rs10798953

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

ZSCAN20 : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0209 (6282/29956,GnomAD)
T==0184 (5363/29118,TOPMED)
T==0237 (1188/5008,1000G)
T==0222 (857/3854,ALSPAC)
T==0223 (828/3708,TWINSUK)

Position: chr1:33471534 (GRCh38.p7) (1p35.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 187 Enhancers around

Promoter: 20 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.33471534T>C
GRCh37.p13 chr 1	NC_000001.10:g.33937135T>C

Gene: ZSCAN20, zinc finger and SCAN domain containing 20(plus strand): 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ZSCAN20 transcript	NM_145238.3:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X3	XM_005271171.3:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X1	XM_006710874.3:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X5	XM_006710876.3:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X2	XM_017002237.1:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X4	XM_017002238.1:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X6	XM_017002239.1:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X7	XM_017002240.1:c.	N/A	Upstream Transcript Variant
ZSCAN20 transcript variant X8	XM_017002241.1:c.	N/A	N/A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.110	C=0.890
1000Genomes	American	Sub	694	T=0.380	C=0.620
1000Genomes	East Asian	Sub	1008	T=0.249	C=0.751
1000Genomes	Europe	Sub	1006	T=0.274	C=0.726
1000Genomes	Global	Study-wide	5008	T=0.237	C=0.763
1000Genomes	South Asian	Sub	978	T=0.260	C=0.740
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.222	C=0.778
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.184	C=0.815
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.223	C=0.777

PMID	Title	Author	Journal
19581569	Genome-wide association study of alcohol dependence.	Treutlein J	Arch Gen Psychiatry

