rs254778

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0330 (9889/29928,GnomAD)
G==0367 (10700/29118,TOPMED)
G==0327 (1637/5008,1000G)
G==0305 (1176/3854,ALSPAC)
G==0311 (1153/3708,TWINSUK)

Position: chr5:88713776 (GRCh38.p7) (5q14.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 105 Enhancers around

Promoter: 282 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.88713776G>A
GRCh37.p13 chr 5	NC_000005.9:g.88009593G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.488	A=0.512
1000Genomes	American	Sub	694	G=0.440	A=0.560
1000Genomes	East Asian	Sub	1008	G=0.064	A=0.936
1000Genomes	Europe	Sub	1006	G=0.312	A=0.688
1000Genomes	Global	Study-wide	5008	G=0.327	A=0.673
1000Genomes	South Asian	Sub	978	G=0.310	A=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.305	A=0.695
The Genome Aggregation Database	African	Sub	8704	G=0.432	A=0.568
The Genome Aggregation Database	American	Sub	836	G=0.410	A=0.590
The Genome Aggregation Database	East Asian	Sub	1622	G=0.054	A=0.946
The Genome Aggregation Database	Europe	Sub	18464	G=0.302	A=0.697
The Genome Aggregation Database	Global	Study-wide	29928	G=0.330	A=0.669
The Genome Aggregation Database	Other	Sub	302	G=0.360	A=0.640
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.367	A=0.632
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.311	A=0.689

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
rs254778	0.000833	alcohol dependence	21314694

eQTL of rs254778 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 rs254778 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 )
chr5	87960402	87960810	E067	-48783
chr5	88025033	88025829	E067	15440
chr5	88025972	88026385	E067	16379
chr5	88026416	88026511	E067	16823
chr5	88028741	88028954	E067	19148
chr5	88032419	88032586	E067	22826
chr5	88047683	88047733	E067	38090
chr5	88025033	88025829	E068	15440
chr5	88025972	88026385	E068	16379
chr5	88026416	88026511	E068	16823
chr5	88026626	88026688	E068	17033
chr5	88026774	88026824	E068	17181
chr5	88027690	88027893	E068	18097
chr5	88027951	88028664	E068	18358
chr5	88028741	88028954	E068	19148
chr5	88025972	88026385	E069	16379
chr5	88026416	88026511	E069	16823
chr5	88027690	88027893	E069	18097
chr5	88027951	88028664	E069	18358
chr5	88028741	88028954	E069	19148
chr5	88057088	88057149	E069	47495
chr5	87994163	87994485	E070	-15108
chr5	87994677	87994789	E070	-14804
chr5	88019876	88020149	E070	10283
chr5	88020175	88020261	E070	10582
chr5	88021055	88021171	E070	11462
chr5	88024466	88024559	E070	14873
chr5	88024750	88024823	E070	15157
chr5	88025033	88025829	E070	15440
chr5	88025972	88026385	E070	16379
chr5	88026416	88026511	E070	16823
chr5	88026626	88026688	E070	17033
chr5	88026774	88026824	E070	17181
chr5	88025033	88025829	E071	15440
chr5	88025972	88026385	E071	16379
chr5	88026416	88026511	E071	16823
chr5	88026626	88026688	E071	17033
chr5	88026774	88026824	E071	17181
chr5	88027690	88027893	E071	18097
chr5	88027951	88028664	E071	18358
chr5	88028741	88028954	E071	19148
chr5	88047683	88047733	E072	38090
