rs1460673

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0461 (13735/29736,GnomAD)
G=0421 (12260/29118,TOPMED)
G=0445 (2228/5008,1000G)
A==0464 (1790/3854,ALSPAC)
A==0462 (1714/3708,TWINSUK)

Position: chr2:163745636 (GRCh38.p7) (2q24.3)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 229 Enhancers around

Promoter: 41 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.163745636A>G
GRCh37.p13 chr 2	NC_000002.11:g.164602146A>G

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.772	G=0.228
1000Genomes	American	Sub	694	A=0.530	G=0.470
1000Genomes	East Asian	Sub	1008	A=0.444	G=0.556
1000Genomes	Europe	Sub	1006	A=0.452	G=0.548
1000Genomes	Global	Study-wide	5008	A=0.555	G=0.445
1000Genomes	South Asian	Sub	978	A=0.500	G=0.500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.464	G=0.536
The Genome Aggregation Database	African	Sub	8666	A=0.702	G=0.298
The Genome Aggregation Database	American	Sub	826	A=0.520	G=0.480
The Genome Aggregation Database	East Asian	Sub	1596	A=0.465	G=0.535
The Genome Aggregation Database	Europe	Sub	18346	A=0.470	G=0.529
The Genome Aggregation Database	Global	Study-wide	29736	A=0.538	G=0.461
The Genome Aggregation Database	Other	Sub	302	A=0.340	G=0.660
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.579	G=0.421
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.462	G=0.538

PMID	Title	Author	Journal
29460428	Genomewide Association Study of Alcohol Dependence and Related Traits in a Thai Population.	Gelernter J	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs1460673	9E-06	alcohol dependence	29460428

