rs34675858

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

MAP4 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0020 (600/29996,GnomAD)
T=0029 (866/29118,TOPMED)
T=0026 (129/5008,1000G)

Position: chr3:47860757 (GRCh38.p7) (3p21.31)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 109 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.47860757C>T
GRCh37.p13 chr 3	NC_000003.11:g.47902247C>T

Gene: MAP4, microtubule associated protein 4(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MAP4 transcript variant 4	NM_001134364.1:c.	N/A	Intron Variant
MAP4 transcript variant 1	NM_002375.4:c.	N/A	Intron Variant
MAP4 transcript variant 3	NM_030885.3:c.	N/A	Genic Downstream Transcript Variant
MAP4 transcript variant X9	XM_005265133.4:c.	N/A	Intron Variant
MAP4 transcript variant X8	XM_005265134.4:c.	N/A	Intron Variant
MAP4 transcript variant X30	XM_005265155.4:c.	N/A	Intron Variant
MAP4 transcript variant X41	XM_005265157.4:c.	N/A	Intron Variant
MAP4 transcript variant X46	XM_005265158.2:c.	N/A	Intron Variant
MAP4 transcript variant X6	XM_006713146.3:c.	N/A	Intron Variant
MAP4 transcript variant X5	XM_006713147.3:c.	N/A	Intron Variant
MAP4 transcript variant X13	XM_006713152.3:c.	N/A	Intron Variant
MAP4 transcript variant X3	XM_011533703.2:c.	N/A	Intron Variant
MAP4 transcript variant X6	XM_011533704.2:c.	N/A	Intron Variant
MAP4 transcript variant X10	XM_011533705.1:c.	N/A	Intron Variant
MAP4 transcript variant X14	XM_011533708.2:c.	N/A	Intron Variant
MAP4 transcript variant X18	XM_011533709.2:c.	N/A	Intron Variant
MAP4 transcript variant X12	XM_011533710.2:c.	N/A	Intron Variant
MAP4 transcript variant X24	XM_011533718.1:c.	N/A	Intron Variant
MAP4 transcript variant X26	XM_011533719.2:c.	N/A	Intron Variant
MAP4 transcript variant X7	XM_017006391.1:c.	N/A	Intron Variant
MAP4 transcript variant X19	XM_017006392.1:c.	N/A	Intron Variant
MAP4 transcript variant X14	XM_017006393.1:c.	N/A	Intron Variant
MAP4 transcript variant X15	XM_017006394.1:c.	N/A	Intron Variant
MAP4 transcript variant X27	XM_017006395.1:c.	N/A	Intron Variant
MAP4 transcript variant X19	XM_017006396.1:c.	N/A	Intron Variant
MAP4 transcript variant X30	XM_017006397.1:c.	N/A	Intron Variant
MAP4 transcript variant X21	XM_017006398.1:c.	N/A	Intron Variant
MAP4 transcript variant X22	XM_017006399.1:c.	N/A	Intron Variant
MAP4 transcript variant X23	XM_017006400.1:c.	N/A	Intron Variant
MAP4 transcript variant X36	XM_017006401.1:c.	N/A	Intron Variant
MAP4 transcript variant X37	XM_017006402.1:c.	N/A	Intron Variant
MAP4 transcript variant X26	XM_017006403.1:c.	N/A	Intron Variant
MAP4 transcript variant X27	XM_017006404.1:c.	N/A	Intron Variant
MAP4 transcript variant X39	XM_017006405.1:c.	N/A	Intron Variant
MAP4 transcript variant X29	XM_017006406.1:c.	N/A	Intron Variant
MAP4 transcript variant X31	XM_017006407.1:c.	N/A	Intron Variant
MAP4 transcript variant X32	XM_017006408.1:c.	N/A	Intron Variant
MAP4 transcript variant X33	XM_017006409.1:c.	N/A	Intron Variant
MAP4 transcript variant X34	XM_017006410.1:c.	N/A	Intron Variant
MAP4 transcript variant X44	XM_017006411.1:c.	N/A	Intron Variant
MAP4 transcript variant X45	XM_017006412.1:c.	N/A	Intron Variant
MAP4 transcript variant X46	XM_017006413.1:c.	N/A	Intron Variant
MAP4 transcript variant X47	XM_017006414.1:c.	N/A	Intron Variant
MAP4 transcript variant X48	XM_017006415.1:c.	N/A	Intron Variant
MAP4 transcript variant X49	XM_017006416.1:c.	N/A	Intron Variant
MAP4 transcript variant X42	XM_017006417.1:c.	N/A	Intron Variant
MAP4 transcript variant X43	XM_017006418.1:c.	N/A	Intron Variant
MAP4 transcript variant X44	XM_017006419.1:c.	N/A	Intron Variant
MAP4 transcript variant X45	XM_017006420.1:c.	N/A	Intron Variant
MAP4 transcript variant X47	XM_017006421.1:c.	N/A	Intron Variant
MAP4 transcript variant X48	XM_017006422.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.907	T=0.093
1000Genomes	American	Sub	694	C=0.990	T=0.010
1000Genomes	East Asian	Sub	1008	C=1.000	T=0.000
1000Genomes	Europe	Sub	1006	C=0.999	T=0.001
1000Genomes	Global	Study-wide	5008	C=0.974	T=0.026
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
The Genome Aggregation Database	African	Sub	8728	C=0.932	T=0.068
The Genome Aggregation Database	American	Sub	838	C=1.000	T=0.000
The Genome Aggregation Database	East Asian	Sub	1622	C=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18506	C=1.000	T=0.000
The Genome Aggregation Database	Global	Study-wide	29996	C=0.980	T=0.020
The Genome Aggregation Database	Other	Sub	302	C=1.000	T=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.970	T=0.029

