rs1362153

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SLC6A9 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0228 (6839/29964,GnomAD)
C=0278 (8095/29118,TOPMED)
C=0264 (1324/5008,1000G)
C=0097 (375/3854,ALSPAC)
C=0092 (341/3708,TWINSUK)

Position: chr1:44003359 (GRCh38.p7) (1p34.1)

Phenotype: AD

Dataset:

GWASdb2 | GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 294 Enhancers around

Promoter: 76 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.44003359T>C
GRCh37.p13 chr 1	NC_000001.10:g.44469031T>C

Gene: SLC6A9, solute carrier family 6 member 9(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC6A9 transcript variant 3	NM_001024845.2:c.	N/A	Intron Variant
SLC6A9 transcript variant 4	NM_001261380.1:c.	N/A	Intron Variant
SLC6A9 transcript variant 1	NM_006934.3:c.	N/A	Intron Variant
SLC6A9 transcript variant 2	NM_201649.3:c.	N/A	Intron Variant
SLC6A9 transcript variant 5	NR_048548.1:n.	N/A	Intron Variant
SLC6A9 transcript variant 6	NR_048549.1:n.	N/A	Intron Variant
SLC6A9 transcript variant X1	XM_011542017.2:c.	N/A	Intron Variant
SLC6A9 transcript variant X1	XM_017002151.1:c.	N/A	Intron Variant
SLC6A9 transcript variant X3	XM_017002152.1:c.	N/A	Intron Variant
SLC6A9 transcript variant X4	XM_017002153.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.402	C=0.598
1000Genomes	American	Sub	694	T=0.830	C=0.170
1000Genomes	East Asian	Sub	1008	T=0.830	C=0.170
1000Genomes	Europe	Sub	1006	T=0.890	C=0.110
1000Genomes	Global	Study-wide	5008	T=0.736	C=0.264
1000Genomes	South Asian	Sub	978	T=0.860	C=0.140
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.903	C=0.097
The Genome Aggregation Database	African	Sub	8722	T=0.475	C=0.525
The Genome Aggregation Database	American	Sub	836	T=0.810	C=0.190
The Genome Aggregation Database	East Asian	Sub	1618	T=0.859	C=0.141
The Genome Aggregation Database	Europe	Sub	18486	T=0.900	C=0.099
The Genome Aggregation Database	Global	Study-wide	29964	T=0.771	C=0.228
The Genome Aggregation Database	Other	Sub	302	T=0.890	C=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.722	C=0.278
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.908	C=0.092

PMID	Title	Author	Journal
24962325	Genome-wide survival analysis of age at onset of alcohol dependence in extended high-risk COGA families.	Kapoor M	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs1362153	7E-06	alcohol dependence (age at onset)	24962325

