rs11121524

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

UBE4B : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0212 (6353/29964,GnomAD)
G=0264 (7690/29118,TOPMED)
G=0197 (988/5008,1000G)
G=0093 (360/3854,ALSPAC)
G=0087 (322/3708,TWINSUK)

Position: chr1:10172476 (GRCh38.p7) (1p36.22)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 214 Enhancers around

Promoter: 9 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.10172476C>G
GRCh37.p13 chr 1	NC_000001.10:g.10232534C>G

Gene: UBE4B, ubiquitination factor E4B(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBE4B transcript variant 1	NM_001105562.2:c.	N/A	Intron Variant
UBE4B transcript variant 2	NM_006048.4:c.	N/A	Intron Variant
UBE4B transcript variant X1	XM_005263422.1:c.	N/A	Intron Variant
UBE4B transcript variant X2	XM_011540488.2:c.	N/A	Intron Variant
UBE4B transcript variant X3	XM_017000035.1:c.	N/A	Intron Variant
UBE4B transcript variant X6	XM_017000036.1:c.	N/A	Intron Variant
UBE4B transcript variant X4	XM_011540489.2:c.	N/A	Genic Downstream Transcript Variant
UBE4B transcript variant X5	XM_011540490.1:c.	N/A	Genic Downstream Transcript Variant
UBE4B transcript variant X7	XR_001736907.1:n.	N/A	Intron Variant
UBE4B transcript variant X8	XR_946516.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.454	G=0.546
1000Genomes	American	Sub	694	C=0.870	G=0.130
1000Genomes	East Asian	Sub	1008	C=0.952	G=0.048
1000Genomes	Europe	Sub	1006	C=0.902	G=0.098
1000Genomes	Global	Study-wide	5008	C=0.803	G=0.197
1000Genomes	South Asian	Sub	978	C=0.970	G=0.030
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.907	G=0.093
The Genome Aggregation Database	African	Sub	8704	C=0.511	G=0.489
The Genome Aggregation Database	American	Sub	838	C=0.880	G=0.120
The Genome Aggregation Database	East Asian	Sub	1618	C=0.934	G=0.066
The Genome Aggregation Database	Europe	Sub	18502	C=0.899	G=0.100
The Genome Aggregation Database	Global	Study-wide	29964	C=0.788	G=0.212
The Genome Aggregation Database	Other	Sub	302	C=0.890	G=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.735	G=0.264
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.913	G=0.087

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
rs11121524	0.000545	alcohol dependence	21314694

eQTL of rs11121524 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:10232534	UBE4B	ENSG00000130939.14	C>G	1.2550e-3	139644	Cerebellum

