rs4951373

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

PIK3C2B : Non Coding Transcript Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0180 (5383/29910,GnomAD)
A=0181 (5272/29118,TOPMED)
A=0282 (1412/5008,1000G)

Position: chr1:204423129 (GRCh38.p7) (1q32.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 242 Enhancers around

Promoter: 132 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.204423129G>A
GRCh37.p13 chr 1	NC_000001.10:g.204392257G>A

Gene: PIK3C2B, phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PIK3C2B transcript	NM_002646.3:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X1	XM_005245257.2:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X2	XM_017001473.1:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X3	XM_011509630.2:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X4	XM_011509631.2:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X5	XM_017001474.1:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X6	XM_005245258.3:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X9	XM_017001475.1:c.	N/A	3 Prime UTR Variant
PIK3C2B transcript variant X10	XM_011509633.2:c.	N/A	Genic Downstream Transcript Variant
PIK3C2B transcript variant X7	XR_241085.2:n.705...XR_241085.2:n.7054C>T	C>T	Non Coding Transcript Variant
PIK3C2B transcript variant X8	XR_241086.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.784	A=0.216
1000Genomes	American	Sub	694	G=0.850	A=0.150
1000Genomes	East Asian	Sub	1008	G=0.417	A=0.583
1000Genomes	Europe	Sub	1006	G=0.872	A=0.128
1000Genomes	Global	Study-wide	5008	G=0.718	A=0.282
1000Genomes	South Asian	Sub	978	G=0.690	A=0.310
The Genome Aggregation Database	African	Sub	8700	G=0.765	A=0.235
The Genome Aggregation Database	American	Sub	838	G=0.880	A=0.120
The Genome Aggregation Database	East Asian	Sub	1616	G=0.398	A=0.602
The Genome Aggregation Database	Europe	Sub	18454	G=0.878	A=0.121
The Genome Aggregation Database	Global	Study-wide	29910	G=0.820	A=0.180
The Genome Aggregation Database	Other	Sub	302	G=0.890	A=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.818	A=0.181

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
rs4951373	0.000064	alcohol dependence(early age of onset)	20201924
rs4951373	0.0000642	alcoholism	pha002892
rs4951373	0.00016	alcohol dependence	20201924

eQTL of rs4951373 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 rs4951373 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	204353743	204353821	E067	-38436
chr1	204353896	204354040	E067	-38217
chr1	204354131	204354337	E067	-37920
chr1	204354437	204354546	E067	-37711
chr1	204397291	204397341	E067	5034
chr1	204404088	204404190	E067	11831
chr1	204404264	204404385	E067	12007
chr1	204414982	204416198	E067	22725
chr1	204423720	204423943	E067	31463
chr1	204423984	204424745	E067	31727
chr1	204424952	204425029	E067	32695
chr1	204425077	204425351	E067	32820
chr1	204425609	204425785	E067	33352
chr1	204425834	204426770	E067	33577
chr1	204427005	204427137	E067	34748
chr1	204427222	204427272	E067	34965
chr1	204431321	204431460	E067	39064
chr1	204431530	204431600	E067	39273
chr1	204432124	204432239	E067	39867
chr1	204432381	204432770	E067	40124
chr1	204432899	204433030	E067	40642
chr1	204433047	204433203	E067	40790
