
A=0190 (705/3708,TWINSUK)

Position: chr3:14459666 (GRCh38.p7) (3p25.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 424 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.14459666G>A
GRCh37.p13 chr 3	NC_000003.11:g.14501174G>A

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	G=0.962	A=0.038
1000Genomes	American	Sub	694	G=0.890	A=0.110
1000Genomes	East Asian	Sub	1008	G=0.616	A=0.384
1000Genomes	Europe	Sub	1006	G=0.821	A=0.179
1000Genomes	Global	Study-wide	5008	G=0.794	A=0.206
1000Genomes	South Asian	Sub	978	G=0.660	A=0.340
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.821	A=0.179
The Genome Aggregation Database	African	Sub	8712	G=0.946	A=0.054
The Genome Aggregation Database	American	Sub	836	G=0.860	A=0.140
The Genome Aggregation Database	East Asian	Sub	1610	G=0.609	A=0.391
The Genome Aggregation Database	Europe	Sub	18426	G=0.835	A=0.164
The Genome Aggregation Database	Global	Study-wide	29886	G=0.857	A=0.142
The Genome Aggregation Database	Other	Sub	302	G=0.920	A=0.080
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.882	A=0.117
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.810	A=0.190

PMID	Title	Author	Journal
21956439	Genome-wide association study of alcohol dependence implicates KIAA0040 on chromosome 1q.	Zuo L	Neuropsychopharmacology

P-Value

SNP ID	p-value	Traits	Study
rs12489456	4E-07	alcohol dependence	21956439

eQTL of rs12489456 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:14501174	SLC6A6	ENSG00000131389.12	G>A	2.1803e-13	57098	Cerebellum
Chr3:14501174	SLC6A6	ENSG00000131389.12	G>A	8.3882e-5	57098	Cerebellar_Hemisphere

meQTL of rs12489456 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	14454341	14455584	E067	-45590
chr3	14472636	14475032	E067	-26142
chr3	14475200	14476695	E067	-24479
chr3	14476959	14477550	E067	-23624
chr3	14477722	14478031	E067	-23143
chr3	14478143	14478565	E067	-22609
chr3	14480420	14480478	E067	-20696
chr3	14480614	14480676	E067	-20498
chr3	14480757	14480851	E067	-20323
chr3	14480880	14481468	E067	-19706
chr3	14481738	14481949	E067	-19225
chr3	14482042	14482400	E067	-18774
chr3	14482519	14482866	E067	-18308
chr3	14483054	14483104	E067	-18070
chr3	14483164	14483347	E067	-17827
chr3	14483351	14483486	E067	-17688
chr3	14483547	14483698	E067	-17476
chr3	14483790	14483840	E067	-17334
chr3	14484088	14484138	E067	-17036
chr3	14484357	14484469	E067	-16705
chr3	14490318	14490456	E067	-10718
chr3	14490668	14490807	E067	-10367
chr3	14490869	14491069	E067	-10105
chr3	14493183	14493247	E067	-7927
chr3	14493276	14493453	E067	-7721
chr3	14493460	14495149	E067	-6025
chr3	14495225	14495659	E067	-5515
chr3	14495735	14495789	E067	-5385
chr3	14495806	14496177	E067	-4997
chr3	14496229	14496396	E067	-4778
chr3	14496473	14496537	E067	-4637
chr3	14496574	14496646	E067	-4528
chr3	14496660	14496814	E067	-4360
chr3	14496866	14496937	E067	-4237
chr3	14497168	14497364	E067	-3810
chr3	14502148	14502555	E067	974
chr3	14503000	14503054	E067	1826
chr3	14503107	14503267	E067	1933
chr3	14503287	14503532	E067	2113
chr3	14503601	14503701	E067	2427
chr3	14454341	14455584	E068	-45590
chr3	14456527	14456796	E068	-44378
chr3	14456800	14456872	E068	-44302
chr3	14457064	14457333	E068	-43841
chr3	14457400	14457551	E068	-43623
chr3	14457562	14457804	E068	-43370
