rs2252790

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

DSE : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0232 (6934/29882,GnomAD)
G==0228 (6656/29118,TOPMED)
G==0122 (612/5008,1000G)
G==0365 (1408/3854,ALSPAC)
G==0363 (1347/3708,TWINSUK)

Position: chr6:116342160 (GRCh38.p7) (6q22.1)

Phenotype: AD

Dataset:

GWASCatalog

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 47 Enhancers around

Promoter: 11 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.116342160G>A
GRCh37.p13 chr 6	NC_000006.11:g.116663323G>A
DSE RefSeqGene	NG_033266.2:g.93009G>A

Gene: DSE, dermatan sulfate epimerase(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DSE transcript variant 2	NM_001080976.2:c.	N/A	Intron Variant
DSE transcript variant 3	NM_001322937.1:c.	N/A	Intron Variant
DSE transcript variant 4	NM_001322938.1:c.	N/A	Intron Variant
DSE transcript variant 6	NM_001322940.1:c.	N/A	Intron Variant
DSE transcript variant 5	NM_001322939.1:c.	N/A	Genic Upstream Transcript Variant
DSE transcript variant 7	NM_001322941.1:c.	N/A	Genic Upstream Transcript Variant
DSE transcript variant 9	NM_001322943.1:c.	N/A	Genic Upstream Transcript Variant
DSE transcript variant 8	NM_001322944.1:c.	N/A	Genic Upstream Transcript Variant
DSE transcript variant 1	NM_013352.3:c.	N/A	Genic Upstream Transcript Variant
DSE transcript variant 11	NR_136521.1:n.	N/A	Intron Variant
DSE transcript variant 12	NR_136522.1:n.	N/A	Intron Variant
DSE transcript variant 13	NR_136523.1:n.	N/A	Intron Variant
DSE transcript variant 14	NR_136524.1:n.	N/A	Intron Variant
DSE transcript variant 10	NR_136520.1:n.	N/A	Genic Downstream Transcript Variant
DSE transcript variant X1	XM_017010795.1:c.	N/A	Intron Variant
DSE transcript variant X2	XM_017010796.1:c.	N/A	Genic Upstream Transcript Variant
DSE transcript variant X3	XM_017010797.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.056	A=0.944
1000Genomes	American	Sub	694	G=0.220	A=0.780
1000Genomes	East Asian	Sub	1008	G=0.002	A=0.998
1000Genomes	Europe	Sub	1006	G=0.340	A=0.660
1000Genomes	Global	Study-wide	5008	G=0.122	A=0.878
1000Genomes	South Asian	Sub	978	G=0.040	A=0.960
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.365	A=0.635
The Genome Aggregation Database	African	Sub	8712	G=0.091	A=0.909
The Genome Aggregation Database	American	Sub	838	G=0.210	A=0.790
The Genome Aggregation Database	East Asian	Sub	1622	G=0.004	A=0.996
The Genome Aggregation Database	Europe	Sub	18410	G=0.319	A=0.680
The Genome Aggregation Database	Global	Study-wide	29882	G=0.232	A=0.768
The Genome Aggregation Database	Other	Sub	300	G=0.280	A=0.720
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.228	A=0.771
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.363	A=0.637

PMID	Title	Author	Journal
28040410	A genome wide association study of fast beta EEG in families of European ancestry.	Meyers JL	Int J Psychophysiol

P-Value

SNP ID	p-value	Traits	Study
rs2252790	3E-08	alcohol dependence	28040410

eQTL of rs2252790 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 rs2252790 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 )
chr6	116647482	116647595	E067	-15728
chr6	116647687	116647861	E067	-15462
chr6	116648061	116648419	E067	-14904
chr6	116648481	116648674	E067	-14649
chr6	116621061	116621111	E068	-42212
chr6	116621185	116621240	E068	-42083
chr6	116647687	116647861	E068	-15462
chr6	116648061	116648419	E068	-14904
chr6	116648481	116648674	E068	-14649
chr6	116649025	116649433	E068	-13890
chr6	116649521	116649686	E068	-13637
chr6	116649732	116650044	E068	-13279
chr6	116650098	116650542	E068	-12781
chr6	116671883	116671973	E068	8560
chr6	116673492	116673536	E068	10169
chr6	116688372	116688488	E068	25049
chr6	116621923	116622044	E069	-41279
chr6	116647687	116647861	E069	-15462
chr6	116648061	116648419	E069	-14904
chr6	116648481	116648674	E069	-14649
chr6	116634260	116634310	E071	-29013
chr6	116634340	116634458	E071	-28865
chr6	116638291	116638619	E071	-24704
chr6	116647482	116647595	E071	-15728
chr6	116647687	116647861	E071	-15462
chr6	116648061	116648419	E071	-14904
chr6	116648481	116648674	E071	-14649
chr6	116649521	116649686	E071	-13637
chr6	116670434	116670651	E071	7111
chr6	116673651	116674468	E071	10328
chr6	116690734	116691109	E071	27411
chr6	116703064	116703144	E071	39741
chr6	116707164	116707329	E071	43841
chr6	116707496	116707546	E071	44173
chr6	116636189	116636400	E072	-26923
chr6	116638291	116638619	E072	-24704
chr6	116647482	116647595	E072	-15728
chr6	116647687	116647861	E072	-15462
chr6	116690734	116691109	E073	27411
chr6	116638291	116638619	E074	-24704
chr6	116647482	116647595	E074	-15728
chr6	116647687	116647861	E074	-15462
chr6	116648061	116648419	E074	-14904
chr6	116648481	116648674	E074	-14649
chr6	116649025	116649433	E074	-13890
chr6	116673492	116673536	E074	10169
chr6	116673651	116674468	E074	10328

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr6	116691133	116693165	E067	27810
chr6	116691133	116693165	E068	27810
chr6	116691133	116693165	E069	27810
chr6	116691133	116693165	E070	27810
chr6	116691133	116693165	E071	27810
chr6	116693215	116693317	E071	29892
chr6	116693594	116693655	E071	30271
chr6	116691133	116693165	E072	27810
chr6	116691133	116693165	E073	27810
chr6	116691133	116693165	E074	27810
chr6	116691133	116693165	E082	27810