eQTL of rs1362153 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 rs1362153 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 )
chr1	44419601	44419710	E067	-49321
chr1	44419814	44420062	E067	-48969
chr1	44423399	44423664	E067	-45367
chr1	44429392	44429440	E067	-39591
chr1	44439427	44439537	E067	-29494
chr1	44441822	44442168	E067	-26863
chr1	44442489	44442559	E067	-26472
chr1	44442756	44442838	E067	-26193
chr1	44443126	44443187	E067	-25844
chr1	44443273	44443620	E067	-25411
chr1	44443792	44443949	E067	-25082
chr1	44443952	44444066	E067	-24965
chr1	44461994	44462167	E067	-6864
chr1	44476633	44477063	E067	7602
chr1	44477192	44477324	E067	8161
chr1	44477369	44477512	E067	8338
chr1	44478030	44478327	E067	8999
chr1	44479028	44479204	E067	9997
chr1	44479243	44479320	E067	10212
chr1	44479444	44479552	E067	10413
chr1	44479704	44479888	E067	10673
chr1	44480232	44480289	E067	11201
chr1	44480312	44480362	E067	11281
chr1	44480920	44480970	E067	11889
chr1	44481661	44481800	E067	12630
chr1	44485029	44485558	E067	15998
chr1	44485799	44486015	E067	16768
chr1	44486910	44487084	E067	17879
chr1	44487620	44487696	E067	18589
chr1	44501443	44501600	E067	32412
chr1	44501610	44502002	E067	32579
chr1	44502029	44502772	E067	32998
chr1	44419814	44420062	E068	-48969
chr1	44423399	44423664	E068	-45367
chr1	44442489	44442559	E068	-26472
chr1	44442756	44442838	E068	-26193
chr1	44443126	44443187	E068	-25844
chr1	44443273	44443620	E068	-25411
chr1	44443792	44443949	E068	-25082
chr1	44443952	44444066	E068	-24965
chr1	44461994	44462167	E068	-6864
chr1	44462499	44462543	E068	-6488
chr1	44471307	44471900	E068	2276
chr1	44476633	44477063	E068	7602
chr1	44477192	44477324	E068	8161
chr1	44477369	44477512	E068	8338
chr1	44478030	44478327	E068	8999
chr1	44479028	44479204	E068	9997
chr1	44479243	44479320	E068	10212
chr1	44479704	44479888	E068	10673
chr1	44480232	44480289	E068	11201
chr1	44480312	44480362	E068	11281
chr1	44480920	44480970	E068	11889
chr1	44485029	44485558	E068	15998
chr1	44485799	44486015	E068	16768
chr1	44486910	44487084	E068	17879
chr1	44487620	44487696	E068	18589
chr1	44501443	44501600	E068	32412
chr1	44501610	44502002	E068	32579
chr1	44502029	44502772	E068	32998
chr1	44512922	44513100	E068	43891
chr1	44419814	44420062	E069	-48969
chr1	44423399	44423664	E069	-45367
chr1	44429392	44429440	E069	-39591
chr1	44443126	44443187	E069	-25844
chr1	44443273	44443620	E069	-25411
chr1	44443792	44443949	E069	-25082
chr1	44443952	44444066	E069	-24965
chr1	44456356	44456416	E069	-12615
chr1	44461395	44461449	E069	-7582
chr1	44461994	44462167	E069	-6864
chr1	44462499	44462543	E069	-6488
chr1	44464998	44465048	E069	-3983
chr1	44476633	44477063	E069	7602
chr1	44477192	44477324	E069	8161
chr1	44477369	44477512	E069	8338
chr1	44478030	44478327	E069	8999
chr1	44479028	44479204	E069	9997
chr1	44479243	44479320	E069	10212
chr1	44479444	44479552	E069	10413
chr1	44479704	44479888	E069	10673
chr1	44485029	44485558	E069	15998
chr1	44485799	44486015	E069	16768
chr1	44486910	44487084	E069	17879
chr1	44487620	44487696	E069	18589
chr1	44494886	44494937	E069	25855
chr1	44501443	44501600	E069	32412
chr1	44501610	44502002	E069	32579
chr1	44502029	44502772	E069	32998
chr1	44502825	44502927	E069	33794
chr1	44502951	44503034	E069	33920
chr1	44513276	44514241	E069	44245
chr1	44442489	44442559	E070	-26472
chr1	44442756	44442838	E070	-26193
chr1	44443126	44443187	E070	-25844