meQTL of rs11121524 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	10189473	10189608	E067	-42926
chr1	10190487	10190564	E067	-41970
chr1	10190873	10190933	E067	-41601
chr1	10220988	10221189	E067	-11345
chr1	10221215	10221438	E067	-11096
chr1	10221547	10221597	E067	-10937
chr1	10221670	10222012	E067	-10522
chr1	10238929	10239682	E067	6395
chr1	10239786	10240317	E067	7252
chr1	10240343	10240433	E067	7809
chr1	10273051	10273095	E067	40517
chr1	10273131	10273171	E067	40597
chr1	10274204	10274288	E067	41670
chr1	10276151	10276414	E067	43617
chr1	10276599	10276836	E067	44065
chr1	10276948	10276998	E067	44414
chr1	10277633	10277673	E067	45099
chr1	10278041	10278565	E067	45507
chr1	10278726	10278780	E067	46192
chr1	10282231	10282488	E067	49697
chr1	10189473	10189608	E068	-42926
chr1	10190873	10190933	E068	-41601
chr1	10212920	10213319	E068	-19215
chr1	10220988	10221189	E068	-11345
chr1	10221215	10221438	E068	-11096
chr1	10221547	10221597	E068	-10937
chr1	10221670	10222012	E068	-10522
chr1	10238657	10238737	E068	6123
chr1	10238785	10238914	E068	6251
chr1	10238929	10239682	E068	6395
chr1	10239786	10240317	E068	7252
chr1	10240343	10240433	E068	7809
chr1	10273051	10273095	E068	40517
chr1	10273131	10273171	E068	40597
chr1	10273485	10273639	E068	40951
chr1	10273832	10273935	E068	41298
chr1	10274078	10274172	E068	41544
chr1	10275996	10276049	E068	43462
chr1	10276151	10276414	E068	43617
chr1	10276599	10276836	E068	44065
chr1	10276948	10276998	E068	44414
chr1	10277633	10277673	E068	45099
chr1	10278041	10278565	E068	45507
chr1	10278726	10278780	E068	46192
chr1	10282231	10282488	E068	49697
chr1	10188134	10188585	E069	-43949
chr1	10189473	10189608	E069	-42926
chr1	10190873	10190933	E069	-41601
chr1	10212920	10213319	E069	-19215
chr1	10220988	10221189	E069	-11345
chr1	10221215	10221438	E069	-11096
chr1	10221547	10221597	E069	-10937
chr1	10221670	10222012	E069	-10522
chr1	10222764	10222835	E069	-9699
chr1	10238657	10238737	E069	6123
chr1	10238785	10238914	E069	6251
chr1	10238929	10239682	E069	6395
chr1	10239786	10240317	E069	7252
chr1	10240343	10240433	E069	7809
chr1	10254191	10254301	E069	21657
chr1	10273051	10273095	E069	40517
chr1	10273131	10273171	E069	40597
chr1	10273485	10273639	E069	40951
chr1	10273832	10273935	E069	41298
chr1	10274078	10274172	E069	41544
chr1	10274204	10274288	E069	41670
chr1	10275996	10276049	E069	43462
chr1	10276151	10276414	E069	43617
chr1	10276599	10276836	E069	44065
chr1	10276948	10276998	E069	44414
chr1	10277633	10277673	E069	45099
chr1	10278041	10278565	E069	45507
chr1	10278726	10278780	E069	46192
chr1	10188134	10188585	E070	-43949
chr1	10238785	10238914	E070	6251
chr1	10240343	10240433	E070	7809
chr1	10273051	10273095	E070	40517
chr1	10273131	10273171	E070	40597
chr1	10274204	10274288	E070	41670
chr1	10275996	10276049	E070	43462
chr1	10276151	10276414	E070	43617
chr1	10276599	10276836	E070	44065
chr1	10276948	10276998	E070	44414
chr1	10277633	10277673	E070	45099
chr1	10278041	10278565	E070	45507
chr1	10278726	10278780	E070	46192
chr1	10188134	10188585	E071	-43949
chr1	10189473	10189608	E071	-42926
chr1	10204403	10204532	E071	-28002
chr1	10212920	10213319	E071	-19215
chr1	10220296	10220411	E071	-12123
chr1	10220988	10221189	E071	-11345
chr1	10221215	10221438	E071	-11096
chr1	10221547	10221597	E071	-10937
chr1	10221670	10222012	E071	-10522
chr1	10238785	10238914	E071	6251
chr1	10238929	10239682	E071	6395
chr1	10239786	10240317	E071	7252
chr1	10240343	10240433	E071	7809
chr1	10273051	10273095	E071	40517
chr1	10273131	10273171	E071	40597
chr1	10273832	10273935	E071	41298
chr1	10274078	10274172	E071	41544
chr1	10274204	10274288	E071	41670
chr1	10275996	10276049	E071	43462
chr1	10277633	10277673	E071	45099
chr1	10278726	10278780	E071	46192
chr1	10280343	10280393	E071	47809
chr1	10280856	10280900	E071	48322
chr1	10282231	10282488	E071	49697
chr1	10189473	10189608	E072	-42926
