rs6421495

Organism: Homo sapiens

Alleles: T>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0101 (3027/29932,GnomAD)
T==0121 (3540/29118,TOPMED)
T==0086 (432/5008,1000G)
T==0100 (384/3854,ALSPAC)
T==0107 (397/3708,TWINSUK)

Position: chr1:56439773 (GRCh38.p7) (1p32.2)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 260 Enhancers around

Promoter: 10 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.56439773T>A
GRCh37.p13 chr 1	NC_000001.10:g.56905445T>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.119	A=0.881
1000Genomes	American	Sub	694	T=0.070	A=0.930
1000Genomes	East Asian	Sub	1008	T=0.034	A=0.966
1000Genomes	Europe	Sub	1006	T=0.114	A=0.886
1000Genomes	Global	Study-wide	5008	T=0.086	A=0.914
1000Genomes	South Asian	Sub	978	T=0.080	A=0.920
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.100	A=0.900
The Genome Aggregation Database	African	Sub	8714	T=0.142	A=0.858
The Genome Aggregation Database	American	Sub	836	T=0.060	A=0.940
The Genome Aggregation Database	East Asian	Sub	1620	T=0.031	A=0.969
The Genome Aggregation Database	Europe	Sub	18460	T=0.090	A=0.909
The Genome Aggregation Database	Global	Study-wide	29932	T=0.101	A=0.898
The Genome Aggregation Database	Other	Sub	302	T=0.080	A=0.920
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.121	A=0.878
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.107	A=0.893

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs6421495	0.000409	alcohol dependence	21314694