chr1	204433603	204433695	E067	41346
chr1	204433765	204433887	E067	41508
chr1	204434047	204434103	E067	41790
chr1	204434679	204436514	E067	42422
chr1	204436673	204436740	E067	44416
chr1	204437436	204437760	E067	45179
chr1	204437894	204437953	E067	45637
chr1	204438564	204438725	E067	46307
chr1	204353743	204353821	E068	-38436
chr1	204353896	204354040	E068	-38217
chr1	204354131	204354337	E068	-37920
chr1	204354437	204354546	E068	-37711
chr1	204375117	204375400	E068	-16857
chr1	204386152	204387828	E068	-4429
chr1	204388318	204388509	E068	-3748
chr1	204412829	204413615	E068	20572
chr1	204414982	204416198	E068	22725
chr1	204423984	204424745	E068	31727
chr1	204424952	204425029	E068	32695
chr1	204425077	204425351	E068	32820
chr1	204425834	204426770	E068	33577
chr1	204427005	204427137	E068	34748
chr1	204432124	204432239	E068	39867
chr1	204432381	204432770	E068	40124
chr1	204432899	204433030	E068	40642
chr1	204433047	204433203	E068	40790
chr1	204433603	204433695	E068	41346
chr1	204433765	204433887	E068	41508
chr1	204434047	204434103	E068	41790
chr1	204434679	204436514	E068	42422
chr1	204436673	204436740	E068	44416
chr1	204437894	204437953	E068	45637
chr1	204438564	204438725	E068	46307
chr1	204353743	204353821	E069	-38436
chr1	204353896	204354040	E069	-38217
chr1	204354131	204354337	E069	-37920
chr1	204354437	204354546	E069	-37711
chr1	204367528	204368096	E069	-24161
chr1	204375117	204375400	E069	-16857
chr1	204400516	204400928	E069	8259
chr1	204400931	204401285	E069	8674
chr1	204406807	204406872	E069	14550
chr1	204406950	204407282	E069	14693
chr1	204407436	204407675	E069	15179
chr1	204407734	204408113	E069	15477
chr1	204408132	204408250	E069	15875
chr1	204414982	204416198	E069	22725
chr1	204423720	204423943	E069	31463
chr1	204423984	204424745	E069	31727
chr1	204424952	204425029	E069	32695
chr1	204425077	204425351	E069	32820
chr1	204425834	204426770	E069	33577
chr1	204428983	204429121	E069	36726
chr1	204430292	204431282	E069	38035
chr1	204431321	204431460	E069	39064
chr1	204431530	204431600	E069	39273
chr1	204432124	204432239	E069	39867
chr1	204432899	204433030	E069	40642
chr1	204433047	204433203	E069	40790
chr1	204433603	204433695	E069	41346
chr1	204433765	204433887	E069	41508
chr1	204434047	204434103	E069	41790
chr1	204434679	204436514	E069	42422
chr1	204436673	204436740	E069	44416
chr1	204437436	204437760	E069	45179
chr1	204437894	204437953	E069	45637
chr1	204438564	204438725	E069	46307
chr1	204353743	204353821	E070	-38436
chr1	204353896	204354040	E070	-38217
chr1	204354131	204354337	E070	-37920
chr1	204375117	204375400	E070	-16857
chr1	204434679	204436514	E070	42422
chr1	204436673	204436740	E070	44416
chr1	204437436	204437760	E070	45179
chr1	204437894	204437953	E070	45637
chr1	204353743	204353821	E071	-38436
chr1	204353896	204354040	E071	-38217
chr1	204354131	204354337	E071	-37920
chr1	204354437	204354546	E071	-37711
chr1	204387938	204388275	E071	-3982
chr1	204388318	204388509	E071	-3748
chr1	204400931	204401285	E071	8674
chr1	204403307	204403713	E071	11050
chr1	204414982	204416198	E071	22725
chr1	204419536	204420687	E071	27279
chr1	204420854	204421091	E071	28597
chr1	204423720	204423943	E071	31463
chr1	204423984	204424745	E071	31727
chr1	204424952	204425029	E071	32695