chr5	88025033	88025829	E073	15440
chr5	88025972	88026385	E073	16379
chr5	88026416	88026511	E073	16823
chr5	88026626	88026688	E073	17033
chr5	88026774	88026824	E073	17181
chr5	88027004	88027062	E073	17411
chr5	88027690	88027893	E073	18097
chr5	88027951	88028664	E073	18358
chr5	88028741	88028954	E073	19148
chr5	88025972	88026385	E074	16379
chr5	88026416	88026511	E074	16823
chr5	88027690	88027893	E074	18097
chr5	88027951	88028664	E074	18358
chr5	88028741	88028954	E074	19148
chr5	87991747	87991797	E081	-17796
chr5	87991945	87992078	E081	-17515
chr5	87992351	87992529	E081	-17064
chr5	87993792	87994016	E081	-15577
chr5	87994163	87994485	E081	-15108
chr5	87994677	87994789	E081	-14804
chr5	87994991	87995041	E081	-14552
chr5	88011366	88011498	E081	1773
chr5	88011643	88012316	E081	2050
chr5	88012361	88012411	E081	2768
chr5	88012456	88012648	E081	2863
chr5	88013111	88013284	E081	3518
chr5	88013409	88013476	E081	3816
chr5	88013773	88013946	E081	4180
chr5	88014116	88014279	E081	4523
chr5	88014320	88014538	E081	4727
chr5	88014591	88014910	E081	4998
chr5	88015339	88015431	E081	5746
chr5	88015567	88015777	E081	5974
chr5	88015832	88015898	E081	6239
chr5	88016429	88016521	E081	6836
chr5	88016711	88016803	E081	7118
chr5	88016870	88017109	E081	7277
chr5	88019876	88020149	E081	10283
chr5	88020175	88020261	E081	10582
chr5	88022841	88022968	E081	13248
chr5	88025033	88025829	E081	15440
chr5	88025972	88026385	E081	16379
chr5	88026416	88026511	E081	16823
chr5	88026626	88026688	E081	17033
chr5	88026774	88026824	E081	17181
chr5	88027690	88027893	E081	18097
chr5	88027951	88028664	E081	18358
chr5	88028741	88028954	E081	19148
chr5	88035853	88036144	E081	26260
chr5	88037824	88038109	E081	28231
chr5	87993792	87994016	E082	-15577
chr5	87994163	87994485	E082	-15108
chr5	88017617	88017676	E082	8024
chr5	88019876	88020149	E082	10283
chr5	88020175	88020261	E082	10582
chr5	88024466	88024559	E082	14873
chr5	88024750	88024823	E082	15157
chr5	88025033	88025829	E082	15440
chr5	88025972	88026385	E082	16379
chr5	88026416	88026511	E082	16823
chr5	88026626	88026688	E082	17033
chr5	88026774	88026824	E082	17181
chr5	88027951	88028664	E082	18358

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr5	87960882	87961136	E067	-48457
chr5	87962435	87964049	E067	-45544
chr5	87964272	87964402	E067	-45191
chr5	87964420	87964473	E067	-45120
chr5	87964515	87964587	E067	-45006
chr5	87964771	87964889	E067	-44704
chr5	87965149	87965762	E067	-43831
chr5	87965807	87965883	E067	-43710
chr5	87965931	87966267	E067	-43326
chr5	87966405	87966624	E067	-42969
chr5	87966682	87966938	E067	-42655
chr5	87966995	87968470	E067	-41123
chr5	87968509	87972389	E067	-37204
chr5	87972437	87972706	E067	-36887
chr5	87972778	87973291	E067	-36302
chr5	87973330	87973647	E067	-35946
chr5	87973787	87974328	E067	-35265
chr5	87974338	87974614	E067	-34979
chr5	87974629	87974755	E067	-34838
chr5	87974764	87975231	E067	-34362
chr5	87975955	87976935	E067	-32658
chr5	87977110	87977684	E067	-31909
chr5	87977726	87977795	E067	-31798
chr5	87977806	87977943	E067	-31650
