rs4794333

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

CDK5RAP3 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0339 (10132/29852,GnomAD)
C=0338 (9864/29118,TOPMED)
C=0276 (1381/5008,1000G)
C=0401 (1547/3854,ALSPAC)
C=0400 (1483/3708,TWINSUK)

Position: chr17:47968129 (GRCh38.p7) (17q21.32)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 380 Enhancers around

Promoter: 25 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 17	NC_000017.11:g.47968129T>C
GRCh37.p13 chr 17	NC_000017.10:g.46045495T>C

Gene: CDK5RAP3, CDK5 regulatory subunit associated protein 3(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CDK5RAP3 transcript variant 4	NM_001278197.1:c.	N/A	Genic Upstream Transcript Variant
CDK5RAP3 transcript variant 5	NM_001278198.1:c.	N/A	Genic Upstream Transcript Variant
CDK5RAP3 transcript variant 1	NM_001278216.1:c.	N/A	Genic Upstream Transcript Variant
CDK5RAP3 transcript variant 2	NM_001278217.1:c.	N/A	Genic Upstream Transcript Variant
CDK5RAP3 transcript variant 3	NM_176096.2:c.	N/A	Genic Upstream Transcript Variant
CDK5RAP3 transcript variant X1	XM_011525297.1:c.	N/A	Intron Variant
CDK5RAP3 transcript variant X2	XM_017025164.1:c.	N/A	Genic Upstream Transcript Variant
CDK5RAP3 transcript variant X3	XM_017025165.1:c.	N/A	Genic Upstream Transcript Variant
CDK5RAP3 transcript variant X4	XM_017025166.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.703	C=0.297
1000Genomes	American	Sub	694	T=0.680	C=0.320
1000Genomes	East Asian	Sub	1008	T=0.932	C=0.068
1000Genomes	Europe	Sub	1006	T=0.619	C=0.381
1000Genomes	Global	Study-wide	5008	T=0.724	C=0.276
1000Genomes	South Asian	Sub	978	T=0.680	C=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.599	C=0.401
The Genome Aggregation Database	African	Sub	8678	T=0.708	C=0.292
The Genome Aggregation Database	American	Sub	836	T=0.720	C=0.280
The Genome Aggregation Database	East Asian	Sub	1618	T=0.939	C=0.061
The Genome Aggregation Database	Europe	Sub	18418	T=0.611	C=0.388
The Genome Aggregation Database	Global	Study-wide	29852	T=0.660	C=0.339
The Genome Aggregation Database	Other	Sub	302	T=0.650	C=0.350
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.661	C=0.338
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.600	C=0.400

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs4794333	0.0003	nicotine smoking	19268276

eQTL of rs4794333 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr17:46045495	CDK5RAP3	ENSG00000108465.10	T>C	1.0311e-10	319	Cerebellum
Chr17:46045495	CDK5RAP3	ENSG00000108465.10	T>C	3.8021e-4	319	Cortex
Chr17:46045495	CDK5RAP3	ENSG00000108465.10	T>C	2.6810e-6	319	Cerebellar_Hemisphere
Chr17:46045495	CDK5RAP3	ENSG00000108465.10	T>C	4.9645e-4	319	Caudate_basal_ganglia
Chr17:46045495	CDK5RAP3	ENSG00000108465.10	T>C	3.9195e-4	319	Hippocampus

