rs12404679

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0156 (4682/29944,GnomAD)
T=0178 (5201/29118,TOPMED)
T=0173 (868/5008,1000G)
T=0143 (553/3854,ALSPAC)
T=0129 (477/3708,TWINSUK)

Position: chr1:42992787 (GRCh38.p7) (1p34.2)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 297 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.42992787C>T
GRCh37.p13 chr 1	NC_000001.10:g.43458458C>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.749	T=0.251
1000Genomes	American	Sub	694	C=0.810	T=0.190
1000Genomes	East Asian	Sub	1008	C=0.911	T=0.089
1000Genomes	Europe	Sub	1006	C=0.873	T=0.127
1000Genomes	Global	Study-wide	5008	C=0.827	T=0.173
1000Genomes	South Asian	Sub	978	C=0.810	T=0.190
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.857	T=0.143
The Genome Aggregation Database	African	Sub	8708	C=0.792	T=0.208
The Genome Aggregation Database	American	Sub	838	C=0.820	T=0.180
The Genome Aggregation Database	East Asian	Sub	1618	C=0.881	T=0.119
The Genome Aggregation Database	Europe	Sub	18478	C=0.865	T=0.134
The Genome Aggregation Database	Global	Study-wide	29944	C=0.843	T=0.156
The Genome Aggregation Database	Other	Sub	302	C=0.840	T=0.160
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.821	T=0.178
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.871	T=0.129

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
rs12404679	4E-07	alcohol consumption measurement	29460428

eQTL of rs12404679 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 rs12404679 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	43408682	43408732	E067	-49726
chr1	43408770	43409649	E067	-48809
chr1	43409681	43409845	E067	-48613
chr1	43409878	43410453	E067	-48005
chr1	43410647	43410727	E067	-47731
chr1	43410988	43411138	E067	-47320
chr1	43411718	43411927	E067	-46531
chr1	43411980	43412446	E067	-46012
chr1	43412677	43412756	E067	-45702
chr1	43412859	43412950	E067	-45508
chr1	43412964	43413064	E067	-45394
chr1	43413104	43413217	E067	-45241
chr1	43413355	43413598	E067	-44860
chr1	43413728	43413805	E067	-44653
chr1	43413903	43413992	E067	-44466
chr1	43414837	43415441	E067	-43017
chr1	43415536	43415612	E067	-42846
chr1	43415719	43416249	E067	-42209
chr1	43417403	43417556	E067	-40902
chr1	43417745	43417796	E067	-40662
chr1	43418017	43419871	E067	-38587
chr1	43426091	43426141	E067	-32317
chr1	43426394	43426491	E067	-31967
chr1	43426555	43426610	E067	-31848
chr1	43426861	43426981	E067	-31477
chr1	43427030	43427177	E067	-31281
chr1	43427184	43427396	E067	-31062
chr1	43427835	43428293	E067	-30165
chr1	43428323	43428778	E067	-29680
chr1	43428791	43429029	E067	-29429
chr1	43429091	43429670	E067	-28788
chr1	43432666	43433261	E067	-25197
chr1	43408682	43408732	E068	-49726
chr1	43408770	43409649	E068	-48809
chr1	43409681	43409845	E068	-48613
chr1	43409878	43410453	E068	-48005
chr1	43410647	43410727	E068	-47731
chr1	43410988	43411138	E068	-47320
chr1	43411718	43411927	E068	-46531
chr1	43411980	43412446	E068	-46012
chr1	43412677	43412756	E068	-45702
chr1	43412859	43412950	E068	-45508
chr1	43412964	43413064	E068	-45394