eQTL of rs1460673 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 rs1460673 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 )
chr2	164558054	164558165	E067	-43981
chr2	164558225	164558314	E067	-43832
chr2	164558322	164558773	E067	-43373
chr2	164558784	164558901	E067	-43245
chr2	164565138	164565209	E067	-36937
chr2	164565472	164565656	E067	-36490
chr2	164565694	164565758	E067	-36388
chr2	164566225	164566275	E067	-35871
chr2	164567816	164567877	E067	-34269
chr2	164567928	164568003	E067	-34143
chr2	164568062	164568122	E067	-34024
chr2	164568267	164568444	E067	-33702
chr2	164571711	164571822	E067	-30324
chr2	164571858	164572049	E067	-30097
chr2	164573760	164573812	E067	-28334
chr2	164574953	164575047	E067	-27099
chr2	164575105	164575177	E067	-26969
chr2	164575247	164575323	E067	-26823
chr2	164575810	164576283	E067	-25863
chr2	164586321	164586440	E067	-15706
chr2	164586484	164586626	E067	-15520
chr2	164587039	164587083	E067	-15063
chr2	164587584	164587795	E067	-14351
chr2	164554014	164554872	E068	-47274
chr2	164554887	164555261	E068	-46885
chr2	164556927	164556986	E068	-45160
chr2	164558054	164558165	E068	-43981
chr2	164558225	164558314	E068	-43832
chr2	164558322	164558773	E068	-43373
chr2	164558784	164558901	E068	-43245
chr2	164560116	164560365	E068	-41781
chr2	164560429	164560504	E068	-41642
chr2	164560543	164560611	E068	-41535
chr2	164565138	164565209	E068	-36937
chr2	164565472	164565656	E068	-36490
chr2	164565694	164565758	E068	-36388
chr2	164566225	164566275	E068	-35871
chr2	164566670	164566778	E068	-35368
chr2	164566913	164566976	E068	-35170
chr2	164567061	164567182	E068	-34964
chr2	164568062	164568122	E068	-34024
chr2	164568267	164568444	E068	-33702
chr2	164571858	164572049	E068	-30097
chr2	164573760	164573812	E068	-28334
chr2	164575247	164575323	E068	-26823
chr2	164575810	164576283	E068	-25863
chr2	164576747	164576899	E068	-25247
chr2	164584832	164585078	E068	-17068
chr2	164585115	164585165	E068	-16981
chr2	164586321	164586440	E068	-15706
chr2	164586484	164586626	E068	-15520
chr2	164587039	164587083	E068	-15063
chr2	164587584	164587795	E068	-14351
chr2	164556927	164556986	E069	-45160
chr2	164558054	164558165	E069	-43981
chr2	164558225	164558314	E069	-43832
chr2	164558322	164558773	E069	-43373
chr2	164558784	164558901	E069	-43245
chr2	164565138	164565209	E069	-36937
chr2	164565472	164565656	E069	-36490
chr2	164565694	164565758	E069	-36388
chr2	164566913	164566976	E069	-35170
chr2	164567061	164567182	E069	-34964
chr2	164569760	164569876	E069	-32270
chr2	164573760	164573812	E069	-28334
chr2	164575810	164576283	E069	-25863
chr2	164584832	164585078	E069	-17068
chr2	164585115	164585165	E069	-16981
chr2	164585212	164585332	E069	-16814
chr2	164586484	164586626	E069	-15520
chr2	164587039	164587083	E069	-15063
chr2	164587584	164587795	E069	-14351
chr2	164587837	164587897	E069	-14249
chr2	164554887	164555261	E070	-46885
chr2	164558054	164558165	E070	-43981
chr2	164558225	164558314	E070	-43832
chr2	164558322	164558773	E070	-43373
chr2	164558784	164558901	E070	-43245
chr2	164559395	164559538	E070	-42608
chr2	164560003	164560062	E070	-42084
chr2	164560116	164560365	E070	-41781
chr2	164560429	164560504	E070	-41642
chr2	164560543	164560611	E070	-41535
chr2	164566913	164566976	E070	-35170
chr2	164567061	164567182	E070	-34964
chr2	164567816	164567877	E070	-34269
chr2	164567928	164568003	E070	-34143
chr2	164568062	164568122	E070	-34024
chr2	164568267	164568444	E070	-33702
chr2	164570421	164570816	E070	-31330
chr2	164571711	164571822	E070	-30324
chr2	164571858	164572049	E070	-30097
chr2	164572431	164572494	E070	-29652
chr2	164572514	164572603	E070	-29543
chr2	164573075	164573125	E070	-29021
chr2	164573760	164573812	E070	-28334
chr2	164574115	164574412	E070	-27734
chr2	164574953	164575047	E070	-27099
chr2	164575105	164575177	E070	-26969
chr2	164575810	164576283	E070	-25863
chr2	164588149	164588215	E070	-13931
chr2	164588255	164589011	E070	-13135
chr2	164594382	164594432	E070	-7714
chr2	164554887	164555261	E071	-46885
chr2	164556927	164556986	E071	-45160
chr2	164558054	164558165	E071	-43981
chr2	164558225	164558314	E071	-43832
chr2	164558322	164558773	E071	-43373
chr2	164558784	164558901	E071	-43245
chr2	164559395	164559538	E071	-42608
chr2	164560003	164560062	E071	-42084
chr2	164560116	164560365	E071	-41781
chr2	164565138	164565209	E071	-36937
chr2	164565472	164565656	E071	-36490
chr2	164565694	164565758	E071	-36388
chr2	164566913	164566976	E071	-35170
chr2	164567061	164567182	E071	-34964
chr2	164567816	164567877	E071	-34269
chr2	164567928	164568003	E071	-34143
chr2	164568062	164568122	E071	-34024
chr2	164568267	164568444	E071	-33702
chr2	164572431	164572494	E071	-29652
chr2	164572514	164572603	E071	-29543
chr2	164573075	164573125	E071	-29021
chr2	164575247	164575323	E071	-26823
chr2	164575810	164576283	E071	-25863
chr2	164576747	164576899	E071	-25247
chr2	164585212	164585332	E071	-16814
chr2	164586321	164586440	E071	-15706
chr2	164586484	164586626	E071	-15520
chr2	164587039	164587083	E071	-15063
chr2	164587584	164587795	E071	-14351
chr2	164587837	164587897	E071	-14249
chr2	164588149	164588215	E071	-13931
chr2	164554014	164554872	E072	-47274
chr2	164554887	164555261	E072	-46885
chr2	164558054	164558165	E072	-43981
chr2	164558225	164558314	E072	-43832
chr2	164558322	164558773	E072	-43373
chr2	164558784	164558901	E072	-43245
chr2	164560003	164560062	E072	-42084
chr2	164560116	164560365	E072	-41781
chr2	164560429	164560504	E072	-41642
chr2	164560543	164560611	E072	-41535
chr2	164560966	164561024	E072	-41122
chr2	164565472	164565656	E072	-36490
chr2	164565694	164565758	E072	-36388
chr2	164566225	164566275	E072	-35871
chr2	164566670	164566778	E072	-35368
chr2	164566913	164566976	E072	-35170
chr2	164567061	164567182	E072	-34964
chr2	164571858	164572049	E072	-30097
chr2	164575810	164576283	E072	-25863
chr2	164576747	164576899	E072	-25247
chr2	164586321	164586440	E072	-15706
chr2	164586484	164586626	E072	-15520
chr2	164554014	164554872	E073	-47274
chr2	164554887	164555261	E073	-46885
chr2	164555270	164555703	E073	-46443
chr2	164566670	164566778	E073	-35368
chr2	164566913	164566976	E073	-35170
chr2	164567061	164567182	E073	-34964
chr2	164568267	164568444	E073	-33702
chr2	164575247	164575323	E073	-26823
chr2	164586321	164586440	E073	-15706
chr2	164586484	164586626	E073	-15520
chr2	164587584	164587795	E073	-14351
chr2	164554014	164554872	E074	-47274
chr2	164556927	164556986	E074	-45160
chr2	164558054	164558165	E074	-43981
chr2	164558225	164558314	E074	-43832
chr2	164558322	164558773	E074	-43373
chr2	164558784	164558901	E074	-43245
chr2	164560003	164560062	E074	-42084
chr2	164560116	164560365	E074	-41781
chr2	164560429	164560504	E074	-41642
chr2	164560543	164560611	E074	-41535
chr2	164565472	164565656	E074	-36490
chr2	164565694	164565758	E074	-36388
chr2	164566225	164566275	E074	-35871
chr2	164566670	164566778	E074	-35368
chr2	164567061	164567182	E074	-34964
chr2	164567816	164567877	E074	-34269
chr2	164567928	164568003	E074	-34143
chr2	164568062	164568122	E074	-34024
chr2	164568267	164568444	E074	-33702
chr2	164571711	164571822	E074	-30324
chr2	164571858	164572049	E074	-30097
chr2	164572431	164572494	E074	-29652
chr2	164572514	164572603	E074	-29543
chr2	164573075	164573125	E074	-29021
chr2	164573760	164573812	E074	-28334
chr2	164574953	164575047	E074	-27099
chr2	164575105	164575177	E074	-26969
chr2	164575247	164575323	E074	-26823
chr2	164576747	164576899	E074	-25247
chr2	164585212	164585332	E074	-16814
chr2	164586321	164586440	E074	-15706
chr2	164586484	164586626	E074	-15520
chr2	164587039	164587083	E074	-15063
chr2	164588149	164588215	E074	-13931
chr2	164588255	164589011	E074	-13135
chr2	164594382	164594432	E074	-7714
chr2	164568267	164568444	E081	-33702
chr2	164571711	164571822	E081	-30324
chr2	164571858	164572049	E081	-30097
chr2	164572431	164572494	E081	-29652
chr2	164573760	164573812	E081	-28334
chr2	164574115	164574412	E081	-27734
chr2	164574439	164574877	E081	-27269
chr2	164574953	164575047	E081	-27099
chr2	164575105	164575177	E081	-26969
chr2	164575247	164575323	E081	-26823
chr2	164575810	164576283	E081	-25863
chr2	164576747	164576899	E081	-25247
chr2	164634747	164634815	E081	32601
chr2	164634917	164635265	E081	32771
chr2	164554014	164554872	E082	-47274
chr2	164572514	164572603	E082	-29543
chr2	164574115	164574412	E082	-27734
chr2	164574439	164574877	E082	-27269
chr2	164574953	164575047	E082	-27099
chr2	164575105	164575177	E082	-26969
chr2	164575247	164575323	E082	-26823
chr2	164575810	164576283	E082	-25863
chr2	164627186	164627240	E082	25040
chr2	164627452	164627699	E082	25306
chr2	164627868	164628014	E082	25722
chr2	164628159	164628442	E082	26013