meQTL of rs4794333 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 )
chr17	46006534	46007266	E067	-38229
chr17	46007364	46007540	E067	-37955
chr17	46007685	46007747	E067	-37748
chr17	46007778	46007831	E067	-37664
chr17	46008055	46008156	E067	-37339
chr17	46015715	46015755	E067	-29740
chr17	46015846	46015946	E067	-29549
chr17	46015951	46016011	E067	-29484
chr17	46022152	46022229	E067	-23266
chr17	46022289	46022515	E067	-22980
chr17	46022544	46022789	E067	-22706
chr17	46022861	46023043	E067	-22452
chr17	46023046	46023134	E067	-22361
chr17	46023141	46023207	E067	-22288
chr17	46025879	46027659	E067	-17836
chr17	46027690	46027869	E067	-17626
chr17	46049571	46049705	E067	4076
chr17	46049827	46049915	E067	4332
chr17	46049922	46049976	E067	4427
chr17	46059981	46060036	E067	14486
chr17	46060083	46060289	E067	14588
chr17	46060383	46060675	E067	14888
chr17	46060857	46060907	E067	15362
chr17	46060931	46061002	E067	15436
chr17	46061068	46061189	E067	15573
chr17	46061265	46061488	E067	15770
chr17	46061587	46061708	E067	16092
chr17	46061779	46061829	E067	16284
chr17	46079643	46081650	E067	34148
chr17	46090678	46090747	E067	45183
chr17	46090769	46091073	E067	45274
chr17	46006346	46006432	E068	-39063
chr17	46006433	46006505	E068	-38990
chr17	46006534	46007266	E068	-38229
chr17	46007364	46007540	E068	-37955
chr17	46007685	46007747	E068	-37748
chr17	46007778	46007831	E068	-37664
chr17	46020040	46020232	E068	-25263
chr17	46020326	46020410	E068	-25085
chr17	46020418	46020479	E068	-25016
chr17	46020537	46020601	E068	-24894
chr17	46022049	46022103	E068	-23392
chr17	46022152	46022229	E068	-23266
chr17	46022289	46022515	E068	-22980
chr17	46022544	46022789	E068	-22706
chr17	46022861	46023043	E068	-22452
chr17	46023046	46023134	E068	-22361
chr17	46023141	46023207	E068	-22288
chr17	46023248	46023798	E068	-21697
chr17	46049571	46049705	E068	4076
chr17	46059382	46059967	E068	13887
chr17	46059981	46060036	E068	14486
chr17	46060083	46060289	E068	14588
chr17	46060383	46060675	E068	14888
chr17	46060857	46060907	E068	15362
chr17	46060931	46061002	E068	15436
chr17	46061068	46061189	E068	15573
chr17	46061265	46061488	E068	15770
chr17	46061587	46061708	E068	16092
chr17	46061779	46061829	E068	16284
chr17	46076954	46077493	E068	31459
chr17	46079352	46079402	E068	33857
chr17	46081765	46081815	E068	36270
chr17	46081821	46081923	E068	36326
chr17	46082084	46082174	E068	36589
chr17	46082438	46082532	E068	36943
chr17	46082550	46082769	E068	37055
chr17	46082791	46082897	E068	37296
chr17	46091931	46092491	E068	46436
chr17	46092493	46092777	E068	46998
chr17	46006346	46006432	E069	-39063
chr17	46006433	46006505	E069	-38990
chr17	46006534	46007266	E069	-38229
chr17	46007364	46007540	E069	-37955
chr17	46007685	46007747	E069	-37748
chr17	46007778	46007831	E069	-37664
chr17	46008055	46008156	E069	-37339
chr17	46017692	46017844	E069	-27651
chr17	46017845	46017897	E069	-27598
chr17	46020040	46020232	E069	-25263
chr17	46020326	46020410	E069	-25085
chr17	46020418	46020479	E069	-25016
chr17	46020537	46020601	E069	-24894
chr17	46020701	46020801	E069	-24694
chr17	46020899	46021105	E069	-24390
chr17	46022152	46022229	E069	-23266
chr17	46022289	46022515	E069	-22980
chr17	46022544	46022789	E069	-22706
chr17	46022861	46023043	E069	-22452
chr17	46023046	46023134	E069	-22361
chr17	46023141	46023207	E069	-22288
chr17	46023248	46023798	E069	-21697
chr17	46025879	46027659	E069	-17836
chr17	46049571	46049705	E069	4076
chr17	46049827	46049915	E069	4332
chr17	46049922	46049976	E069	4427
chr17	46058049	46058167	E069	12554
chr17	46058233	46058336	E069	12738
chr17	46061265	46061488	E069	15770