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs34675858	0.00066	alcohol dependence	20201924

eQTL of rs34675858 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 rs34675858 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 )
chr3	47855433	47855474	E067	-46773
chr3	47865776	47865949	E067	-36298
chr3	47868308	47868358	E067	-33889
chr3	47877385	47877475	E067	-24772
chr3	47878456	47878518	E067	-23729
chr3	47878536	47878673	E067	-23574
chr3	47878733	47878870	E067	-23377
chr3	47879254	47879606	E067	-22641
chr3	47919471	47919521	E067	17224
chr3	47930652	47930714	E067	28405
chr3	47931612	47931918	E067	29365
chr3	47934545	47934595	E067	32298
chr3	47934774	47934948	E067	32527
chr3	47865776	47865949	E068	-36298
chr3	47868308	47868358	E068	-33889
chr3	47879254	47879606	E068	-22641
chr3	47891946	47892048	E068	-10199
chr3	47892499	47892831	E068	-9416
chr3	47892875	47892919	E068	-9328
chr3	47892925	47893015	E068	-9232
chr3	47893126	47893269	E068	-8978
chr3	47893559	47893664	E068	-8583
chr3	47893671	47893731	E068	-8516
chr3	47893861	47893925	E068	-8322
chr3	47894092	47894153	E068	-8094
chr3	47916493	47916700	E068	14246
chr3	47917183	47917259	E068	14936
chr3	47919471	47919521	E068	17224
chr3	47930652	47930714	E068	28405
chr3	47934774	47934948	E068	32527
chr3	47951054	47951368	E068	48807
chr3	47951705	47951765	E068	49458
chr3	47855433	47855474	E069	-46773
chr3	47865776	47865949	E069	-36298
chr3	47868308	47868358	E069	-33889
chr3	47879254	47879606	E069	-22641
chr3	47909873	47910114	E069	7626
chr3	47914454	47914661	E069	12207
chr3	47915118	47915241	E069	12871
chr3	47916058	47916108	E069	13811
chr3	47919471	47919521	E069	17224
chr3	47930652	47930714	E069	28405
chr3	47934545	47934595	E069	32298
chr3	47934774	47934948	E069	32527
chr3	47865776	47865949	E070	-36298
chr3	47934774	47934948	E070	32527
chr3	47865776	47865949	E071	-36298
chr3	47868308	47868358	E071	-33889
chr3	47878456	47878518	E071	-23729
chr3	47878536	47878673	E071	-23574
chr3	47878733	47878870	E071	-23377
chr3	47879254	47879606	E071	-22641
chr3	47880096	47880195	E071	-22052
chr3	47899016	47899071	E071	-3176
chr3	47909873	47910114	E071	7626
chr3	47916493	47916700	E071	14246
chr3	47918941	47919006	E071	16694
chr3	47919471	47919521	E071	17224
chr3	47934545	47934595	E071	32298
chr3	47934774	47934948	E071	32527
chr3	47941204	47941282	E071	38957
chr3	47865776	47865949	E072	-36298