chr1	43413104	43413217	E068	-45241
chr1	43413355	43413598	E068	-44860
chr1	43413728	43413805	E068	-44653
chr1	43413903	43413992	E068	-44466
chr1	43414126	43414217	E068	-44241
chr1	43414837	43415441	E068	-43017
chr1	43415719	43416249	E068	-42209
chr1	43416933	43417040	E068	-41418
chr1	43417276	43417348	E068	-41110
chr1	43417403	43417556	E068	-40902
chr1	43417745	43417796	E068	-40662
chr1	43427482	43427719	E068	-30739
chr1	43427835	43428293	E068	-30165
chr1	43428323	43428778	E068	-29680
chr1	43428791	43429029	E068	-29429
chr1	43429091	43429670	E068	-28788
chr1	43459113	43459969	E068	655
chr1	43408682	43408732	E069	-49726
chr1	43408770	43409649	E069	-48809
chr1	43409681	43409845	E069	-48613
chr1	43409878	43410453	E069	-48005
chr1	43410647	43410727	E069	-47731
chr1	43410988	43411138	E069	-47320
chr1	43411718	43411927	E069	-46531
chr1	43411980	43412446	E069	-46012
chr1	43412677	43412756	E069	-45702
chr1	43412859	43412950	E069	-45508
chr1	43412964	43413064	E069	-45394
chr1	43413104	43413217	E069	-45241
chr1	43413355	43413598	E069	-44860
chr1	43413728	43413805	E069	-44653
chr1	43413903	43413992	E069	-44466
chr1	43414126	43414217	E069	-44241
chr1	43414837	43415441	E069	-43017
chr1	43415536	43415612	E069	-42846
chr1	43415719	43416249	E069	-42209
chr1	43418017	43419871	E069	-38587
chr1	43420244	43420339	E069	-38119
chr1	43420448	43420522	E069	-37936
chr1	43420572	43420622	E069	-37836
chr1	43420739	43420799	E069	-37659
chr1	43420863	43420970	E069	-37488
chr1	43425678	43425810	E069	-32648
chr1	43425824	43426036	E069	-32422
chr1	43426091	43426141	E069	-32317
chr1	43426394	43426491	E069	-31967
chr1	43426555	43426610	E069	-31848
chr1	43426861	43426981	E069	-31477
chr1	43427030	43427177	E069	-31281
chr1	43427184	43427396	E069	-31062
chr1	43427482	43427719	E069	-30739
chr1	43427835	43428293	E069	-30165
chr1	43428323	43428778	E069	-29680
chr1	43428791	43429029	E069	-29429
chr1	43429091	43429670	E069	-28788
chr1	43412677	43412756	E070	-45702
chr1	43412859	43412950	E070	-45508
chr1	43412964	43413064	E070	-45394
chr1	43413104	43413217	E070	-45241
chr1	43413355	43413598	E070	-44860
chr1	43413728	43413805	E070	-44653
chr1	43413903	43413992	E070	-44466
chr1	43414837	43415441	E070	-43017
chr1	43415536	43415612	E070	-42846
chr1	43415719	43416249	E070	-42209
chr1	43504189	43504593	E070	45731
chr1	43504875	43504994	E070	46417
chr1	43408682	43408732	E071	-49726
chr1	43408770	43409649	E071	-48809
chr1	43409681	43409845	E071	-48613
chr1	43409878	43410453	E071	-48005
chr1	43410647	43410727	E071	-47731
chr1	43410988	43411138	E071	-47320
chr1	43411718	43411927	E071	-46531
chr1	43411980	43412446	E071	-46012
chr1	43412677	43412756	E071	-45702
chr1	43412859	43412950	E071	-45508
chr1	43412964	43413064	E071	-45394
chr1	43413104	43413217	E071	-45241
chr1	43413355	43413598	E071	-44860
chr1	43413728	43413805	E071	-44653
chr1	43413903	43413992	E071	-44466
chr1	43414126	43414217	E071	-44241
chr1	43414837	43415441	E071	-43017
chr1	43415536	43415612	E071	-42846
chr1	43415719	43416249	E071	-42209
chr1	43416933	43417040	E071	-41418
chr1	43417276	43417348	E071	-41110