chr17	46061587	46061708	E069	16092
chr17	46061779	46061829	E069	16284
chr17	46078607	46078943	E069	33112
chr17	46079192	46079306	E069	33697
chr17	46079352	46079402	E069	33857
chr17	46079643	46081650	E069	34148
chr17	46082438	46082532	E069	36943
chr17	46090678	46090747	E069	45183
chr17	46090769	46091073	E069	45274
chr17	46091543	46091876	E069	46048
chr17	46049571	46049705	E070	4076
chr17	46055695	46056163	E070	10200
chr17	46056194	46056323	E070	10699
chr17	46056336	46056416	E070	10841
chr17	46064627	46065269	E070	19132
chr17	46065368	46065532	E070	19873
chr17	46068159	46068285	E070	22664
chr17	46068303	46069440	E070	22808
chr17	46071853	46072127	E070	26358
chr17	46072143	46072270	E070	26648
chr17	46072545	46073427	E070	27050
chr17	46073520	46073588	E070	28025
chr17	46073685	46073842	E070	28190
chr17	46078607	46078943	E070	33112
chr17	46079192	46079306	E070	33697
chr17	46079352	46079402	E070	33857
chr17	46081765	46081815	E070	36270
chr17	46081821	46081923	E070	36326
chr17	46082084	46082174	E070	36589
chr17	46082438	46082532	E070	36943
chr17	46082550	46082769	E070	37055
chr17	46082791	46082897	E070	37296
chr17	46082902	46082960	E070	37407
chr17	46088529	46088672	E070	43034
chr17	46090678	46090747	E070	45183
chr17	46090769	46091073	E070	45274
chr17	46091098	46091526	E070	45603
chr17	46091543	46091876	E070	46048
chr17	46091931	46092491	E070	46436
chr17	46092493	46092777	E070	46998
chr17	46006346	46006432	E071	-39063
chr17	46006433	46006505	E071	-38990
chr17	46006534	46007266	E071	-38229
chr17	46007364	46007540	E071	-37955
chr17	46007685	46007747	E071	-37748
chr17	46007778	46007831	E071	-37664
chr17	46015846	46015946	E071	-29549
chr17	46015951	46016011	E071	-29484
chr17	46017416	46017554	E071	-27941
chr17	46022152	46022229	E071	-23266
chr17	46022289	46022515	E071	-22980
chr17	46022544	46022789	E071	-22706
chr17	46022861	46023043	E071	-22452
chr17	46023046	46023134	E071	-22361
chr17	46023141	46023207	E071	-22288
chr17	46023248	46023798	E071	-21697
chr17	46023803	46024842	E071	-20653
chr17	46025879	46027659	E071	-17836
chr17	46027690	46027869	E071	-17626
chr17	46049571	46049705	E071	4076
chr17	46049827	46049915	E071	4332
chr17	46049922	46049976	E071	4427
chr17	46050040	46050090	E071	4545
chr17	46050169	46050289	E071	4674
chr17	46050322	46050458	E071	4827
chr17	46057888	46057938	E071	12393
chr17	46058049	46058167	E071	12554
chr17	46060857	46060907	E071	15362
chr17	46060931	46061002	E071	15436
chr17	46061068	46061189	E071	15573
chr17	46061265	46061488	E071	15770
chr17	46065368	46065532	E071	19873
chr17	46079643	46081650	E071	34148
chr17	46081765	46081815	E071	36270
chr17	46081821	46081923	E071	36326
chr17	46082084	46082174	E071	36589
chr17	46090678	46090747	E071	45183
chr17	46090769	46091073	E071	45274
chr17	46091098	46091526	E071	45603
chr17	46091543	46091876	E071	46048
chr17	46091931	46092491	E071	46436
chr17	46006346	46006432	E072	-39063
chr17	46006433	46006505	E072	-38990
chr17	46006534	46007266	E072	-38229
chr17	46007364	46007540	E072	-37955
chr17	46007685	46007747	E072	-37748
chr17	46007778	46007831	E072	-37664
chr17	46015414	46015547	E072	-29948
chr17	46015715	46015755	E072	-29740
chr17	46017692	46017844	E072	-27651
chr17	46017845	46017897	E072	-27598
chr17	46020040	46020232	E072	-25263
chr17	46020326	46020410	E072	-25085
chr17	46020418	46020479	E072	-25016
chr17	46020537	46020601	E072	-24894
chr17	46020701	46020801	E072	-24694
chr17	46022152	46022229	E072	-23266
chr17	46022289	46022515	E072	-22980
chr17	46022544	46022789	E072	-22706
chr17	46022861	46023043	E072	-22452
chr17	46023046	46023134	E072	-22361
chr17	46023141	46023207	E072	-22288