chr1	44443273	44443620	E070	-25411
chr1	44443792	44443949	E070	-25082
chr1	44443952	44444066	E070	-24965
chr1	44478030	44478327	E070	8999
chr1	44479028	44479204	E070	9997
chr1	44479243	44479320	E070	10212
chr1	44479444	44479552	E070	10413
chr1	44485029	44485558	E070	15998
chr1	44485799	44486015	E070	16768
chr1	44494886	44494937	E070	25855
chr1	44501610	44502002	E070	32579
chr1	44502029	44502772	E070	32998
chr1	44502825	44502927	E070	33794
chr1	44502951	44503034	E070	33920
chr1	44503143	44503208	E070	34112
chr1	44419601	44419710	E071	-49321
chr1	44419814	44420062	E071	-48969
chr1	44423399	44423664	E071	-45367
chr1	44429392	44429440	E071	-39591
chr1	44441822	44442168	E071	-26863
chr1	44442489	44442559	E071	-26472
chr1	44442756	44442838	E071	-26193
chr1	44443126	44443187	E071	-25844
chr1	44443273	44443620	E071	-25411
chr1	44443792	44443949	E071	-25082
chr1	44443952	44444066	E071	-24965
chr1	44456356	44456416	E071	-12615
chr1	44460528	44460842	E071	-8189
chr1	44461395	44461449	E071	-7582
chr1	44461994	44462167	E071	-6864
chr1	44462499	44462543	E071	-6488
chr1	44462935	44463280	E071	-5751
chr1	44463371	44463523	E071	-5508
chr1	44471307	44471900	E071	2276
chr1	44476633	44477063	E071	7602
chr1	44477192	44477324	E071	8161
chr1	44477369	44477512	E071	8338
chr1	44478030	44478327	E071	8999
chr1	44479028	44479204	E071	9997
chr1	44479243	44479320	E071	10212
chr1	44479444	44479552	E071	10413
chr1	44479704	44479888	E071	10673
chr1	44480232	44480289	E071	11201
chr1	44480312	44480362	E071	11281
chr1	44480920	44480970	E071	11889
chr1	44485029	44485558	E071	15998
chr1	44485799	44486015	E071	16768
chr1	44486910	44487084	E071	17879
chr1	44487620	44487696	E071	18589
chr1	44494886	44494937	E071	25855
chr1	44497891	44498046	E071	28860
chr1	44501443	44501600	E071	32412
chr1	44501610	44502002	E071	32579
chr1	44502029	44502772	E071	32998
chr1	44502825	44502927	E071	33794
chr1	44502951	44503034	E071	33920
chr1	44513276	44514241	E071	44245
chr1	44514297	44514429	E071	45266
chr1	44419601	44419710	E072	-49321
chr1	44423399	44423664	E072	-45367
chr1	44429392	44429440	E072	-39591
chr1	44441822	44442168	E072	-26863
chr1	44442489	44442559	E072	-26472
chr1	44442756	44442838	E072	-26193
chr1	44443126	44443187	E072	-25844
chr1	44443273	44443620	E072	-25411
chr1	44443792	44443949	E072	-25082
chr1	44443952	44444066	E072	-24965
chr1	44449344	44449429	E072	-19602
chr1	44456356	44456416	E072	-12615
chr1	44461994	44462167	E072	-6864
chr1	44462499	44462543	E072	-6488
chr1	44471307	44471900	E072	2276
chr1	44476633	44477063	E072	7602
chr1	44477192	44477324	E072	8161
chr1	44477369	44477512	E072	8338
chr1	44478030	44478327	E072	8999
chr1	44479028	44479204	E072	9997
chr1	44479243	44479320	E072	10212
chr1	44479444	44479552	E072	10413
chr1	44480232	44480289	E072	11201
chr1	44480312	44480362	E072	11281
chr1	44480920	44480970	E072	11889
chr1	44481661	44481800	E072	12630
chr1	44485029	44485558	E072	15998
chr1	44485799	44486015	E072	16768
chr1	44486910	44487084	E072	17879
chr1	44487620	44487696	E072	18589
chr1	44501443	44501600	E072	32412
chr1	44501610	44502002	E072	32579
chr1	44502029	44502772	E072	32998
chr1	44513276	44514241	E072	44245
chr1	44514297	44514429	E072	45266
chr1	44419814	44420062	E073	-48969
chr1	44423399	44423664	E073	-45367
chr1	44429392	44429440	E073	-39591
chr1	44443126	44443187	E073	-25844
chr1	44443273	44443620	E073	-25411
chr1	44443792	44443949	E073	-25082
