rs2163618

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

EML6 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0128 (3835/29958,GnomAD)
G==0138 (4023/29116,TOPMED)
G==0130 (652/5008,1000G)
G==0108 (417/3854,ALSPAC)
G==0104 (387/3708,TWINSUK)

Position: chr2:54884552 (GRCh38.p7) (2p16.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 140 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.54884552G>A
GRCh37.p13 chr 2	NC_000002.11:g.55111689G>A

Gene: EML6, echinoderm microtubule associated protein like 6(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
EML6 transcript	NM_001039753.2:c.	N/A	Intron Variant
EML6 transcript variant X1	XM_017004098.1:c.	N/A	Intron Variant
EML6 transcript variant X2	XM_017004099.1:c.	N/A	Intron Variant
EML6 transcript variant X3	XM_017004100.1:c.	N/A	Intron Variant
EML6 transcript variant X4	XM_017004101.1:c.	N/A	Intron Variant
EML6 transcript variant X5	XM_017004102.1:c.	N/A	Intron Variant
EML6 transcript variant X7	XR_001738743.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.166	A=0.834
1000Genomes	American	Sub	694	G=0.110	A=0.890
1000Genomes	East Asian	Sub	1008	G=0.102	A=0.898
1000Genomes	Europe	Sub	1006	G=0.099	A=0.901
1000Genomes	Global	Study-wide	5008	G=0.130	A=0.870
1000Genomes	South Asian	Sub	978	G=0.150	A=0.850
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.108	A=0.892
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.138	A=0.861
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.104	A=0.896

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
rs2163618	0.000304	alcohol dependence	20201924