chr17	46023248	46023798	E072	-21697
chr17	46023803	46024842	E072	-20653
chr17	46025879	46027659	E072	-17836
chr17	46049571	46049705	E072	4076
chr17	46049827	46049915	E072	4332
chr17	46049922	46049976	E072	4427
chr17	46060383	46060675	E072	14888
chr17	46060857	46060907	E072	15362
chr17	46060931	46061002	E072	15436
chr17	46061068	46061189	E072	15573
chr17	46061265	46061488	E072	15770
chr17	46061587	46061708	E072	16092
chr17	46065368	46065532	E072	19873
chr17	46079643	46081650	E072	34148
chr17	46081765	46081815	E072	36270
chr17	46081821	46081923	E072	36326
chr17	46082084	46082174	E072	36589
chr17	46082438	46082532	E072	36943
chr17	46082550	46082769	E072	37055
chr17	46006433	46006505	E073	-38990
chr17	46006534	46007266	E073	-38229
chr17	46007364	46007540	E073	-37955
chr17	46017416	46017554	E073	-27941
chr17	46017692	46017844	E073	-27651
chr17	46017845	46017897	E073	-27598
chr17	46020040	46020232	E073	-25263
chr17	46020326	46020410	E073	-25085
chr17	46020418	46020479	E073	-25016
chr17	46020537	46020601	E073	-24894
chr17	46020701	46020801	E073	-24694
chr17	46022049	46022103	E073	-23392
chr17	46022152	46022229	E073	-23266
chr17	46022289	46022515	E073	-22980
chr17	46022544	46022789	E073	-22706
chr17	46022861	46023043	E073	-22452
chr17	46023046	46023134	E073	-22361
chr17	46023141	46023207	E073	-22288
chr17	46023248	46023798	E073	-21697
chr17	46049571	46049705	E073	4076
chr17	46049827	46049915	E073	4332
chr17	46049922	46049976	E073	4427
chr17	46050040	46050090	E073	4545
chr17	46050169	46050289	E073	4674
chr17	46059981	46060036	E073	14486
chr17	46060083	46060289	E073	14588
chr17	46060383	46060675	E073	14888
chr17	46060857	46060907	E073	15362
chr17	46060931	46061002	E073	15436
chr17	46061068	46061189	E073	15573
chr17	46061265	46061488	E073	15770
chr17	46061587	46061708	E073	16092
chr17	46061779	46061829	E073	16284
chr17	46065368	46065532	E073	19873
chr17	46079192	46079306	E073	33697
chr17	46079352	46079402	E073	33857
chr17	46079643	46081650	E073	34148
chr17	46081765	46081815	E073	36270
chr17	46081821	46081923	E073	36326
chr17	46082084	46082174	E073	36589
chr17	46082438	46082532	E073	36943
chr17	46082550	46082769	E073	37055
chr17	46082791	46082897	E073	37296
chr17	46090678	46090747	E073	45183
chr17	46090769	46091073	E073	45274
chr17	46091098	46091526	E073	45603
chr17	46091543	46091876	E073	46048
chr17	46006346	46006432	E074	-39063
chr17	46006433	46006505	E074	-38990
chr17	46006534	46007266	E074	-38229
chr17	46007364	46007540	E074	-37955
chr17	46007685	46007747	E074	-37748
chr17	46007778	46007831	E074	-37664
chr17	46020040	46020232	E074	-25263
chr17	46022289	46022515	E074	-22980
chr17	46022544	46022789	E074	-22706
chr17	46022861	46023043	E074	-22452
chr17	46023046	46023134	E074	-22361
chr17	46023141	46023207	E074	-22288
chr17	46023248	46023798	E074	-21697
chr17	46023803	46024842	E074	-20653
chr17	46025879	46027659	E074	-17836
chr17	46049571	46049705	E074	4076
chr17	46049827	46049915	E074	4332
chr17	46049922	46049976	E074	4427
chr17	46050040	46050090	E074	4545
chr17	46050169	46050289	E074	4674
chr17	46065368	46065532	E074	19873
chr17	46079643	46081650	E074	34148
chr17	46025879	46027659	E081	-17836
chr17	46049571	46049705	E081	4076
chr17	46049827	46049915	E081	4332
chr17	46049922	46049976	E081	4427
chr17	46055695	46056163	E081	10200
chr17	46056194	46056323	E081	10699
chr17	46063648	46064518	E081	18153
chr17	46064627	46065269	E081	19132
chr17	46065368	46065532	E081	19873
chr17	46068159	46068285	E081	22664
chr17	46068303	46069440	E081	22808
chr17	46071853	46072127	E081	26358
chr17	46072143	46072270	E081	26648
chr17	46072545	46073427	E081	27050
chr17	46073520	46073588	E081	28025