chr1	43417403	43417556	E071	-40902
chr1	43417745	43417796	E071	-40662
chr1	43418017	43419871	E071	-38587
chr1	43420244	43420339	E071	-38119
chr1	43420448	43420522	E071	-37936
chr1	43420572	43420622	E071	-37836
chr1	43420739	43420799	E071	-37659
chr1	43420863	43420970	E071	-37488
chr1	43421773	43421886	E071	-36572
chr1	43426394	43426491	E071	-31967
chr1	43426555	43426610	E071	-31848
chr1	43427030	43427177	E071	-31281
chr1	43427482	43427719	E071	-30739
chr1	43427835	43428293	E071	-30165
chr1	43428323	43428778	E071	-29680
chr1	43428791	43429029	E071	-29429
chr1	43429091	43429670	E071	-28788
chr1	43501571	43501646	E071	43113
chr1	43501776	43501948	E071	43318
chr1	43502147	43502433	E071	43689
chr1	43502463	43502513	E071	44005
chr1	43408682	43408732	E072	-49726
chr1	43408770	43409649	E072	-48809
chr1	43409681	43409845	E072	-48613
chr1	43409878	43410453	E072	-48005
chr1	43410647	43410727	E072	-47731
chr1	43410988	43411138	E072	-47320
chr1	43411718	43411927	E072	-46531
chr1	43411980	43412446	E072	-46012
chr1	43412677	43412756	E072	-45702
chr1	43412859	43412950	E072	-45508
chr1	43412964	43413064	E072	-45394
chr1	43413104	43413217	E072	-45241
chr1	43413355	43413598	E072	-44860
chr1	43413728	43413805	E072	-44653
chr1	43413903	43413992	E072	-44466
chr1	43414126	43414217	E072	-44241
chr1	43414837	43415441	E072	-43017
chr1	43415536	43415612	E072	-42846
chr1	43415719	43416249	E072	-42209
chr1	43417745	43417796	E072	-40662
chr1	43420244	43420339	E072	-38119
chr1	43420448	43420522	E072	-37936
chr1	43420572	43420622	E072	-37836
chr1	43420739	43420799	E072	-37659
chr1	43420863	43420970	E072	-37488
chr1	43421102	43421407	E072	-37051
chr1	43421408	43421682	E072	-36776
chr1	43421773	43421886	E072	-36572
chr1	43426091	43426141	E072	-32317
chr1	43426394	43426491	E072	-31967
chr1	43426555	43426610	E072	-31848
chr1	43426861	43426981	E072	-31477
chr1	43427030	43427177	E072	-31281
chr1	43427184	43427396	E072	-31062
chr1	43427482	43427719	E072	-30739
chr1	43427835	43428293	E072	-30165
chr1	43428323	43428778	E072	-29680
chr1	43428791	43429029	E072	-29429
chr1	43429091	43429670	E072	-28788
chr1	43408682	43408732	E073	-49726
chr1	43408770	43409649	E073	-48809
chr1	43409681	43409845	E073	-48613
chr1	43409878	43410453	E073	-48005
chr1	43410647	43410727	E073	-47731
chr1	43410988	43411138	E073	-47320
chr1	43411718	43411927	E073	-46531
chr1	43411980	43412446	E073	-46012
chr1	43412859	43412950	E073	-45508
chr1	43412964	43413064	E073	-45394
chr1	43413104	43413217	E073	-45241
chr1	43413355	43413598	E073	-44860
chr1	43413728	43413805	E073	-44653
chr1	43413903	43413992	E073	-44466
chr1	43414126	43414217	E073	-44241
chr1	43414837	43415441	E073	-43017
chr1	43415536	43415612	E073	-42846
chr1	43415719	43416249	E073	-42209
chr1	43416933	43417040	E073	-41418
chr1	43417276	43417348	E073	-41110
chr1	43417403	43417556	E073	-40902
chr1	43417745	43417796	E073	-40662
chr1	43418017	43419871	E073	-38587
chr1	43420244	43420339	E073	-38119
chr1	43426394	43426491	E073	-31967
chr1	43427482	43427719	E073	-30739
chr1	43427835	43428293	E073	-30165
chr1	43428323	43428778	E073	-29680