chr1	204425077	204425351	E071	32820
chr1	204425609	204425785	E071	33352
chr1	204425834	204426770	E071	33577
chr1	204427005	204427137	E071	34748
chr1	204427222	204427272	E071	34965
chr1	204430292	204431282	E071	38035
chr1	204431321	204431460	E071	39064
chr1	204431530	204431600	E071	39273
chr1	204432124	204432239	E071	39867
chr1	204432381	204432770	E071	40124
chr1	204432899	204433030	E071	40642
chr1	204433047	204433203	E071	40790
chr1	204433603	204433695	E071	41346
chr1	204433765	204433887	E071	41508
chr1	204434047	204434103	E071	41790
chr1	204434679	204436514	E071	42422
chr1	204436673	204436740	E071	44416
chr1	204437436	204437760	E071	45179
chr1	204437894	204437953	E071	45637
chr1	204438564	204438725	E071	46307
chr1	204347804	204347877	E072	-44380
chr1	204353743	204353821	E072	-38436
chr1	204353896	204354040	E072	-38217
chr1	204354131	204354337	E072	-37920
chr1	204354437	204354546	E072	-37711
chr1	204367528	204368096	E072	-24161
chr1	204375117	204375400	E072	-16857
chr1	204394908	204395046	E072	2651
chr1	204395162	204395424	E072	2905
chr1	204395502	204395614	E072	3245
chr1	204400516	204400928	E072	8259
chr1	204400931	204401285	E072	8674
chr1	204414982	204416198	E072	22725
chr1	204423720	204423943	E072	31463
chr1	204423984	204424745	E072	31727
chr1	204424952	204425029	E072	32695
chr1	204425077	204425351	E072	32820
chr1	204425609	204425785	E072	33352
chr1	204425834	204426770	E072	33577
chr1	204428983	204429121	E072	36726
chr1	204430292	204431282	E072	38035
chr1	204431321	204431460	E072	39064
chr1	204431530	204431600	E072	39273
chr1	204432124	204432239	E072	39867
chr1	204432381	204432770	E072	40124
chr1	204432899	204433030	E072	40642
chr1	204433047	204433203	E072	40790
chr1	204433603	204433695	E072	41346
chr1	204433765	204433887	E072	41508
chr1	204434047	204434103	E072	41790
chr1	204434679	204436514	E072	42422
chr1	204436673	204436740	E072	44416
chr1	204437436	204437760	E072	45179
chr1	204438564	204438725	E072	46307
chr1	204353743	204353821	E073	-38436
chr1	204353896	204354040	E073	-38217
chr1	204354131	204354337	E073	-37920
chr1	204375117	204375400	E073	-16857
chr1	204400359	204400431	E073	8102
chr1	204400516	204400928	E073	8259
chr1	204414982	204416198	E073	22725
chr1	204423720	204423943	E073	31463
chr1	204423984	204424745	E073	31727
chr1	204424952	204425029	E073	32695
chr1	204425077	204425351	E073	32820
chr1	204425834	204426770	E073	33577
chr1	204431321	204431460	E073	39064
chr1	204431530	204431600	E073	39273
chr1	204432124	204432239	E073	39867
chr1	204432381	204432770	E073	40124
chr1	204432899	204433030	E073	40642
chr1	204433047	204433203	E073	40790
chr1	204433603	204433695	E073	41346
chr1	204433765	204433887	E073	41508
chr1	204434679	204436514	E073	42422
chr1	204436673	204436740	E073	44416
chr1	204437436	204437760	E073	45179
chr1	204437894	204437953	E073	45637
chr1	204438564	204438725	E073	46307
chr1	204353743	204353821	E074	-38436
chr1	204353896	204354040	E074	-38217
chr1	204354131	204354337	E074	-37920
chr1	204354437	204354546	E074	-37711
chr1	204375117	204375400	E074	-16857
chr1	204400516	204400928	E074	8259
chr1	204414982	204416198	E074	22725
chr1	204420854	204421091	E074	28597
chr1	204423720	204423943	E074	31463
chr1	204423984	204424745	E074	31727
