rs3755233

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

NRP2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0159 (4761/29936,GnomAD)
A=0201 (5875/29118,TOPMED)
A=0190 (953/5008,1000G)
A=0105 (404/3854,ALSPAC)
A=0117 (433/3708,TWINSUK)

Position: chr2:205775107 (GRCh38.p7) (2q33.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 204 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.205775107G>A
GRCh37.p13 chr 2	NC_000002.11:g.206639831G>A
NRP2 RefSeqGene	NG_029567.1:g.97608G>A

Gene: NRP2, neuropilin 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
NRP2 transcript variant 2	NM_003872.2:c.	N/A	Intron Variant
NRP2 transcript variant 4	NM_018534.3:c.	N/A	Intron Variant
NRP2 transcript variant 1	NM_201266.1:c.	N/A	Intron Variant
NRP2 transcript variant 5	NM_201267.1:c.	N/A	Intron Variant
NRP2 transcript variant 3	NM_201279.1:c.	N/A	Intron Variant
NRP2 transcript variant 6	NM_201264.1:c.	N/A	Genic Downstream Transcript Variant
NRP2 transcript variant X1	XM_005246933.3:c.	N/A	Intron Variant
NRP2 transcript variant X2	XM_005246934.3:c.	N/A	Intron Variant
NRP2 transcript variant X3	XM_017005185.1:c.	N/A	Intron Variant
NRP2 transcript variant X4	XM_017005186.1:c.	N/A	Intron Variant
NRP2 transcript variant X5	XM_017005187.1:c.	N/A	Intron Variant
NRP2 transcript variant X6	XM_017005188.1:c.	N/A	Intron Variant
NRP2 transcript variant X7	XR_923055.2:n.	N/A	Intron Variant
NRP2 transcript variant X8	XR_923056.2:n.	N/A	Intron Variant
NRP2 transcript variant X9	XR_923057.2:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.670	A=0.330
1000Genomes	American	Sub	694	G=0.830	A=0.170
1000Genomes	East Asian	Sub	1008	G=0.795	A=0.205
1000Genomes	Europe	Sub	1006	G=0.895	A=0.105
1000Genomes	Global	Study-wide	5008	G=0.810	A=0.190
1000Genomes	South Asian	Sub	978	G=0.920	A=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.895	A=0.105
The Genome Aggregation Database	African	Sub	8698	G=0.729	A=0.271
The Genome Aggregation Database	American	Sub	836	G=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1622	G=0.785	A=0.215
The Genome Aggregation Database	Europe	Sub	18478	G=0.899	A=0.100
The Genome Aggregation Database	Global	Study-wide	29936	G=0.841	A=0.159
The Genome Aggregation Database	Other	Sub	302	G=0.890	A=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.798	A=0.201
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.883	A=0.117

PMID	Title	Author	Journal
20158304	A genomewide association study of nicotine and alcohol dependence in Australian and Dutch populations.	Lind PA	Twin Res Hum Genet
21183627	Genomic predictors of the maximal O(2) uptake response to standardized exercise training programs.	Bouchard C	J Appl Physiol (1985)

P-Value

SNP ID	p-value	Traits	Study
rs3755233	2.13E-05	alcohol and nictotine co-dependence	20158304