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	164584359	164584461	E067	-17685
chr2	164589097	164589737	E067	-12409
chr2	164589876	164590536	E067	-11610
chr2	164590569	164591072	E067	-11074
chr2	164591152	164593959	E067	-8187
chr2	164584359	164584461	E068	-17685
chr2	164589097	164589737	E068	-12409
chr2	164589876	164590536	E068	-11610
chr2	164590569	164591072	E068	-11074
chr2	164591152	164593959	E068	-8187
chr2	164584359	164584461	E069	-17685
chr2	164589097	164589737	E069	-12409
chr2	164589876	164590536	E069	-11610
chr2	164590569	164591072	E069	-11074
chr2	164591152	164593959	E069	-8187
chr2	164589097	164589737	E070	-12409
chr2	164589876	164590536	E070	-11610
chr2	164590569	164591072	E070	-11074
chr2	164591152	164593959	E070	-8187
chr2	164584359	164584461	E071	-17685
chr2	164589097	164589737	E071	-12409
chr2	164589876	164590536	E071	-11610
chr2	164590569	164591072	E071	-11074
chr2	164591152	164593959	E071	-8187
chr2	164584359	164584461	E072	-17685
chr2	164589097	164589737	E072	-12409
chr2	164589876	164590536	E072	-11610
chr2	164590569	164591072	E072	-11074
chr2	164591152	164593959	E072	-8187
chr2	164589097	164589737	E073	-12409
chr2	164589876	164590536	E073	-11610
chr2	164590569	164591072	E073	-11074
chr2	164591152	164593959	E073	-8187
chr2	164584359	164584461	E074	-17685
chr2	164589097	164589737	E074	-12409
chr2	164589876	164590536	E074	-11610
chr2	164590569	164591072	E074	-11074
chr2	164591152	164593959	E074	-8187
chr2	164589876	164590536	E082	-11610
chr2	164590569	164591072	E082	-11074
chr2	164591152	164593959	E082	-8187