chr1	10190487	10190564	E072	-41970
chr1	10190873	10190933	E072	-41601
chr1	10212920	10213319	E072	-19215
chr1	10220296	10220411	E072	-12123
chr1	10220988	10221189	E072	-11345
chr1	10221215	10221438	E072	-11096
chr1	10221547	10221597	E072	-10937
chr1	10221670	10222012	E072	-10522
chr1	10222764	10222835	E072	-9699
chr1	10238785	10238914	E072	6251
chr1	10238929	10239682	E072	6395
chr1	10239786	10240317	E072	7252
chr1	10240343	10240433	E072	7809
chr1	10254191	10254301	E072	21657
chr1	10273051	10273095	E072	40517
chr1	10273131	10273171	E072	40597
chr1	10273832	10273935	E072	41298
chr1	10274078	10274172	E072	41544
chr1	10274204	10274288	E072	41670
chr1	10275996	10276049	E072	43462
chr1	10276948	10276998	E072	44414
chr1	10277633	10277673	E072	45099
chr1	10278041	10278565	E072	45507
chr1	10278726	10278780	E072	46192
chr1	10190873	10190933	E073	-41601
chr1	10220988	10221189	E073	-11345
chr1	10221215	10221438	E073	-11096
chr1	10221547	10221597	E073	-10937
chr1	10221670	10222012	E073	-10522
chr1	10238929	10239682	E073	6395
chr1	10239786	10240317	E073	7252
chr1	10240343	10240433	E073	7809
chr1	10273051	10273095	E073	40517
chr1	10273131	10273171	E073	40597
chr1	10273485	10273639	E073	40951
chr1	10274204	10274288	E073	41670
chr1	10275996	10276049	E073	43462
chr1	10276151	10276414	E073	43617
chr1	10276599	10276836	E073	44065
chr1	10276948	10276998	E073	44414
chr1	10277633	10277673	E073	45099
chr1	10278726	10278780	E073	46192
chr1	10282231	10282488	E073	49697
chr1	10188134	10188585	E074	-43949
chr1	10189473	10189608	E074	-42926
chr1	10205012	10205073	E074	-27461
chr1	10212920	10213319	E074	-19215
chr1	10220988	10221189	E074	-11345
chr1	10221215	10221438	E074	-11096
chr1	10221547	10221597	E074	-10937
chr1	10221670	10222012	E074	-10522
chr1	10238074	10238166	E074	5540
chr1	10238657	10238737	E074	6123
chr1	10238785	10238914	E074	6251
chr1	10238929	10239682	E074	6395
chr1	10239786	10240317	E074	7252
chr1	10240343	10240433	E074	7809
chr1	10241242	10241570	E074	8708
chr1	10273051	10273095	E074	40517
chr1	10273131	10273171	E074	40597
chr1	10273485	10273639	E074	40951
chr1	10273832	10273935	E074	41298
chr1	10274204	10274288	E074	41670
chr1	10276948	10276998	E074	44414
chr1	10277633	10277673	E074	45099
chr1	10278041	10278565	E074	45507
chr1	10278726	10278780	E074	46192
chr1	10282231	10282488	E074	49697
chr1	10220988	10221189	E081	-11345
chr1	10221215	10221438	E081	-11096
chr1	10221547	10221597	E081	-10937
chr1	10221670	10222012	E081	-10522
chr1	10238074	10238166	E081	5540
chr1	10238657	10238737	E081	6123
chr1	10238785	10238914	E081	6251
chr1	10238929	10239682	E081	6395
chr1	10239786	10240317	E081	7252
chr1	10240343	10240433	E081	7809
chr1	10261421	10261633	E081	28887
chr1	10273051	10273095	E081	40517
chr1	10273131	10273171	E081	40597
chr1	10273485	10273639	E081	40951
chr1	10273832	10273935	E081	41298
chr1	10274078	10274172	E081	41544
chr1	10274204	10274288	E081	41670
chr1	10275996	10276049	E081	43462
chr1	10276151	10276414	E081	43617
chr1	10276599	10276836	E081	44065
chr1	10276948	10276998	E081	44414
chr1	10277633	10277673	E081	45099
chr1	10278041	10278565	E081	45507
chr1	10220988	10221189	E082	-11345
chr1	10221215	10221438	E082	-11096
chr1	10221547	10221597	E082	-10937
chr1	10221670	10222012	E082	-10522
chr1	10240343	10240433	E082	7809
chr1	10269337	10269397	E082	36803
chr1	10275996	10276049	E082	43462
chr1	10276151	10276414	E082	43617
chr1	10276599	10276836	E082	44065
chr1	10276948	10276998	E082	44414
chr1	10277633	10277673	E082	45099
chr1	10278041	10278565	E082	45507

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	10269694	10272466	E067	37160
chr1	10269694	10272466	E068	37160
chr1	10269694	10272466	E069	37160
chr1	10269694	10272466	E070	37160
chr1	10269694	10272466	E071	37160
chr1	10269694	10272466	E072	37160
chr1	10269694	10272466	E073	37160
chr1	10269694	10272466	E074	37160
chr1	10269694	10272466	E082	37160