eQTL of rs3755233 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 rs3755233 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 )
chr2	206593269	206593511	E067	-46320
chr2	206593821	206593948	E067	-45883
chr2	206598461	206598688	E067	-41143
chr2	206598751	206598817	E067	-41014
chr2	206598970	206599053	E067	-40778
chr2	206599188	206599790	E067	-40041
chr2	206599990	206600030	E067	-39801
chr2	206622693	206623264	E067	-16567
chr2	206623295	206623542	E067	-16289
chr2	206628222	206629543	E067	-10288
chr2	206639780	206639864	E067	0
chr2	206639868	206640550	E067	37
chr2	206594326	206594403	E068	-45428
chr2	206594697	206594831	E068	-45000
chr2	206594873	206596788	E068	-43043
chr2	206598751	206598817	E068	-41014
chr2	206598970	206599053	E068	-40778
chr2	206599188	206599790	E068	-40041
chr2	206616326	206616874	E068	-22957
chr2	206616979	206617064	E068	-22767
chr2	206617296	206617350	E068	-22481
chr2	206619644	206620034	E068	-19797
chr2	206620052	206620161	E068	-19670
chr2	206620416	206620552	E068	-19279
chr2	206620586	206621012	E068	-18819
chr2	206623295	206623542	E068	-16289
chr2	206630026	206630118	E068	-9713
chr2	206630159	206630209	E068	-9622
chr2	206631014	206631134	E068	-8697
chr2	206635298	206636270	E068	-3561
chr2	206636324	206636429	E068	-3402
chr2	206639868	206640550	E068	37
chr2	206640771	206640860	E068	940
chr2	206646207	206646362	E068	6376
chr2	206646368	206646540	E068	6537
chr2	206646705	206646804	E068	6874
chr2	206646958	206647011	E068	7127
chr2	206648603	206648712	E068	8772
chr2	206648760	206649070	E068	8929
chr2	206592882	206593015	E069	-46816
chr2	206593169	206593260	E069	-46571
chr2	206593269	206593511	E069	-46320
chr2	206593821	206593948	E069	-45883
chr2	206594326	206594403	E069	-45428
chr2	206594697	206594831	E069	-45000
chr2	206597733	206598232	E069	-41599
chr2	206598461	206598688	E069	-41143
chr2	206598751	206598817	E069	-41014
chr2	206617296	206617350	E069	-22481
chr2	206617744	206617883	E069	-21948
chr2	206618618	206618697	E069	-21134
chr2	206618754	206618826	E069	-21005
chr2	206619008	206619305	E069	-20526
chr2	206619347	206619467	E069	-20364
chr2	206628067	206628148	E069	-11683
chr2	206592882	206593015	E070	-46816
chr2	206593169	206593260	E070	-46571
chr2	206593269	206593511	E070	-46320
chr2	206593821	206593948	E070	-45883
chr2	206594326	206594403	E070	-45428
chr2	206599188	206599790	E070	-40041
chr2	206619347	206619467	E070	-20364
chr2	206619644	206620034	E070	-19797
chr2	206620052	206620161	E070	-19670
chr2	206620416	206620552	E070	-19279
chr2	206620586	206621012	E070	-18819
chr2	206627717	206627850	E070	-11981
chr2	206628067	206628148	E070	-11683
chr2	206631459	206631506	E070	-8325
chr2	206631577	206631795	E070	-8036
chr2	206638848	206639057	E070	-774
chr2	206639578	206639639	E070	-192
chr2	206639780	206639864	E070	0
chr2	206639868	206640550	E070	37
chr2	206640771	206640860	E070	940
chr2	206640863	206641287	E070	1032
chr2	206645299	206645789	E070	5468
chr2	206646001	206646145	E070	6170
chr2	206646207	206646362	E070	6376
chr2	206646368	206646540	E070	6537
chr2	206646705	206646804	E070	6874
chr2	206646958	206647011	E070	7127
chr2	206680634	206680737	E070	40803
chr2	206681125	206681595	E070	41294
chr2	206593169	206593260	E071	-46571
chr2	206593269	206593511	E071	-46320
chr2	206593821	206593948	E071	-45883
chr2	206594326	206594403	E071	-45428
chr2	206594697	206594831	E071	-45000
chr2	206594873	206596788	E071	-43043
chr2	206597210	206597332	E071	-42499
chr2	206597386	206597430	E071	-42401
chr2	206597475	206597559	E071	-42272
chr2	206597733	206598232	E071	-41599
chr2	206598461	206598688	E071	-41143
chr2	206598751	206598817	E071	-41014
chr2	206598970	206599053	E071	-40778
chr2	206599188	206599790	E071	-40041
chr2	206599990	206600030	E071	-39801
chr2	206616223	206616318	E071	-23513