chr1	44443952	44444066	E073	-24965
chr1	44461994	44462167	E073	-6864
chr1	44462499	44462543	E073	-6488
chr1	44471307	44471900	E073	2276
chr1	44476633	44477063	E073	7602
chr1	44477192	44477324	E073	8161
chr1	44477369	44477512	E073	8338
chr1	44478030	44478327	E073	8999
chr1	44479028	44479204	E073	9997
chr1	44479243	44479320	E073	10212
chr1	44479444	44479552	E073	10413
chr1	44479704	44479888	E073	10673
chr1	44480232	44480289	E073	11201
chr1	44480312	44480362	E073	11281
chr1	44480920	44480970	E073	11889
chr1	44481661	44481800	E073	12630
chr1	44485029	44485558	E073	15998
chr1	44486910	44487084	E073	17879
chr1	44487620	44487696	E073	18589
chr1	44494886	44494937	E073	25855
chr1	44499812	44499852	E073	30781
chr1	44501443	44501600	E073	32412
chr1	44501610	44502002	E073	32579
chr1	44502029	44502772	E073	32998
chr1	44513276	44514241	E073	44245
chr1	44419601	44419710	E074	-49321
chr1	44419814	44420062	E074	-48969
chr1	44423399	44423664	E074	-45367
chr1	44429392	44429440	E074	-39591
chr1	44435041	44435100	E074	-33931
chr1	44435109	44435149	E074	-33882
chr1	44442756	44442838	E074	-26193
chr1	44443126	44443187	E074	-25844
chr1	44443273	44443620	E074	-25411
chr1	44443792	44443949	E074	-25082
chr1	44443952	44444066	E074	-24965
chr1	44456356	44456416	E074	-12615
chr1	44461994	44462167	E074	-6864
chr1	44462499	44462543	E074	-6488
chr1	44462935	44463280	E074	-5751
chr1	44463371	44463523	E074	-5508
chr1	44463542	44463673	E074	-5358
chr1	44463925	44464016	E074	-5015
chr1	44464998	44465048	E074	-3983
chr1	44476633	44477063	E074	7602
chr1	44477192	44477324	E074	8161
chr1	44477369	44477512	E074	8338
chr1	44478030	44478327	E074	8999
chr1	44479243	44479320	E074	10212
chr1	44479444	44479552	E074	10413
chr1	44480920	44480970	E074	11889
chr1	44485029	44485558	E074	15998
chr1	44485799	44486015	E074	16768
chr1	44486910	44487084	E074	17879
chr1	44487620	44487696	E074	18589
chr1	44494886	44494937	E074	25855
chr1	44501443	44501600	E074	32412
chr1	44501610	44502002	E074	32579
chr1	44502029	44502772	E074	32998
chr1	44502825	44502927	E074	33794
chr1	44502951	44503034	E074	33920
chr1	44503143	44503208	E074	34112
chr1	44513276	44514241	E074	44245
chr1	44514297	44514429	E074	45266
chr1	44441822	44442168	E081	-26863
chr1	44442489	44442559	E081	-26472
chr1	44442756	44442838	E081	-26193
chr1	44443126	44443187	E081	-25844
chr1	44443273	44443620	E081	-25411
chr1	44443792	44443949	E081	-25082
chr1	44443952	44444066	E081	-24965
chr1	44454465	44454724	E081	-14307
chr1	44476633	44477063	E081	7602
chr1	44477192	44477324	E081	8161
chr1	44477369	44477512	E081	8338
chr1	44478030	44478327	E081	8999
chr1	44479028	44479204	E081	9997
chr1	44479243	44479320	E081	10212
chr1	44479444	44479552	E081	10413
chr1	44479704	44479888	E081	10673
chr1	44480232	44480289	E081	11201
chr1	44480312	44480362	E081	11281
chr1	44480920	44480970	E081	11889
chr1	44481661	44481800	E081	12630
chr1	44485799	44486015	E081	16768
chr1	44494230	44494415	E081	25199
chr1	44494886	44494937	E081	25855
chr1	44501610	44502002	E081	32579
chr1	44502029	44502772	E081	32998
chr1	44513276	44514241	E081	44245
chr1	44443273	44443620	E082	-25411
chr1	44478030	44478327	E082	8999
chr1	44479028	44479204	E082	9997
chr1	44479243	44479320	E082	10212
chr1	44479444	44479552	E082	10413
chr1	44479704	44479888	E082	10673
chr1	44485029	44485558	E082	15998
chr1	44485799	44486015	E082	16768
chr1	44501610	44502002	E082	32579
chr1	44502029	44502772	E082	32998