chr1	204424952	204425029	E074	32695
chr1	204425077	204425351	E074	32820
chr1	204425834	204426770	E074	33577
chr1	204427005	204427137	E074	34748
chr1	204427222	204427272	E074	34965
chr1	204428983	204429121	E074	36726
chr1	204430292	204431282	E074	38035
chr1	204431321	204431460	E074	39064
chr1	204431530	204431600	E074	39273
chr1	204432124	204432239	E074	39867
chr1	204432381	204432770	E074	40124
chr1	204432899	204433030	E074	40642
chr1	204433047	204433203	E074	40790
chr1	204434047	204434103	E074	41790
chr1	204434679	204436514	E074	42422
chr1	204436673	204436740	E074	44416
chr1	204437436	204437760	E074	45179
chr1	204437894	204437953	E074	45637
chr1	204438564	204438725	E074	46307
chr1	204353743	204353821	E081	-38436
chr1	204353896	204354040	E081	-38217
chr1	204354131	204354337	E081	-37920
chr1	204354437	204354546	E081	-37711
chr1	204400516	204400928	E081	8259
chr1	204400931	204401285	E081	8674
chr1	204423720	204423943	E081	31463
chr1	204423984	204424745	E081	31727
chr1	204424952	204425029	E081	32695
chr1	204434679	204436514	E081	42422
chr1	204437436	204437760	E081	45179
chr1	204437894	204437953	E081	45637
chr1	204353743	204353821	E082	-38436
chr1	204353896	204354040	E082	-38217
chr1	204354131	204354337	E082	-37920
chr1	204354437	204354546	E082	-37711
chr1	204414982	204416198	E082	22725
chr1	204423720	204423943	E082	31463
chr1	204423984	204424745	E082	31727
chr1	204424952	204425029	E082	32695
chr1	204425077	204425351	E082	32820
chr1	204434679	204436514	E082	42422
chr1	204437894	204437953	E082	45637

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	204346903	204347783	E067	-44474
chr1	204376004	204376052	E067	-16205
chr1	204376646	204376716	E067	-15541
chr1	204376855	204377048	E067	-15209
chr1	204377121	204377180	E067	-15077
chr1	204377188	204377490	E067	-14767
chr1	204377496	204377642	E067	-14615
chr1	204377746	204377907	E067	-14350
chr1	204377969	204378019	E067	-14238
chr1	204378306	204378548	E067	-13709
chr1	204378652	204378769	E067	-13488
chr1	204378935	204379049	E067	-13208
chr1	204379114	204379401	E067	-12856
chr1	204379470	204381851	E067	-10406
chr1	204346218	204346859	E068	-45398
chr1	204346903	204347783	E068	-44474
chr1	204376004	204376052	E068	-16205
chr1	204376646	204376716	E068	-15541
chr1	204376855	204377048	E068	-15209
chr1	204377121	204377180	E068	-15077
chr1	204377188	204377490	E068	-14767
chr1	204377496	204377642	E068	-14615
chr1	204377746	204377907	E068	-14350
chr1	204377969	204378019	E068	-14238
chr1	204378306	204378548	E068	-13709
chr1	204378652	204378769	E068	-13488
chr1	204378935	204379049	E068	-13208
chr1	204379114	204379401	E068	-12856
chr1	204379470	204381851	E068	-10406
chr1	204346218	204346859	E069	-45398
chr1	204346903	204347783	E069	-44474
chr1	204376004	204376052	E069	-16205
chr1	204376646	204376716	E069	-15541
chr1	204376855	204377048	E069	-15209
chr1	204377121	204377180	E069	-15077
chr1	204377188	204377490	E069	-14767
chr1	204377496	204377642	E069	-14615
chr1	204377746	204377907	E069	-14350
chr1	204377969	204378019	E069	-14238
chr1	204378306	204378548	E069	-13709
chr1	204378652	204378769	E069	-13488
chr1	204378935	204379049	E069	-13208
chr1	204379114	204379401	E069	-12856
chr1	204379470	204381851	E069	-10406
chr1	204376004	204376052	E070	-16205