chr3	14459895	14460091	E068	-41083
chr3	14466875	14467045	E068	-34129
chr3	14467126	14467185	E068	-33989
chr3	14467385	14467966	E068	-33208
chr3	14468677	14468727	E068	-32447
chr3	14468733	14468845	E068	-32329
chr3	14468990	14469057	E068	-32117
chr3	14469334	14469411	E068	-31763
chr3	14469462	14469524	E068	-31650
chr3	14472350	14472454	E068	-28720
chr3	14472636	14475032	E068	-26142
chr3	14475200	14476695	E068	-24479
chr3	14476759	14476847	E068	-24327
chr3	14476959	14477550	E068	-23624
chr3	14477722	14478031	E068	-23143
chr3	14478143	14478565	E068	-22609
chr3	14480191	14480247	E068	-20927
chr3	14480303	14480366	E068	-20808
chr3	14480420	14480478	E068	-20696
chr3	14480614	14480676	E068	-20498
chr3	14480757	14480851	E068	-20323
chr3	14480880	14481468	E068	-19706
chr3	14481738	14481949	E068	-19225
chr3	14482042	14482400	E068	-18774
chr3	14482519	14482866	E068	-18308
chr3	14483054	14483104	E068	-18070
chr3	14483164	14483347	E068	-17827
chr3	14483351	14483486	E068	-17688
chr3	14483547	14483698	E068	-17476
chr3	14490318	14490456	E068	-10718
chr3	14490668	14490807	E068	-10367
chr3	14490869	14491069	E068	-10105
chr3	14492774	14493110	E068	-8064
chr3	14493183	14493247	E068	-7927
chr3	14493276	14493453	E068	-7721
chr3	14493460	14495149	E068	-6025
chr3	14495225	14495659	E068	-5515
chr3	14495735	14495789	E068	-5385
chr3	14495806	14496177	E068	-4997
chr3	14496229	14496396	E068	-4778
chr3	14496473	14496537	E068	-4637
chr3	14496574	14496646	E068	-4528
chr3	14496660	14496814	E068	-4360
chr3	14496866	14496937	E068	-4237
chr3	14497168	14497364	E068	-3810
chr3	14501625	14501711	E068	451
chr3	14501752	14502058	E068	578
chr3	14502148	14502555	E068	974
chr3	14503000	14503054	E068	1826
chr3	14523439	14523499	E068	22265
chr3	14523538	14523603	E068	22364
chr3	14523651	14523828	E068	22477
chr3	14454341	14455584	E069	-45590
chr3	14456527	14456796	E069	-44378
chr3	14456800	14456872	E069	-44302
chr3	14457064	14457333	E069	-43841
chr3	14457400	14457551	E069	-43623
chr3	14457562	14457804	E069	-43370
chr3	14469662	14470158	E069	-31016
chr3	14470161	14470211	E069	-30963
chr3	14470302	14470402	E069	-30772
chr3	14470596	14470646	E069	-30528
chr3	14470816	14471083	E069	-30091
chr3	14471194	14471332	E069	-29842
chr3	14472350	14472454	E069	-28720
chr3	14472636	14475032	E069	-26142
chr3	14475200	14476695	E069	-24479
chr3	14476759	14476847	E069	-24327
chr3	14476959	14477550	E069	-23624
chr3	14477722	14478031	E069	-23143
chr3	14478143	14478565	E069	-22609
chr3	14480191	14480247	E069	-20927
chr3	14480303	14480366	E069	-20808
chr3	14480420	14480478	E069	-20696
chr3	14480614	14480676	E069	-20498
chr3	14480757	14480851	E069	-20323
chr3	14480880	14481468	E069	-19706
chr3	14481738	14481949	E069	-19225
chr3	14482042	14482400	E069	-18774
chr3	14482519	14482866	E069	-18308
chr3	14483054	14483104	E069	-18070
chr3	14483164	14483347	E069	-17827
chr3	14483351	14483486	E069	-17688
chr3	14483547	14483698	E069	-17476
chr3	14483790	14483840	E069	-17334
chr3	14484088	14484138	E069	-17036
chr3	14490318	14490456	E069	-10718
chr3	14490668	14490807	E069	-10367
chr3	14490869	14491069	E069	-10105
chr3	14493276	14493453	E069	-7721
chr3	14493460	14495149	E069	-6025
chr3	14495225	14495659	E069	-5515
chr3	14495735	14495789	E069	-5385
chr3	14495806	14496177	E069	-4997