P-Value

SNP ID	p-value	Traits	Study
rs10798953	2.04E-05	alcohol dependence	19581569

eQTL of rs10798953 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 rs10798953 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	33893960	33894028	E067	-43107
chr1	33894679	33894757	E067	-42378
chr1	33900520	33900743	E067	-36392
chr1	33900799	33901006	E067	-36129
chr1	33901196	33901331	E067	-35804
chr1	33902335	33902593	E067	-34542
chr1	33902619	33902935	E067	-34200
chr1	33925245	33926344	E067	-10791
chr1	33926494	33927260	E067	-9875
chr1	33933683	33933869	E067	-3266
chr1	33933926	33933976	E067	-3159
chr1	33934254	33934429	E067	-2706
chr1	33934707	33934815	E067	-2320
chr1	33935969	33936667	E067	-468
chr1	33937063	33937152	E067	0
chr1	33937222	33937272	E067	87
chr1	33937389	33937480	E067	254
chr1	33939229	33939275	E067	2094
chr1	33939437	33939515	E067	2302
chr1	33939595	33940051	E067	2460
chr1	33892642	33892906	E068	-44229
chr1	33897365	33897492	E068	-39643
chr1	33900520	33900743	E068	-36392
chr1	33900799	33901006	E068	-36129
chr1	33902335	33902593	E068	-34542
chr1	33902619	33902935	E068	-34200
chr1	33906846	33906967	E068	-30168
chr1	33933683	33933869	E068	-3266
chr1	33933926	33933976	E068	-3159
chr1	33934254	33934429	E068	-2706
chr1	33935969	33936667	E068	-468
chr1	33937222	33937272	E068	87
chr1	33937389	33937480	E068	254
chr1	33939229	33939275	E068	2094
chr1	33892642	33892906	E069	-44229
chr1	33893960	33894028	E069	-43107
chr1	33894189	33894265	E069	-42870
chr1	33894403	33894553	E069	-42582
chr1	33894679	33894757	E069	-42378
chr1	33897365	33897492	E069	-39643
chr1	33900520	33900743	E069	-36392
chr1	33900799	33901006	E069	-36129
chr1	33901196	33901331	E069	-35804
chr1	33902335	33902593	E069	-34542
chr1	33902619	33902935	E069	-34200
chr1	33925245	33926344	E069	-10791
chr1	33931577	33931655	E069	-5480
chr1	33931879	33932027	E069	-5108
chr1	33933217	33933277	E069	-3858
chr1	33933455	33933540	E069	-3595
chr1	33933683	33933869	E069	-3266
chr1	33933926	33933976	E069	-3159
chr1	33934254	33934429	E069	-2706
chr1	33935969	33936667	E069	-468
chr1	33937063	33937152	E069	0
chr1	33937222	33937272	E069	87
chr1	33937389	33937480	E069	254
chr1	33939229	33939275	E069	2094
chr1	33939437	33939515	E069	2302
chr1	33933455	33933540	E070	-3595
chr1	33933683	33933869	E070	-3266
chr1	33933926	33933976	E070	-3159
chr1	33935969	33936667	E070	-468
chr1	33939229	33939275	E070	2094
chr1	33939437	33939515	E070	2302
chr1	33939595	33940051	E070	2460
chr1	33893960	33894028	E071	-43107
chr1	33899052	33899843	E071	-37292
chr1	33900043	33900235	E071	-36900
chr1	33900520	33900743	E071	-36392
chr1	33900799	33901006	E071	-36129
chr1	33901196	33901331	E071	-35804
chr1	33902335	33902593	E071	-34542
chr1	33902619	33902935	E071	-34200
chr1	33912367	33912534	E071	-24601
chr1	33921163	33922127	E071	-15008
chr1	33922240	33922330	E071	-14805
chr1	33922380	33922446	E071	-14689
chr1	33922659	33922724	E071	-14411
chr1	33925245	33926344	E071	-10791
chr1	33926494	33927260	E071	-9875
chr1	33931091	33931238	E071	-5897
chr1	33931577	33931655	E071	-5480
chr1	33931879	33932027	E071	-5108
chr1	33933217	33933277	E071	-3858
chr1	33933455	33933540	E071	-3595
chr1	33933683	33933869	E071	-3266
chr1	33933926	33933976	E071	-3159
chr1	33934254	33934429	E071	-2706
chr1	33934707	33934815	E071	-2320
chr1	33935969	33936667	E071	-468
chr1	33937222	33937272	E071	87
chr1	33939229	33939275	E071	2094
chr1	33939437	33939515	E071	2302
chr1	33939595	33940051	E071	2460
chr1	33894189	33894265	E072	-42870
chr1	33900799	33901006	E072	-36129
chr1	33901196	33901331	E072	-35804
chr1	33902335	33902593	E072	-34542
chr1	33902619	33902935	E072	-34200
chr1	33908761	33908948	E072	-28187
chr1	33909028	33909234	E072	-27901
chr1	33909264	33909756	E072	-27379
chr1	33925245	33926344	E072	-10791
chr1	33926494	33927260	E072	-9875
chr1	33933217	33933277	E072	-3858
chr1	33933455	33933540	E072	-3595
chr1	33933683	33933869	E072	-3266
chr1	33933926	33933976	E072	-3159
chr1	33934254	33934429	E072	-2706
chr1	33934707	33934815	E072	-2320
chr1	33935969	33936667	E072	-468
chr1	33937222	33937272	E072	87
chr1	33937389	33937480	E072	254
chr1	33939229	33939275	E072	2094
chr1	33939437	33939515	E072	2302
chr1	33982609	33982853	E072	45474
chr1	33892642	33892906	E073	-44229
chr1	33893960	33894028	E073	-43107
chr1	33894189	33894265	E073	-42870
chr1	33897365	33897492	E073	-39643
chr1	33902335	33902593	E073	-34542
chr1	33902619	33902935	E073	-34200
chr1	33908761	33908948	E073	-28187
chr1	33909028	33909234	E073	-27901
chr1	33925245	33926344	E073	-10791
chr1	33933455	33933540	E073	-3595
chr1	33933683	33933869	E073	-3266
chr1	33933926	33933976	E073	-3159
chr1	33934254	33934429	E073	-2706
chr1	33935969	33936667	E073	-468
chr1	33982609	33982853	E073	45474
chr1	33983302	33983465	E073	46167
chr1	33983631	33983693	E073	46496
chr1	33893960	33894028	E074	-43107
chr1	33894189	33894265	E074	-42870
chr1	33894679	33894757	E074	-42378
chr1	33900799	33901006	E074	-36129
chr1	33901196	33901331	E074	-35804
chr1	33902335	33902593	E074	-34542
chr1	33902619	33902935	E074	-34200
chr1	33912367	33912534	E074	-24601
chr1	33921163	33922127	E074	-15008
chr1	33925245	33926344	E074	-10791
chr1	33931577	33931655	E074	-5480
chr1	33931879	33932027	E074	-5108
chr1	33933217	33933277	E074	-3858
chr1	33933455	33933540	E074	-3595
chr1	33933683	33933869	E074	-3266
chr1	33933926	33933976	E074	-3159
chr1	33934254	33934429	E074	-2706
chr1	33934707	33934815	E074	-2320
chr1	33935969	33936667	E074	-468
chr1	33937063	33937152	E074	0
chr1	33937222	33937272	E074	87
chr1	33937389	33937480	E074	254
chr1	33939229	33939275	E074	2094
chr1	33893960	33894028	E081	-43107
chr1	33894189	33894265	E081	-42870
chr1	33894403	33894553	E081	-42582
chr1	33902335	33902593	E081	-34542
chr1	33902619	33902935	E081	-34200
chr1	33934254	33934429	E081	-2706
chr1	33934707	33934815	E081	-2320
chr1	33935969	33936667	E081	-468
chr1	33937222	33937272	E081	87
chr1	33937389	33937480	E081	254
chr1	33939229	33939275	E081	2094
chr1	33977475	33977525	E081	40340
chr1	33977667	33977760	E081	40532
chr1	33977842	33978401	E081	40707
chr1	33983302	33983465	E081	46167
chr1	33983631	33983693	E081	46496
chr1	33894189	33894265	E082	-42870
chr1	33894403	33894553	E082	-42582
chr1	33894679	33894757	E082	-42378
chr1	33934707	33934815	E082	-2320
chr1	33935969	33936667	E082	-468
chr1	33937063	33937152	E082	0
chr1	33937222	33937272	E082	87
chr1	33939229	33939275	E082	2094
chr1	33939437	33939515	E082	2302
chr1	33939595	33940051	E082	2460
chr1	33977475	33977525	E082	40340
chr1	33977667	33977760	E082	40532
chr1	33977842	33978401	E082	40707
chr1	33983302	33983465	E082	46167

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	33895604	33897276	E067	-39859
chr1	33937639	33938682	E067	504
chr1	33895604	33897276	E068	-39859
chr1	33937639	33938682	E068	504
chr1	33895604	33897276	E069	-39859
chr1	33937639	33938682	E069	504
chr1	33895604	33897276	E070	-39859
chr1	33937639	33938682	E070	504
chr1	33895604	33897276	E071	-39859
chr1	33937639	33938682	E071	504
chr1	33895604	33897276	E072	-39859
chr1	33937639	33938682	E072	504
chr1	33895604	33897276	E073	-39859
chr1	33937639	33938682	E073	504
chr1	33895604	33897276	E074	-39859
chr1	33937639	33938682	E074	504
chr1	33895604	33897276	E081	-39859
chr1	33937639	33938682	E081	504
chr1	33895604	33897276	E082	-39859
chr1	33937639	33938682	E082	504