chr1	43428791	43429029	E073	-29429
chr1	43408682	43408732	E074	-49726
chr1	43408770	43409649	E074	-48809
chr1	43409681	43409845	E074	-48613
chr1	43409878	43410453	E074	-48005
chr1	43410647	43410727	E074	-47731
chr1	43410988	43411138	E074	-47320
chr1	43411718	43411927	E074	-46531
chr1	43411980	43412446	E074	-46012
chr1	43412677	43412756	E074	-45702
chr1	43412859	43412950	E074	-45508
chr1	43412964	43413064	E074	-45394
chr1	43413104	43413217	E074	-45241
chr1	43413355	43413598	E074	-44860
chr1	43413728	43413805	E074	-44653
chr1	43413903	43413992	E074	-44466
chr1	43414126	43414217	E074	-44241
chr1	43414837	43415441	E074	-43017
chr1	43415536	43415612	E074	-42846
chr1	43415719	43416249	E074	-42209
chr1	43417403	43417556	E074	-40902
chr1	43417745	43417796	E074	-40662
chr1	43418017	43419871	E074	-38587
chr1	43420448	43420522	E074	-37936
chr1	43420572	43420622	E074	-37836
chr1	43420863	43420970	E074	-37488
chr1	43421102	43421407	E074	-37051
chr1	43421408	43421682	E074	-36776
chr1	43421773	43421886	E074	-36572
chr1	43425678	43425810	E074	-32648
chr1	43425824	43426036	E074	-32422
chr1	43426091	43426141	E074	-32317
chr1	43426394	43426491	E074	-31967
chr1	43426555	43426610	E074	-31848
chr1	43426861	43426981	E074	-31477
chr1	43427482	43427719	E074	-30739
chr1	43427835	43428293	E074	-30165
chr1	43428323	43428778	E074	-29680
chr1	43428791	43429029	E074	-29429
chr1	43429091	43429670	E074	-28788
chr1	43501571	43501646	E074	43113
chr1	43501776	43501948	E074	43318
chr1	43502147	43502433	E074	43689
chr1	43502463	43502513	E074	44005
chr1	43502625	43502707	E074	44167
chr1	43502718	43502758	E074	44260
chr1	43502773	43502871	E074	44315
chr1	43502904	43502975	E074	44446
chr1	43508056	43508144	E074	49598
chr1	43410647	43410727	E081	-47731
chr1	43414837	43415441	E081	-43017
chr1	43415536	43415612	E081	-42846
chr1	43437488	43437977	E081	-20481
chr1	43472768	43475141	E081	14310
chr1	43501776	43501948	E081	43318
chr1	43502147	43502433	E081	43689
chr1	43502463	43502513	E081	44005
chr1	43502625	43502707	E081	44167
chr1	43502718	43502758	E081	44260
chr1	43502773	43502871	E081	44315
chr1	43502904	43502975	E081	44446
chr1	43503101	43503545	E081	44643
chr1	43504189	43504593	E081	45731
chr1	43504875	43504994	E081	46417
chr1	43505104	43505279	E081	46646
chr1	43505445	43505565	E081	46987
chr1	43409878	43410453	E082	-48005
chr1	43421102	43421407	E082	-37051
chr1	43421408	43421682	E082	-36776
chr1	43501776	43501948	E082	43318
chr1	43502147	43502433	E082	43689
chr1	43502463	43502513	E082	44005
chr1	43502625	43502707	E082	44167
chr1	43502718	43502758	E082	44260
chr1	43502773	43502871	E082	44315
chr1	43502904	43502975	E082	44446
chr1	43503101	43503545	E082	44643
chr1	43505445	43505565	E082	46987

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	43422468	43425407	E067	-33051
chr1	43422468	43425407	E068	-33051
chr1	43422468	43425407	E069	-33051
chr1	43422468	43425407	E070	-33051
chr1	43422468	43425407	E071	-33051
chr1	43422468	43425407	E072	-33051
chr1	43422468	43425407	E073	-33051
chr1	43422468	43425407	E074	-33051
chr1	43422468	43425407	E082	-33051