chr3	14496229	14496396	E069	-4778
chr3	14496473	14496537	E069	-4637
chr3	14496574	14496646	E069	-4528
chr3	14496660	14496814	E069	-4360
chr3	14496866	14496937	E069	-4237
chr3	14502148	14502555	E069	974
chr3	14503000	14503054	E069	1826
chr3	14503107	14503267	E069	1933
chr3	14503287	14503532	E069	2113
chr3	14503601	14503701	E069	2427
chr3	14550360	14550939	E069	49186
chr3	14550960	14551052	E069	49786
chr3	14480191	14480247	E070	-20927
chr3	14480303	14480366	E070	-20808
chr3	14480420	14480478	E070	-20696
chr3	14480614	14480676	E070	-20498
chr3	14480757	14480851	E070	-20323
chr3	14480880	14481468	E070	-19706
chr3	14481738	14481949	E070	-19225
chr3	14482519	14482866	E070	-18308
chr3	14483054	14483104	E070	-18070
chr3	14483164	14483347	E070	-17827
chr3	14493276	14493453	E070	-7721
chr3	14493460	14495149	E070	-6025
chr3	14497168	14497364	E070	-3810
chr3	14550960	14551052	E070	49786
chr3	14453548	14453748	E071	-47426
chr3	14453758	14453840	E071	-47334
chr3	14454341	14455584	E071	-45590
chr3	14457400	14457551	E071	-43623
chr3	14457562	14457804	E071	-43370
chr3	14457981	14458058	E071	-43116
chr3	14458075	14458166	E071	-43008
chr3	14466875	14467045	E071	-34129
chr3	14468733	14468845	E071	-32329
chr3	14468990	14469057	E071	-32117
chr3	14469334	14469411	E071	-31763
chr3	14469462	14469524	E071	-31650
chr3	14469662	14470158	E071	-31016
chr3	14470161	14470211	E071	-30963
chr3	14470302	14470402	E071	-30772
chr3	14470596	14470646	E071	-30528
chr3	14470816	14471083	E071	-30091
chr3	14471194	14471332	E071	-29842
chr3	14471360	14471434	E071	-29740
chr3	14472350	14472454	E071	-28720
chr3	14472636	14475032	E071	-26142
chr3	14475200	14476695	E071	-24479
chr3	14477722	14478031	E071	-23143
chr3	14478143	14478565	E071	-22609
chr3	14480191	14480247	E071	-20927
chr3	14480303	14480366	E071	-20808
chr3	14480420	14480478	E071	-20696
chr3	14480614	14480676	E071	-20498
chr3	14480757	14480851	E071	-20323
chr3	14480880	14481468	E071	-19706
chr3	14481738	14481949	E071	-19225
chr3	14482042	14482400	E071	-18774
chr3	14482519	14482866	E071	-18308
chr3	14483054	14483104	E071	-18070
chr3	14483164	14483347	E071	-17827
chr3	14483351	14483486	E071	-17688
chr3	14483547	14483698	E071	-17476
chr3	14490318	14490456	E071	-10718
chr3	14490668	14490807	E071	-10367
chr3	14490869	14491069	E071	-10105
chr3	14493276	14493453	E071	-7721
chr3	14493460	14495149	E071	-6025
chr3	14495225	14495659	E071	-5515
chr3	14495735	14495789	E071	-5385
chr3	14495806	14496177	E071	-4997
chr3	14496229	14496396	E071	-4778
chr3	14496473	14496537	E071	-4637
chr3	14496574	14496646	E071	-4528
chr3	14496660	14496814	E071	-4360
chr3	14496866	14496937	E071	-4237
chr3	14497168	14497364	E071	-3810
chr3	14497505	14497574	E071	-3600
chr3	14501752	14502058	E071	578
chr3	14502148	14502555	E071	974
chr3	14503000	14503054	E071	1826
chr3	14503107	14503267	E071	1933
chr3	14503287	14503532	E071	2113
chr3	14503601	14503701	E071	2427
chr3	14454341	14455584	E072	-45590
chr3	14470596	14470646	E072	-30528
chr3	14470816	14471083	E072	-30091
chr3	14472350	14472454	E072	-28720
chr3	14472636	14475032	E072	-26142
chr3	14475200	14476695	E072	-24479
chr3	14476759	14476847	E072	-24327
chr3	14476959	14477550	E072	-23624
chr3	14477722	14478031	E072	-23143
chr3	14478143	14478565	E072	-22609
chr3	14480191	14480247	E072	-20927