chr5	87978124	87978312	E067	-31281
chr5	87978451	87978503	E067	-31090
chr5	87978695	87979310	E067	-30283
chr5	87979948	87982866	E067	-26727
chr5	88018437	88019006	E067	8844
chr5	87960882	87961136	E068	-48457
chr5	87962435	87964049	E068	-45544
chr5	87964272	87964402	E068	-45191
chr5	87964420	87964473	E068	-45120
chr5	87964515	87964587	E068	-45006
chr5	87964771	87964889	E068	-44704
chr5	87965149	87965762	E068	-43831
chr5	87965807	87965883	E068	-43710
chr5	87965931	87966267	E068	-43326
chr5	87966405	87966624	E068	-42969
chr5	87966682	87966938	E068	-42655
chr5	87966995	87968470	E068	-41123
chr5	87968509	87972389	E068	-37204
chr5	87972437	87972706	E068	-36887
chr5	87972778	87973291	E068	-36302
chr5	87973330	87973647	E068	-35946
chr5	87973787	87974328	E068	-35265
chr5	87974338	87974614	E068	-34979
chr5	87974629	87974755	E068	-34838
chr5	87974764	87975231	E068	-34362
chr5	87975955	87976935	E068	-32658
chr5	87977110	87977684	E068	-31909
chr5	87978695	87979310	E068	-30283
chr5	87979948	87982866	E068	-26727
chr5	87960882	87961136	E069	-48457
chr5	87962435	87964049	E069	-45544
chr5	87964272	87964402	E069	-45191
chr5	87964420	87964473	E069	-45120
chr5	87964515	87964587	E069	-45006
chr5	87964771	87964889	E069	-44704
chr5	87965149	87965762	E069	-43831
chr5	87965807	87965883	E069	-43710
chr5	87965931	87966267	E069	-43326
chr5	87966405	87966624	E069	-42969
chr5	87966682	87966938	E069	-42655
chr5	87966995	87968470	E069	-41123
chr5	87968509	87972389	E069	-37204
chr5	87972437	87972706	E069	-36887
chr5	87972778	87973291	E069	-36302
chr5	87973330	87973647	E069	-35946
chr5	87973787	87974328	E069	-35265
chr5	87974338	87974614	E069	-34979
chr5	87974629	87974755	E069	-34838
chr5	87974764	87975231	E069	-34362
chr5	87975955	87976935	E069	-32658
chr5	87977110	87977684	E069	-31909
chr5	87977726	87977795	E069	-31798
chr5	87977806	87977943	E069	-31650
chr5	87978124	87978312	E069	-31281
chr5	87978451	87978503	E069	-31090
chr5	87978695	87979310	E069	-30283
chr5	87979948	87982866	E069	-26727
chr5	87982969	87983128	E069	-26465
chr5	87983182	87984117	E069	-25476
chr5	87984132	87984467	E069	-25126
chr5	87964420	87964473	E070	-45120
chr5	87964515	87964587	E070	-45006
chr5	87964771	87964889	E070	-44704
chr5	87965149	87965762	E070	-43831
chr5	87966405	87966624	E070	-42969
chr5	87966682	87966938	E070	-42655
chr5	87966995	87968470	E070	-41123
chr5	87968509	87972389	E070	-37204
chr5	87972437	87972706	E070	-36887
chr5	87972778	87973291	E070	-36302
chr5	87973330	87973647	E070	-35946
chr5	87973787	87974328	E070	-35265
chr5	87974338	87974614	E070	-34979
chr5	87974629	87974755	E070	-34838
chr5	87974764	87975231	E070	-34362
chr5	87975955	87976935	E070	-32658
chr5	87977110	87977684	E070	-31909
chr5	87977726	87977795	E070	-31798
chr5	87977806	87977943	E070	-31650
chr5	87978124	87978312	E070	-31281
chr5	87978451	87978503	E070	-31090
chr5	87978695	87979310	E070	-30283
chr5	87979948	87982866	E070	-26727
chr5	87982969	87983128	E070	-26465
chr5	87983182	87984117	E070	-25476
chr5	87984132	87984467	E070	-25126