chr17	46073685	46073842	E081	28190
chr17	46073856	46073957	E081	28361
chr17	46074040	46074205	E081	28545
chr17	46076396	46076663	E081	30901
chr17	46076954	46077493	E081	31459
chr17	46077517	46077860	E081	32022
chr17	46078607	46078943	E081	33112
chr17	46079192	46079306	E081	33697
chr17	46079352	46079402	E081	33857
chr17	46079643	46081650	E081	34148
chr17	46081765	46081815	E081	36270
chr17	46081821	46081923	E081	36326
chr17	46082084	46082174	E081	36589
chr17	46082438	46082532	E081	36943
chr17	46082550	46082769	E081	37055
chr17	46082791	46082897	E081	37296
chr17	46082902	46082960	E081	37407
chr17	46083336	46083396	E081	37841
chr17	46083475	46083562	E081	37980
chr17	46083628	46083689	E081	38133
chr17	46084381	46084528	E081	38886
chr17	46087411	46087484	E081	41916
chr17	46087566	46087635	E081	42071
chr17	46088346	46088406	E081	42851
chr17	46088529	46088672	E081	43034
chr17	46090678	46090747	E081	45183
chr17	46090769	46091073	E081	45274
chr17	46091098	46091526	E081	45603
chr17	46091543	46091876	E081	46048
chr17	46091931	46092491	E081	46436
chr17	46092493	46092777	E081	46998
chr17	46093517	46093816	E081	48022
chr17	46093848	46094170	E081	48353
chr17	46049827	46049915	E082	4332
chr17	46049922	46049976	E082	4427
chr17	46056194	46056323	E082	10699
chr17	46056336	46056416	E082	10841
chr17	46056498	46056538	E082	11003
chr17	46056584	46056650	E082	11089
chr17	46064627	46065269	E082	19132
chr17	46065368	46065532	E082	19873
chr17	46068159	46068285	E082	22664
chr17	46068303	46069440	E082	22808
chr17	46069595	46069954	E082	24100
chr17	46070394	46070527	E082	24899
chr17	46070661	46070774	E082	25166
chr17	46070875	46070925	E082	25380
chr17	46071491	46071578	E082	25996
chr17	46071640	46071848	E082	26145
chr17	46071853	46072127	E082	26358
chr17	46072143	46072270	E082	26648
chr17	46072545	46073427	E082	27050
chr17	46073520	46073588	E082	28025
chr17	46073685	46073842	E082	28190
chr17	46076954	46077493	E082	31459
chr17	46077517	46077860	E082	32022
chr17	46078607	46078943	E082	33112
chr17	46079192	46079306	E082	33697
chr17	46079352	46079402	E082	33857
chr17	46081821	46081923	E082	36326
chr17	46082084	46082174	E082	36589
chr17	46082438	46082532	E082	36943
chr17	46082550	46082769	E082	37055
chr17	46082791	46082897	E082	37296
chr17	46082902	46082960	E082	37407
chr17	46083336	46083396	E082	37841
chr17	46083475	46083562	E082	37980
chr17	46083628	46083689	E082	38133
chr17	46087411	46087484	E082	41916
chr17	46087566	46087635	E082	42071
chr17	46090678	46090747	E082	45183
chr17	46090769	46091073	E082	45274
chr17	46091098	46091526	E082	45603
chr17	46091543	46091876	E082	46048
chr17	46091931	46092491	E082	46436
chr17	46092493	46092777	E082	46998

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr17	46018287	46019736	E067	-25759
chr17	46047367	46049081	E067	1872
chr17	46018287	46019736	E068	-25759
chr17	46047367	46049081	E068	1872
chr17	46088687	46090632	E068	43192
chr17	46018287	46019736	E069	-25759
chr17	46047367	46049081	E069	1872
chr17	46018287	46019736	E070	-25759
chr17	46047367	46049081	E070	1872
chr17	46088687	46090632	E070	43192
chr17	46018287	46019736	E071	-25759
chr17	46047367	46049081	E071	1872
chr17	46018287	46019736	E072	-25759
chr17	46047367	46049081	E072	1872
chr17	46088687	46090632	E072	43192
chr17	46018287	46019736	E073	-25759
chr17	46047367	46049081	E073	1872
chr17	46088687	46090632	E073	43192
chr17	46018287	46019736	E074	-25759
chr17	46047367	46049081	E074	1872
chr17	46018287	46019736	E081	-25759
chr17	46047367	46049081	E081	1872
chr17	46018287	46019736	E082	-25759
chr17	46047367	46049081	E082	1872
chr17	46088687	46090632	E082	43192