chr3	14480303	14480366	E072	-20808
chr3	14480420	14480478	E072	-20696
chr3	14480614	14480676	E072	-20498
chr3	14480757	14480851	E072	-20323
chr3	14480880	14481468	E072	-19706
chr3	14481738	14481949	E072	-19225
chr3	14482042	14482400	E072	-18774
chr3	14482519	14482866	E072	-18308
chr3	14483054	14483104	E072	-18070
chr3	14483164	14483347	E072	-17827
chr3	14483351	14483486	E072	-17688
chr3	14483547	14483698	E072	-17476
chr3	14483790	14483840	E072	-17334
chr3	14484088	14484138	E072	-17036
chr3	14490318	14490456	E072	-10718
chr3	14490668	14490807	E072	-10367
chr3	14490869	14491069	E072	-10105
chr3	14492655	14492740	E072	-8434
chr3	14492774	14493110	E072	-8064
chr3	14493183	14493247	E072	-7927
chr3	14493276	14493453	E072	-7721
chr3	14493460	14495149	E072	-6025
chr3	14495225	14495659	E072	-5515
chr3	14495735	14495789	E072	-5385
chr3	14495806	14496177	E072	-4997
chr3	14496229	14496396	E072	-4778
chr3	14496574	14496646	E072	-4528
chr3	14496660	14496814	E072	-4360
chr3	14496866	14496937	E072	-4237
chr3	14497168	14497364	E072	-3810
chr3	14501752	14502058	E072	578
chr3	14502148	14502555	E072	974
chr3	14503000	14503054	E072	1826
chr3	14503107	14503267	E072	1933
chr3	14503287	14503532	E072	2113
chr3	14510255	14510305	E072	9081
chr3	14454341	14455584	E073	-45590
chr3	14456527	14456796	E073	-44378
chr3	14456800	14456872	E073	-44302
chr3	14457064	14457333	E073	-43841
chr3	14457400	14457551	E073	-43623
chr3	14470302	14470402	E073	-30772
chr3	14472636	14475032	E073	-26142
chr3	14475200	14476695	E073	-24479
chr3	14476759	14476847	E073	-24327
chr3	14476959	14477550	E073	-23624
chr3	14478143	14478565	E073	-22609
chr3	14480191	14480247	E073	-20927
chr3	14480303	14480366	E073	-20808
chr3	14480420	14480478	E073	-20696
chr3	14480614	14480676	E073	-20498
chr3	14480757	14480851	E073	-20323
chr3	14480880	14481468	E073	-19706
chr3	14481738	14481949	E073	-19225
chr3	14482042	14482400	E073	-18774
chr3	14482519	14482866	E073	-18308
chr3	14483054	14483104	E073	-18070
chr3	14483164	14483347	E073	-17827
chr3	14483351	14483486	E073	-17688
chr3	14483547	14483698	E073	-17476
chr3	14490318	14490456	E073	-10718
chr3	14493460	14495149	E073	-6025
chr3	14495225	14495659	E073	-5515
chr3	14495735	14495789	E073	-5385
chr3	14495806	14496177	E073	-4997
chr3	14496229	14496396	E073	-4778
chr3	14496473	14496537	E073	-4637
chr3	14496574	14496646	E073	-4528
chr3	14502148	14502555	E073	974
chr3	14503000	14503054	E073	1826
chr3	14503107	14503267	E073	1933
chr3	14503287	14503532	E073	2113
chr3	14503601	14503701	E073	2427
chr3	14529478	14529525	E073	28304
chr3	14550360	14550939	E073	49186
chr3	14550960	14551052	E073	49786
chr3	14454341	14455584	E074	-45590
chr3	14456527	14456796	E074	-44378
chr3	14456800	14456872	E074	-44302
chr3	14457064	14457333	E074	-43841
chr3	14457400	14457551	E074	-43623
chr3	14457562	14457804	E074	-43370
chr3	14469334	14469411	E074	-31763
chr3	14469462	14469524	E074	-31650
chr3	14469662	14470158	E074	-31016
chr3	14470161	14470211	E074	-30963
chr3	14470302	14470402	E074	-30772
chr3	14470596	14470646	E074	-30528
chr3	14470816	14471083	E074	-30091
chr3	14471194	14471332	E074	-29842
chr3	14471360	14471434	E074	-29740
chr3	14471548	14471708	E074	-29466
chr3	14471755	14471903	E074	-29271
chr3	14472350	14472454	E074	-28720