chr5	87960882	87961136	E071	-48457
chr5	87962435	87964049	E071	-45544
chr5	87964272	87964402	E071	-45191
chr5	87964420	87964473	E071	-45120
chr5	87964515	87964587	E071	-45006
chr5	87964771	87964889	E071	-44704
chr5	87965149	87965762	E071	-43831
chr5	87966405	87966624	E071	-42969
chr5	87966682	87966938	E071	-42655
chr5	87966995	87968470	E071	-41123
chr5	87968509	87972389	E071	-37204
chr5	87972437	87972706	E071	-36887
chr5	87972778	87973291	E071	-36302
chr5	87973787	87974328	E071	-35265
chr5	87974338	87974614	E071	-34979
chr5	87974629	87974755	E071	-34838
chr5	87974764	87975231	E071	-34362
chr5	87975955	87976935	E071	-32658
chr5	87977110	87977684	E071	-31909
chr5	87977726	87977795	E071	-31798
chr5	87977806	87977943	E071	-31650
chr5	87978124	87978312	E071	-31281
chr5	87978451	87978503	E071	-31090
chr5	87978695	87979310	E071	-30283
chr5	87979948	87982866	E071	-26727
chr5	87982969	87983128	E071	-26465
chr5	87983182	87984117	E071	-25476
chr5	87984132	87984467	E071	-25126
chr5	88018437	88019006	E071	8844
chr5	87960882	87961136	E072	-48457
chr5	87962435	87964049	E072	-45544
chr5	87964272	87964402	E072	-45191
chr5	87964420	87964473	E072	-45120
chr5	87964515	87964587	E072	-45006
chr5	87964771	87964889	E072	-44704
chr5	87965149	87965762	E072	-43831
chr5	87965807	87965883	E072	-43710
chr5	87965931	87966267	E072	-43326
chr5	87966405	87966624	E072	-42969
chr5	87966682	87966938	E072	-42655
chr5	87966995	87968470	E072	-41123
chr5	87968509	87972389	E072	-37204
chr5	87972437	87972706	E072	-36887
chr5	87972778	87973291	E072	-36302
chr5	87973330	87973647	E072	-35946
chr5	87973787	87974328	E072	-35265
chr5	87974338	87974614	E072	-34979
chr5	87974629	87974755	E072	-34838
chr5	87974764	87975231	E072	-34362
chr5	87975955	87976935	E072	-32658
chr5	87977110	87977684	E072	-31909
chr5	87977726	87977795	E072	-31798
chr5	87977806	87977943	E072	-31650
chr5	87978124	87978312	E072	-31281
chr5	87978451	87978503	E072	-31090
chr5	87978695	87979310	E072	-30283
chr5	87979948	87982866	E072	-26727
chr5	87982969	87983128	E072	-26465
chr5	87983182	87984117	E072	-25476
chr5	88018437	88019006	E072	8844
chr5	87960882	87961136	E073	-48457
chr5	87962435	87964049	E073	-45544
chr5	87964272	87964402	E073	-45191
chr5	87964420	87964473	E073	-45120
chr5	87964515	87964587	E073	-45006
chr5	87964771	87964889	E073	-44704
chr5	87965149	87965762	E073	-43831
chr5	87965807	87965883	E073	-43710
chr5	87965931	87966267	E073	-43326
chr5	87966405	87966624	E073	-42969
chr5	87966682	87966938	E073	-42655
chr5	87966995	87968470	E073	-41123
chr5	87968509	87972389	E073	-37204
chr5	87972437	87972706	E073	-36887
chr5	87972778	87973291	E073	-36302
chr5	87973330	87973647	E073	-35946
chr5	87973787	87974328	E073	-35265
chr5	87974338	87974614	E073	-34979
chr5	87974629	87974755	E073	-34838
chr5	87974764	87975231	E073	-34362
chr5	87975955	87976935	E073	-32658
chr5	87977110	87977684	E073	-31909
chr5	87977726	87977795	E073	-31798
chr5	87977806	87977943	E073	-31650
chr5	87978124	87978312	E073	-31281
chr5	87978451	87978503	E073	-31090