chr1	204376646	204376716	E070	-15541
chr1	204376855	204377048	E070	-15209
chr1	204377121	204377180	E070	-15077
chr1	204377188	204377490	E070	-14767
chr1	204377496	204377642	E070	-14615
chr1	204377746	204377907	E070	-14350
chr1	204377969	204378019	E070	-14238
chr1	204378306	204378548	E070	-13709
chr1	204378652	204378769	E070	-13488
chr1	204378935	204379049	E070	-13208
chr1	204379114	204379401	E070	-12856
chr1	204379470	204381851	E070	-10406
chr1	204346218	204346859	E071	-45398
chr1	204346903	204347783	E071	-44474
chr1	204376004	204376052	E071	-16205
chr1	204376646	204376716	E071	-15541
chr1	204376855	204377048	E071	-15209
chr1	204377121	204377180	E071	-15077
chr1	204377188	204377490	E071	-14767
chr1	204377496	204377642	E071	-14615
chr1	204377746	204377907	E071	-14350
chr1	204377969	204378019	E071	-14238
chr1	204378306	204378548	E071	-13709
chr1	204378652	204378769	E071	-13488
chr1	204379470	204381851	E071	-10406
chr1	204346218	204346859	E072	-45398
chr1	204346903	204347783	E072	-44474
chr1	204376004	204376052	E072	-16205
chr1	204376646	204376716	E072	-15541
chr1	204376855	204377048	E072	-15209
chr1	204377121	204377180	E072	-15077
chr1	204377188	204377490	E072	-14767
chr1	204377496	204377642	E072	-14615
chr1	204377746	204377907	E072	-14350
chr1	204377969	204378019	E072	-14238
chr1	204378306	204378548	E072	-13709
chr1	204379470	204381851	E072	-10406
chr1	204346903	204347783	E073	-44474
chr1	204376646	204376716	E073	-15541
chr1	204376855	204377048	E073	-15209
chr1	204377121	204377180	E073	-15077
chr1	204377188	204377490	E073	-14767
chr1	204377496	204377642	E073	-14615
chr1	204377746	204377907	E073	-14350
chr1	204377969	204378019	E073	-14238
chr1	204378306	204378548	E073	-13709
chr1	204378652	204378769	E073	-13488
chr1	204378935	204379049	E073	-13208
chr1	204379114	204379401	E073	-12856
chr1	204379470	204381851	E073	-10406
chr1	204345908	204346085	E074	-46172
chr1	204346218	204346859	E074	-45398
chr1	204346903	204347783	E074	-44474
chr1	204376004	204376052	E074	-16205
chr1	204376646	204376716	E074	-15541
chr1	204376855	204377048	E074	-15209
chr1	204377121	204377180	E074	-15077
chr1	204377188	204377490	E074	-14767
chr1	204377496	204377642	E074	-14615
chr1	204377746	204377907	E074	-14350
chr1	204377969	204378019	E074	-14238
chr1	204378306	204378548	E074	-13709
chr1	204378652	204378769	E074	-13488
chr1	204378935	204379049	E074	-13208
chr1	204379114	204379401	E074	-12856
chr1	204379470	204381851	E074	-10406
chr1	204376646	204376716	E081	-15541
chr1	204376855	204377048	E081	-15209
chr1	204377121	204377180	E081	-15077
chr1	204377188	204377490	E081	-14767
chr1	204377496	204377642	E081	-14615
chr1	204377746	204377907	E081	-14350
chr1	204377969	204378019	E081	-14238
chr1	204378306	204378548	E081	-13709
chr1	204376004	204376052	E082	-16205
chr1	204376646	204376716	E082	-15541
chr1	204376855	204377048	E082	-15209
chr1	204377121	204377180	E082	-15077
chr1	204377188	204377490	E082	-14767
chr1	204377496	204377642	E082	-14615
chr1	204377746	204377907	E082	-14350
chr1	204377969	204378019	E082	-14238
chr1	204378306	204378548	E082	-13709
chr1	204378652	204378769	E082	-13488
chr1	204378935	204379049	E082	-13208
chr1	204379114	204379401	E082	-12856
chr1	204379470	204381851	E082	-10406