chr3	14472636	14475032	E074	-26142
chr3	14475200	14476695	E074	-24479
chr3	14476759	14476847	E074	-24327
chr3	14476959	14477550	E074	-23624
chr3	14477722	14478031	E074	-23143
chr3	14478143	14478565	E074	-22609
chr3	14480191	14480247	E074	-20927
chr3	14480303	14480366	E074	-20808
chr3	14480420	14480478	E074	-20696
chr3	14480614	14480676	E074	-20498
chr3	14480757	14480851	E074	-20323
chr3	14480880	14481468	E074	-19706
chr3	14481738	14481949	E074	-19225
chr3	14482042	14482400	E074	-18774
chr3	14482519	14482866	E074	-18308
chr3	14483054	14483104	E074	-18070
chr3	14483164	14483347	E074	-17827
chr3	14483351	14483486	E074	-17688
chr3	14483547	14483698	E074	-17476
chr3	14483790	14483840	E074	-17334
chr3	14490318	14490456	E074	-10718
chr3	14490668	14490807	E074	-10367
chr3	14490869	14491069	E074	-10105
chr3	14493183	14493247	E074	-7927
chr3	14493276	14493453	E074	-7721
chr3	14493460	14495149	E074	-6025
chr3	14495225	14495659	E074	-5515
chr3	14495735	14495789	E074	-5385
chr3	14495806	14496177	E074	-4997
chr3	14496229	14496396	E074	-4778
chr3	14496473	14496537	E074	-4637
chr3	14496574	14496646	E074	-4528
chr3	14496660	14496814	E074	-4360
chr3	14496866	14496937	E074	-4237
chr3	14497168	14497364	E074	-3810
chr3	14501752	14502058	E074	578
chr3	14502148	14502555	E074	974
chr3	14503000	14503054	E074	1826
chr3	14503107	14503267	E074	1933
chr3	14503287	14503532	E074	2113
chr3	14503601	14503701	E074	2427
chr3	14509507	14509817	E074	8333
chr3	14475200	14476695	E081	-24479
chr3	14476759	14476847	E081	-24327
chr3	14480191	14480247	E081	-20927
chr3	14480303	14480366	E081	-20808
chr3	14480420	14480478	E081	-20696
chr3	14480614	14480676	E081	-20498
chr3	14480757	14480851	E081	-20323
chr3	14480880	14481468	E081	-19706
chr3	14481738	14481949	E081	-19225
chr3	14482042	14482400	E081	-18774
chr3	14482519	14482866	E081	-18308
chr3	14483054	14483104	E081	-18070
chr3	14483164	14483347	E081	-17827
chr3	14493276	14493453	E081	-7721
chr3	14493460	14495149	E081	-6025
chr3	14495225	14495659	E081	-5515
chr3	14495735	14495789	E081	-5385
chr3	14495806	14496177	E081	-4997
chr3	14496229	14496396	E081	-4778
chr3	14496473	14496537	E081	-4637
chr3	14496574	14496646	E081	-4528
chr3	14496660	14496814	E081	-4360
chr3	14496866	14496937	E081	-4237
chr3	14497168	14497364	E081	-3810
chr3	14502148	14502555	E081	974
chr3	14528303	14528427	E081	27129
chr3	14528779	14528823	E081	27605
chr3	14528917	14529037	E081	27743
chr3	14529039	14529100	E081	27865
chr3	14529147	14529227	E081	27973
chr3	14529336	14529380	E081	28162
chr3	14529478	14529525	E081	28304
chr3	14529693	14529751	E081	28519
chr3	14529798	14529886	E081	28624
chr3	14530004	14530121	E081	28830
chr3	14530190	14530691	E081	29016
chr3	14531005	14531143	E081	29831
chr3	14531371	14531441	E081	30197
chr3	14475200	14476695	E082	-24479
chr3	14480191	14480247	E082	-20927
chr3	14480303	14480366	E082	-20808
chr3	14480420	14480478	E082	-20696
chr3	14480614	14480676	E082	-20498
chr3	14480757	14480851	E082	-20323
chr3	14480880	14481468	E082	-19706
chr3	14482519	14482866	E082	-18308
chr3	14493460	14495149	E082	-6025
chr3	14495225	14495659	E082	-5515
chr3	14495735	14495789	E082	-5385
chr3	14495806	14496177	E082	-4997
chr3	14496229	14496396	E082	-4778
chr3	14496473	14496537	E082	-4637
chr3	14496574	14496646	E082	-4528