eQTL of rs2163618 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 rs2163618 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	55065130	55065613	E067	-46076
chr2	55065677	55066051	E067	-45638
chr2	55066159	55066203	E067	-45486
chr2	55107113	55107476	E067	-4213
chr2	55109039	55109218	E067	-2471
chr2	55126998	55127272	E067	15309
chr2	55127354	55127481	E067	15665
chr2	55133800	55133850	E067	22111
chr2	55133929	55134193	E067	22240
chr2	55153963	55154053	E067	42274
chr2	55154128	55154219	E067	42439
chr2	55154364	55154427	E067	42675
chr2	55154452	55154510	E067	42763
chr2	55065130	55065613	E068	-46076
chr2	55065677	55066051	E068	-45638
chr2	55066159	55066203	E068	-45486
chr2	55066717	55066980	E068	-44709
chr2	55067242	55067445	E068	-44244
chr2	55067608	55067648	E068	-44041
chr2	55067839	55067883	E068	-43806
chr2	55068000	55068490	E068	-43199
chr2	55127354	55127481	E068	15665
chr2	55133800	55133850	E068	22111
chr2	55133929	55134193	E068	22240
chr2	55153963	55154053	E068	42274
chr2	55154128	55154219	E068	42439
chr2	55154364	55154427	E068	42675
chr2	55154452	55154510	E068	42763
chr2	55157227	55157288	E068	45538
chr2	55065130	55065613	E069	-46076
chr2	55065677	55066051	E069	-45638
chr2	55066159	55066203	E069	-45486
chr2	55066717	55066980	E069	-44709
chr2	55068000	55068490	E069	-43199
chr2	55107113	55107476	E069	-4213
chr2	55109039	55109218	E069	-2471
chr2	55124669	55124843	E069	12980
chr2	55126734	55126956	E069	15045
chr2	55126998	55127272	E069	15309
chr2	55127354	55127481	E069	15665
chr2	55133800	55133850	E069	22111
chr2	55133929	55134193	E069	22240
chr2	55153590	55153856	E069	41901
chr2	55153963	55154053	E069	42274
chr2	55154128	55154219	E069	42439
chr2	55154364	55154427	E069	42675
chr2	55069691	55069967	E070	-41722
chr2	55107113	55107476	E070	-4213
chr2	55107679	55107826	E070	-3863
chr2	55109039	55109218	E070	-2471
chr2	55119175	55119281	E070	7486
chr2	55065130	55065613	E071	-46076
chr2	55065677	55066051	E071	-45638
chr2	55066159	55066203	E071	-45486
chr2	55066717	55066980	E071	-44709
chr2	55068000	55068490	E071	-43199
chr2	55107113	55107476	E071	-4213
chr2	55107679	55107826	E071	-3863
chr2	55109039	55109218	E071	-2471
chr2	55119175	55119281	E071	7486
chr2	55123813	55124165	E071	12124
chr2	55126589	55126692	E071	14900
chr2	55126734	55126956	E071	15045
chr2	55126998	55127272	E071	15309
chr2	55127354	55127481	E071	15665
chr2	55128481	55129139	E071	16792
chr2	55133800	55133850	E071	22111
chr2	55133929	55134193	E071	22240
chr2	55153963	55154053	E071	42274
chr2	55154128	55154219	E071	42439
chr2	55154364	55154427	E071	42675
chr2	55154452	55154510	E071	42763
chr2	55065130	55065613	E072	-46076
chr2	55065677	55066051	E072	-45638
chr2	55066159	55066203	E072	-45486
chr2	55066717	55066980	E072	-44709
chr2	55068000	55068490	E072	-43199
chr2	55119175	55119281	E072	7486
chr2	55124669	55124843	E072	12980
chr2	55126734	55126956	E072	15045
chr2	55126998	55127272	E072	15309
chr2	55127354	55127481	E072	15665
chr2	55133800	55133850	E072	22111
chr2	55133929	55134193	E072	22240
chr2	55153590	55153856	E072	41901
chr2	55153963	55154053	E072	42274
chr2	55154128	55154219	E072	42439
chr2	55127354	55127481	E073	15665
chr2	55133800	55133850	E073	22111
chr2	55133929	55134193	E073	22240
chr2	55153590	55153856	E073	41901
chr2	55153963	55154053	E073	42274
chr2	55154128	55154219	E073	42439
chr2	55154364	55154427	E073	42675
chr2	55154452	55154510	E073	42763
chr2	55065130	55065613	E074	-46076
chr2	55065677	55066051	E074	-45638
chr2	55066159	55066203	E074	-45486
chr2	55066717	55066980	E074	-44709
chr2	55107113	55107476	E074	-4213
chr2	55126734	55126956	E074	15045
chr2	55126998	55127272	E074	15309
chr2	55127354	55127481	E074	15665
chr2	55133800	55133850	E074	22111
chr2	55133929	55134193	E074	22240
chr2	55153590	55153856	E074	41901
chr2	55153963	55154053	E074	42274
chr2	55154128	55154219	E074	42439
chr2	55154364	55154427	E074	42675
chr2	55154452	55154510	E074	42763
chr2	55065130	55065613	E081	-46076
chr2	55065677	55066051	E081	-45638
chr2	55071499	55071577	E081	-40112
chr2	55098692	55098779	E081	-12910
chr2	55099022	55099137	E081	-12552
chr2	55099655	55100222	E081	-11467
chr2	55100482	55100646	E081	-11043
chr2	55107113	55107476	E081	-4213
chr2	55124669	55124843	E081	12980
chr2	55125678	55125878	E081	13989
chr2	55126055	55126268	E081	14366
chr2	55126589	55126692	E081	14900
chr2	55126734	55126956	E081	15045
chr2	55126998	55127272	E081	15309
chr2	55132513	55132587	E081	20824
chr2	55132703	55132933	E081	21014
chr2	55132972	55133046	E081	21283
chr2	55133114	55133164	E081	21425
chr2	55133800	55133850	E081	22111
chr2	55133929	55134193	E081	22240
chr2	55099655	55100222	E082	-11467
chr2	55107113	55107476	E082	-4213
chr2	55125678	55125878	E082	13989
chr2	55126055	55126268	E082	14366
chr2	55126589	55126692	E082	14900
chr2	55126734	55126956	E082	15045
chr2	55126998	55127272	E082	15309
chr2	55127354	55127481	E082	15665
chr2	55133800	55133850	E082	22111
chr2	55133929	55134193	E082	22240