chr3	47879254	47879606	E072	-22641
chr3	47892499	47892831	E072	-9416
chr3	47892875	47892919	E072	-9328
chr3	47892925	47893015	E072	-9232
chr3	47909873	47910114	E072	7626
chr3	47930652	47930714	E072	28405
chr3	47938151	47938605	E072	35904
chr3	47951054	47951368	E072	48807
chr3	47951705	47951765	E072	49458
chr3	47868308	47868358	E073	-33889
chr3	47879254	47879606	E073	-22641
chr3	47892499	47892831	E073	-9416
chr3	47892875	47892919	E073	-9328
chr3	47892925	47893015	E073	-9232
chr3	47914454	47914661	E073	12207
chr3	47916493	47916700	E073	14246
chr3	47917183	47917259	E073	14936
chr3	47934545	47934595	E073	32298
chr3	47934774	47934948	E073	32527
chr3	47951705	47951765	E073	49458
chr3	47865776	47865949	E074	-36298
chr3	47879254	47879606	E074	-22641
chr3	47909873	47910114	E074	7626
chr3	47915118	47915241	E074	12871
chr3	47915358	47915439	E074	13111
chr3	47915516	47915599	E074	13269
chr3	47916493	47916700	E074	14246
chr3	47918941	47919006	E074	16694
chr3	47919471	47919521	E074	17224
chr3	47930652	47930714	E074	28405
chr3	47931038	47931088	E074	28791
chr3	47931612	47931918	E074	29365
chr3	47931933	47932869	E074	29686
chr3	47932973	47933282	E074	30726
chr3	47938151	47938605	E074	35904
chr3	47865776	47865949	E081	-36298
chr3	47926122	47926499	E081	23875
chr3	47927354	47927406	E081	25107
chr3	47929052	47929107	E081	26805
chr3	47930652	47930714	E081	28405
chr3	47932973	47933282	E081	30726
chr3	47934545	47934595	E081	32298
chr3	47934774	47934948	E081	32527
chr3	47942859	47943023	E081	40612
chr3	47943831	47943885	E081	41584
chr3	47865776	47865949	E082	-36298
chr3	47934774	47934948	E082	32527

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr3	47865978	47867113	E067	-35134
chr3	47867123	47867259	E067	-34988
chr3	47865978	47867113	E068	-35134
chr3	47867123	47867259	E068	-34988
chr3	47865978	47867113	E069	-35134
chr3	47867123	47867259	E069	-34988
chr3	47865978	47867113	E070	-35134
chr3	47867123	47867259	E070	-34988
chr3	47865978	47867113	E071	-35134
chr3	47867123	47867259	E071	-34988
chr3	47865978	47867113	E072	-35134
chr3	47867123	47867259	E072	-34988
chr3	47865978	47867113	E073	-35134
chr3	47867123	47867259	E073	-34988
chr3	47865978	47867113	E074	-35134
chr3	47867123	47867259	E074	-34988
chr3	47865978	47867113	E081	-35134
chr3	47867123	47867259	E081	-34988
chr3	47865978	47867113	E082	-35134
chr3	47867123	47867259	E082	-34988