chr2	206616326	206616874	E071	-22957
chr2	206616979	206617064	E071	-22767
chr2	206618618	206618697	E071	-21134
chr2	206618754	206618826	E071	-21005
chr2	206619008	206619305	E071	-20526
chr2	206619347	206619467	E071	-20364
chr2	206619644	206620034	E071	-19797
chr2	206620416	206620552	E071	-19279
chr2	206622102	206622176	E071	-17655
chr2	206622693	206623264	E071	-16567
chr2	206623295	206623542	E071	-16289
chr2	206623685	206623735	E071	-16096
chr2	206623836	206624041	E071	-15790
chr2	206634869	206635001	E071	-4830
chr2	206639578	206639639	E071	-192
chr2	206639780	206639864	E071	0
chr2	206639868	206640550	E071	37
chr2	206648760	206649070	E071	8929
chr2	206593269	206593511	E072	-46320
chr2	206593821	206593948	E072	-45883
chr2	206598751	206598817	E072	-41014
chr2	206598970	206599053	E072	-40778
chr2	206599188	206599790	E072	-40041
chr2	206599990	206600030	E072	-39801
chr2	206593269	206593511	E073	-46320
chr2	206593821	206593948	E073	-45883
chr2	206594326	206594403	E073	-45428
chr2	206618754	206618826	E073	-21005
chr2	206619008	206619305	E073	-20526
chr2	206619347	206619467	E073	-20364
chr2	206619644	206620034	E073	-19797
chr2	206628067	206628148	E073	-11683
chr2	206628222	206629543	E073	-10288
chr2	206664825	206666224	E073	24994
chr2	206592882	206593015	E074	-46816
chr2	206593169	206593260	E074	-46571
chr2	206593269	206593511	E074	-46320
chr2	206593821	206593948	E074	-45883
chr2	206594326	206594403	E074	-45428
chr2	206594697	206594831	E074	-45000
chr2	206594873	206596788	E074	-43043
chr2	206621744	206621845	E074	-17986
chr2	206622693	206623264	E074	-16567
chr2	206623295	206623542	E074	-16289
chr2	206623685	206623735	E074	-16096
chr2	206628067	206628148	E074	-11683
chr2	206633449	206634846	E074	-4985
chr2	206639578	206639639	E074	-192
chr2	206639780	206639864	E074	0
chr2	206648603	206648712	E074	8772
chr2	206648760	206649070	E074	8929
chr2	206592882	206593015	E081	-46816
chr2	206593169	206593260	E081	-46571
chr2	206593269	206593511	E081	-46320
chr2	206593821	206593948	E081	-45883
chr2	206594326	206594403	E081	-45428
chr2	206594697	206594831	E081	-45000
chr2	206594873	206596788	E081	-43043
chr2	206624848	206625257	E081	-14574
chr2	206625390	206625654	E081	-14177
chr2	206627283	206627374	E081	-12457
chr2	206627717	206627850	E081	-11981
chr2	206628067	206628148	E081	-11683
chr2	206628222	206629543	E081	-10288
chr2	206630026	206630118	E081	-9713
chr2	206630159	206630209	E081	-9622
chr2	206631014	206631134	E081	-8697
chr2	206631277	206631358	E081	-8473
chr2	206631459	206631506	E081	-8325
chr2	206631577	206631795	E081	-8036
chr2	206631960	206632067	E081	-7764
chr2	206632108	206632276	E081	-7555
chr2	206635298	206636270	E081	-3561
chr2	206636324	206636429	E081	-3402
chr2	206636517	206636706	E081	-3125
chr2	206636781	206637076	E081	-2755
chr2	206638848	206639057	E081	-774
chr2	206639578	206639639	E081	-192
chr2	206639780	206639864	E081	0
chr2	206640771	206640860	E081	940
chr2	206640863	206641287	E081	1032
chr2	206666238	206666549	E081	26407
chr2	206670406	206670541	E081	30575
chr2	206672486	206672562	E081	32655
chr2	206673334	206673565	E081	33503
chr2	206592882	206593015	E082	-46816
chr2	206593169	206593260	E082	-46571
chr2	206593269	206593511	E082	-46320
chr2	206593821	206593948	E082	-45883
chr2	206594326	206594403	E082	-45428
chr2	206594873	206596788	E082	-43043
chr2	206625390	206625654	E082	-14177
chr2	206627283	206627374	E082	-12457
chr2	206627717	206627850	E082	-11981
chr2	206628067	206628148	E082	-11683
chr2	206630026	206630118	E082	-9713
chr2	206630159	206630209	E082	-9622
chr2	206631014	206631134	E082	-8697
chr2	206638848	206639057	E082	-774
chr2	206639578	206639639	E082	-192
chr2	206639780	206639864	E082	0
chr2	206639868	206640550	E082	37
chr2	206640771	206640860	E082	940
chr2	206672486	206672562	E082	32655