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	44435208	44435974	E067	-33057
chr1	44435991	44436130	E067	-32901
chr1	44439641	44441641	E067	-27390
chr1	44444197	44444979	E067	-24052
chr1	44445121	44445214	E067	-23817
chr1	44445325	44445903	E067	-23128
chr1	44456665	44458034	E067	-10997
chr1	44495208	44497696	E067	26177
chr1	44435208	44435974	E068	-33057
chr1	44435991	44436130	E068	-32901
chr1	44439641	44441641	E068	-27390
chr1	44444197	44444979	E068	-24052
chr1	44445121	44445214	E068	-23817
chr1	44445325	44445903	E068	-23128
chr1	44456665	44458034	E068	-10997
chr1	44495208	44497696	E068	26177
chr1	44435208	44435974	E069	-33057
chr1	44435991	44436130	E069	-32901
chr1	44439641	44441641	E069	-27390
chr1	44444197	44444979	E069	-24052
chr1	44445121	44445214	E069	-23817
chr1	44445325	44445903	E069	-23128
chr1	44456665	44458034	E069	-10997
chr1	44495208	44497696	E069	26177
chr1	44435208	44435974	E070	-33057
chr1	44435991	44436130	E070	-32901
chr1	44439641	44441641	E070	-27390
chr1	44444197	44444979	E070	-24052
chr1	44445121	44445214	E070	-23817
chr1	44445325	44445903	E070	-23128
chr1	44456665	44458034	E070	-10997
chr1	44495208	44497696	E070	26177
chr1	44435208	44435974	E071	-33057
chr1	44435991	44436130	E071	-32901
chr1	44439641	44441641	E071	-27390
chr1	44444197	44444979	E071	-24052
chr1	44445121	44445214	E071	-23817
chr1	44445325	44445903	E071	-23128
chr1	44456665	44458034	E071	-10997
chr1	44495208	44497696	E071	26177
chr1	44435208	44435974	E072	-33057
chr1	44435991	44436130	E072	-32901
chr1	44439641	44441641	E072	-27390
chr1	44444197	44444979	E072	-24052
chr1	44445121	44445214	E072	-23817
chr1	44445325	44445903	E072	-23128
chr1	44456665	44458034	E072	-10997
chr1	44495208	44497696	E072	26177
chr1	44435208	44435974	E073	-33057
chr1	44435991	44436130	E073	-32901
chr1	44439641	44441641	E073	-27390
chr1	44444197	44444979	E073	-24052
chr1	44445121	44445214	E073	-23817
chr1	44445325	44445903	E073	-23128
chr1	44456665	44458034	E073	-10997
chr1	44495208	44497696	E073	26177
chr1	44435208	44435974	E074	-33057
chr1	44435991	44436130	E074	-32901
chr1	44439641	44441641	E074	-27390
chr1	44445121	44445214	E074	-23817
chr1	44445325	44445903	E074	-23128
chr1	44456665	44458034	E074	-10997
chr1	44495208	44497696	E074	26177
chr1	44435208	44435974	E081	-33057
chr1	44435991	44436130	E081	-32901
chr1	44444197	44444979	E081	-24052
chr1	44445121	44445214	E081	-23817
chr1	44445325	44445903	E081	-23128
chr1	44435208	44435974	E082	-33057
chr1	44435991	44436130	E082	-32901
chr1	44439641	44441641	E082	-27390
chr1	44444197	44444979	E082	-24052
chr1	44445121	44445214	E082	-23817
chr1	44445325	44445903	E082	-23128
chr1	44456665	44458034	E082	-10997
chr1	44495208	44497696	E082	26177