chr5	87978695	87979310	E073	-30283
chr5	87979948	87982866	E073	-26727
chr5	87984132	87984467	E073	-25126
chr5	87962435	87964049	E074	-45544
chr5	87964272	87964402	E074	-45191
chr5	87964420	87964473	E074	-45120
chr5	87964515	87964587	E074	-45006
chr5	87965149	87965762	E074	-43831
chr5	87965807	87965883	E074	-43710
chr5	87965931	87966267	E074	-43326
chr5	87966405	87966624	E074	-42969
chr5	87966682	87966938	E074	-42655
chr5	87966995	87968470	E074	-41123
chr5	87968509	87972389	E074	-37204
chr5	87972437	87972706	E074	-36887
chr5	87972778	87973291	E074	-36302
chr5	87973330	87973647	E074	-35946
chr5	87973787	87974328	E074	-35265
chr5	87974338	87974614	E074	-34979
chr5	87974629	87974755	E074	-34838
chr5	87974764	87975231	E074	-34362
chr5	87975955	87976935	E074	-32658
chr5	87977110	87977684	E074	-31909
chr5	87978695	87979310	E074	-30283
chr5	87979948	87982866	E074	-26727
chr5	87960882	87961136	E081	-48457
chr5	87962435	87964049	E081	-45544
chr5	87964272	87964402	E081	-45191
chr5	87964420	87964473	E081	-45120
chr5	87964515	87964587	E081	-45006
chr5	87964771	87964889	E081	-44704
chr5	87965149	87965762	E081	-43831
chr5	87965807	87965883	E081	-43710
chr5	87965931	87966267	E081	-43326
chr5	87966405	87966624	E081	-42969
chr5	87966682	87966938	E081	-42655
chr5	87966995	87968470	E081	-41123
chr5	87968509	87972389	E081	-37204
chr5	87972437	87972706	E081	-36887
chr5	87972778	87973291	E081	-36302
chr5	87973330	87973647	E081	-35946
chr5	87973787	87974328	E081	-35265
chr5	87974338	87974614	E081	-34979
chr5	87974629	87974755	E081	-34838
chr5	87974764	87975231	E081	-34362
chr5	87975955	87976935	E081	-32658
chr5	87977110	87977684	E081	-31909
chr5	87977726	87977795	E081	-31798
chr5	87977806	87977943	E081	-31650
chr5	87978124	87978312	E081	-31281
chr5	87978451	87978503	E081	-31090
chr5	87978695	87979310	E081	-30283
chr5	87979948	87982866	E081	-26727
chr5	87982969	87983128	E081	-26465
chr5	87983182	87984117	E081	-25476
chr5	87984132	87984467	E081	-25126
chr5	87964272	87964402	E082	-45191
chr5	87964420	87964473	E082	-45120
chr5	87964515	87964587	E082	-45006
chr5	87964771	87964889	E082	-44704
chr5	87965149	87965762	E082	-43831
chr5	87965807	87965883	E082	-43710
chr5	87965931	87966267	E082	-43326
chr5	87966405	87966624	E082	-42969
chr5	87966682	87966938	E082	-42655
chr5	87966995	87968470	E082	-41123
chr5	87968509	87972389	E082	-37204
chr5	87972437	87972706	E082	-36887
chr5	87972778	87973291	E082	-36302
chr5	87973330	87973647	E082	-35946
chr5	87973787	87974328	E082	-35265
chr5	87974338	87974614	E082	-34979
chr5	87974629	87974755	E082	-34838
chr5	87974764	87975231	E082	-34362
chr5	87975955	87976935	E082	-32658
chr5	87977110	87977684	E082	-31909
chr5	87977726	87977795	E082	-31798
chr5	87977806	87977943	E082	-31650
chr5	87978124	87978312	E082	-31281
chr5	87978451	87978503	E082	-31090
chr5	87978695	87979310	E082	-30283
chr5	87979948	87982866	E082	-26727
chr5	87982969	87983128	E082	-26465
chr5	87983182	87984117	E082	-25476
chr5	87984132	87984467	E082	-25126
chr5	88018437	88019006	E082	8844