eQTL of rs6421495 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 rs6421495 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	56865402	56865477	E067	-39968
chr1	56898006	56898165	E067	-7280
chr1	56898244	56898508	E067	-6937
chr1	56898559	56899076	E067	-6369
chr1	56899264	56899410	E067	-6035
chr1	56899723	56900011	E067	-5434
chr1	56900218	56900576	E067	-4869
chr1	56900629	56900832	E067	-4613
chr1	56900920	56901011	E067	-4434
chr1	56901139	56901208	E067	-4237
chr1	56901237	56901297	E067	-4148
chr1	56901412	56902306	E067	-3139
chr1	56902515	56903353	E067	-2092
chr1	56903449	56903499	E067	-1946
chr1	56903557	56903617	E067	-1828
chr1	56903712	56904010	E067	-1435
chr1	56904015	56904075	E067	-1370
chr1	56905164	56905227	E067	-218
chr1	56905336	56905493	E067	0
chr1	56905507	56905570	E067	62
chr1	56905733	56905819	E067	288
chr1	56916866	56916960	E067	11421
chr1	56917056	56917665	E067	11611
chr1	56917692	56918343	E067	12247
chr1	56937849	56937973	E067	32404
chr1	56939395	56939653	E067	33950
chr1	56939677	56939816	E067	34232
chr1	56939817	56939982	E067	34372
chr1	56944196	56944246	E067	38751
chr1	56877233	56877318	E068	-28127
chr1	56898006	56898165	E068	-7280
chr1	56898244	56898508	E068	-6937
chr1	56898559	56899076	E068	-6369
chr1	56899264	56899410	E068	-6035
chr1	56899723	56900011	E068	-5434
chr1	56900218	56900576	E068	-4869
chr1	56900629	56900832	E068	-4613
chr1	56900920	56901011	E068	-4434
chr1	56901139	56901208	E068	-4237
chr1	56901237	56901297	E068	-4148
chr1	56901412	56902306	E068	-3139
chr1	56902515	56903353	E068	-2092
chr1	56903449	56903499	E068	-1946
chr1	56903557	56903617	E068	-1828
chr1	56903712	56904010	E068	-1435
chr1	56904015	56904075	E068	-1370
chr1	56904643	56904782	E068	-663
chr1	56904912	56905116	E068	-329
chr1	56905164	56905227	E068	-218
chr1	56905336	56905493	E068	0
chr1	56905507	56905570	E068	62
chr1	56905733	56905819	E068	288
chr1	56908157	56908496	E068	2712
chr1	56916866	56916960	E068	11421
chr1	56917056	56917665	E068	11611
chr1	56917692	56918343	E068	12247
chr1	56936015	56936154	E068	30570
chr1	56938648	56938838	E068	33203
chr1	56939395	56939653	E068	33950
chr1	56939677	56939816	E068	34232
chr1	56939817	56939982	E068	34372
chr1	56942673	56942723	E068	37228
chr1	56944196	56944246	E068	38751
chr1	56877233	56877318	E069	-28127
chr1	56877378	56877753	E069	-27692
chr1	56883413	56883669	E069	-21776
chr1	56883701	56884195	E069	-21250
chr1	56898006	56898165	E069	-7280
chr1	56898244	56898508	E069	-6937
chr1	56898559	56899076	E069	-6369
chr1	56899264	56899410	E069	-6035
chr1	56899723	56900011	E069	-5434
chr1	56900218	56900576	E069	-4869
chr1	56900629	56900832	E069	-4613
chr1	56900920	56901011	E069	-4434
chr1	56901139	56901208	E069	-4237
chr1	56901237	56901297	E069	-4148
chr1	56901412	56902306	E069	-3139
chr1	56902515	56903353	E069	-2092
chr1	56903449	56903499	E069	-1946
chr1	56903557	56903617	E069	-1828
chr1	56903712	56904010	E069	-1435
chr1	56904015	56904075	E069	-1370
chr1	56904643	56904782	E069	-663
chr1	56904912	56905116	E069	-329
chr1	56905164	56905227	E069	-218
chr1	56905336	56905493	E069	0
chr1	56905507	56905570	E069	62
chr1	56905733	56905819	E069	288
chr1	56908157	56908496	E069	2712
chr1	56917056	56917665	E069	11611
chr1	56917692	56918343	E069	12247
chr1	56939395	56939653	E069	33950
chr1	56939677	56939816	E069	34232
chr1	56939817	56939982	E069	34372
chr1	56942673	56942723	E069	37228
chr1	56944196	56944246	E069	38751
chr1	56944662	56944766	E069	39217
chr1	56945487	56945638	E069	40042
chr1	56898244	56898508	E070	-6937
chr1	56898559	56899076	E070	-6369
chr1	56900629	56900832	E070	-4613
chr1	56900920	56901011	E070	-4434
chr1	56901139	56901208	E070	-4237
chr1	56901237	56901297	E070	-4148
chr1	56901412	56902306	E070	-3139
chr1	56902515	56903353	E070	-2092
chr1	56917056	56917665	E070	11611
chr1	56936302	56936354	E070	30857
chr1	56939012	56939095	E070	33567
chr1	56939395	56939653	E070	33950
chr1	56865028	56865351	E071	-40094
chr1	56882352	56882540	E071	-22905
chr1	56898006	56898165	E071	-7280
chr1	56898244	56898508	E071	-6937
chr1	56898559	56899076	E071	-6369
chr1	56899264	56899410	E071	-6035
chr1	56899723	56900011	E071	-5434
chr1	56900218	56900576	E071	-4869
chr1	56900629	56900832	E071	-4613
chr1	56900920	56901011	E071	-4434
chr1	56901139	56901208	E071	-4237
chr1	56901237	56901297	E071	-4148
chr1	56902515	56903353	E071	-2092
chr1	56903449	56903499	E071	-1946
chr1	56903557	56903617	E071	-1828
chr1	56903712	56904010	E071	-1435
chr1	56904015	56904075	E071	-1370
chr1	56904643	56904782	E071	-663
chr1	56904912	56905116	E071	-329
chr1	56905164	56905227	E071	-218
chr1	56905336	56905493	E071	0
chr1	56905507	56905570	E071	62
chr1	56905733	56905819	E071	288
chr1	56907687	56907799	E071	2242
chr1	56908157	56908496	E071	2712
chr1	56916866	56916960	E071	11421
chr1	56917056	56917665	E071	11611
chr1	56917692	56918343	E071	12247
chr1	56918391	56918702	E071	12946
chr1	56918783	56918992	E071	13338
chr1	56935514	56935698	E071	30069
chr1	56935763	56935940	E071	30318
chr1	56936015	56936154	E071	30570
chr1	56936302	56936354	E071	30857
chr1	56936404	56936676	E071	30959
chr1	56938648	56938838	E071	33203
chr1	56939395	56939653	E071	33950
chr1	56939677	56939816	E071	34232
chr1	56939817	56939982	E071	34372
chr1	56942673	56942723	E071	37228
chr1	56877233	56877318	E072	-28127
chr1	56877378	56877753	E072	-27692
chr1	56883105	56883403	E072	-22042
chr1	56883413	56883669	E072	-21776
chr1	56883701	56884195	E072	-21250
chr1	56898006	56898165	E072	-7280
chr1	56898244	56898508	E072	-6937
chr1	56898559	56899076	E072	-6369
chr1	56899264	56899410	E072	-6035
chr1	56900218	56900576	E072	-4869
chr1	56900629	56900832	E072	-4613
chr1	56900920	56901011	E072	-4434
chr1	56901139	56901208	E072	-4237
chr1	56901237	56901297	E072	-4148
chr1	56901412	56902306	E072	-3139
chr1	56902515	56903353	E072	-2092
chr1	56903449	56903499	E072	-1946
chr1	56903557	56903617	E072	-1828
chr1	56903712	56904010	E072	-1435
chr1	56904015	56904075	E072	-1370
chr1	56904643	56904782	E072	-663
chr1	56904912	56905116	E072	-329
chr1	56905164	56905227	E072	-218
chr1	56905336	56905493	E072	0
chr1	56905507	56905570	E072	62
chr1	56905733	56905819	E072	288
chr1	56908157	56908496	E072	2712
chr1	56916866	56916960	E072	11421
chr1	56917056	56917665	E072	11611
chr1	56917692	56918343	E072	12247
chr1	56918391	56918702	E072	12946
chr1	56939395	56939653	E072	33950
chr1	56939677	56939816	E072	34232
chr1	56939817	56939982	E072	34372
chr1	56944196	56944246	E072	38751
chr1	56898244	56898508	E073	-6937
chr1	56900629	56900832	E073	-4613
chr1	56900920	56901011	E073	-4434
chr1	56901139	56901208	E073	-4237
chr1	56901237	56901297	E073	-4148
chr1	56901412	56902306	E073	-3139
chr1	56905164	56905227	E073	-218
chr1	56905336	56905493	E073	0
chr1	56905507	56905570	E073	62
chr1	56905733	56905819	E073	288
chr1	56917056	56917665	E073	11611
chr1	56917692	56918343	E073	12247
chr1	56939395	56939653	E073	33950
chr1	56939677	56939816	E073	34232
chr1	56939817	56939982	E073	34372
chr1	56942673	56942723	E073	37228
chr1	56944196	56944246	E073	38751
chr1	56865028	56865351	E074	-40094
chr1	56865402	56865477	E074	-39968
chr1	56865515	56865610	E074	-39835
chr1	56877233	56877318	E074	-28127
chr1	56877378	56877753	E074	-27692
chr1	56883105	56883403	E074	-22042
chr1	56883413	56883669	E074	-21776
chr1	56883701	56884195	E074	-21250
chr1	56890477	56891228	E074	-14217
chr1	56898006	56898165	E074	-7280
chr1	56898244	56898508	E074	-6937
chr1	56898559	56899076	E074	-6369
chr1	56899264	56899410	E074	-6035
chr1	56899723	56900011	E074	-5434
chr1	56900218	56900576	E074	-4869
chr1	56900629	56900832	E074	-4613
chr1	56900920	56901011	E074	-4434
chr1	56901139	56901208	E074	-4237
chr1	56901237	56901297	E074	-4148
chr1	56901412	56902306	E074	-3139
chr1	56902515	56903353	E074	-2092
chr1	56903449	56903499	E074	-1946
chr1	56903557	56903617	E074	-1828
chr1	56903712	56904010	E074	-1435
chr1	56904015	56904075	E074	-1370
chr1	56904643	56904782	E074	-663
chr1	56904912	56905116	E074	-329
chr1	56905164	56905227	E074	-218
chr1	56905336	56905493	E074	0
chr1	56905507	56905570	E074	62
chr1	56905733	56905819	E074	288
chr1	56907295	56907555	E074	1850
chr1	56907687	56907799	E074	2242
chr1	56908157	56908496	E074	2712
chr1	56912332	56912688	E074	6887
chr1	56912738	56912836	E074	7293
chr1	56915781	56915908	E074	10336
chr1	56915986	56916321	E074	10541
chr1	56916866	56916960	E074	11421
chr1	56917056	56917665	E074	11611
chr1	56917692	56918343	E074	12247
chr1	56939012	56939095	E074	33567
chr1	56939395	56939653	E074	33950
chr1	56939677	56939816	E074	34232
chr1	56939817	56939982	E074	34372
chr1	56942673	56942723	E074	37228
chr1	56944196	56944246	E074	38751
chr1	56901139	56901208	E081	-4237
chr1	56901237	56901297	E081	-4148
chr1	56901412	56902306	E081	-3139
chr1	56942673	56942723	E081	37228
chr1	56900218	56900576	E082	-4869
chr1	56900629	56900832	E082	-4613
chr1	56900920	56901011	E082	-4434
chr1	56901139	56901208	E082	-4237
chr1	56901237	56901297	E082	-4148
chr1	56901412	56902306	E082	-3139

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	56942816	56943778	E067	37371
chr1	56942816	56943778	E068	37371
chr1	56942816	56943778	E069	37371
chr1	56942816	56943778	E070	37371
chr1	56942816	56943778	E071	37371
chr1	56942816	56943778	E072	37371
chr1	56942816	56943778	E073	37371
chr1	56942816	56943778	E074	37371
chr1	56942816	56943778	E081	37371
chr1	56942816	56943778	E082	37371