rs506598

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

RASGRF2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0361 (10809/29914,GnomAD)
A=0385 (11238/29118,TOPMED)
A=0356 (1785/5008,1000G)
A=0374 (1443/3854,ALSPAC)
A=0366 (1356/3708,TWINSUK)

Position: chr5:81019851 (GRCh38.p7) (5q14.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 147 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 5	NC_000005.10:g.81019851G>A
GRCh37.p13 chr 5	NC_000005.9:g.80315670G>A
RASGRF2 RefSeqGene	NG_030334.1:g.64163G>A

Gene: RASGRF2, Ras protein specific guanine nucleotide releasing factor 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RASGRF2 transcript	NM_006909.2:c.	N/A	Intron Variant
RASGRF2 transcript variant X2	XM_005248565.1:c.	N/A	Intron Variant
RASGRF2 transcript variant X1	XM_017009682.1:c.	N/A	Intron Variant
RASGRF2 transcript variant X5	XM_017009683.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.598	A=0.402
1000Genomes	American	Sub	694	G=0.560	A=0.440
1000Genomes	East Asian	Sub	1008	G=0.711	A=0.289
1000Genomes	Europe	Sub	1006	G=0.638	A=0.362
1000Genomes	Global	Study-wide	5008	G=0.644	A=0.356
1000Genomes	South Asian	Sub	978	G=0.700	A=0.300
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.626	A=0.374
The Genome Aggregation Database	African	Sub	8698	G=0.611	A=0.389
The Genome Aggregation Database	American	Sub	836	G=0.520	A=0.480
The Genome Aggregation Database	East Asian	Sub	1614	G=0.685	A=0.315
The Genome Aggregation Database	Europe	Sub	18466	G=0.653	A=0.346
The Genome Aggregation Database	Global	Study-wide	29914	G=0.638	A=0.361
The Genome Aggregation Database	Other	Sub	300	G=0.610	A=0.390
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.614	A=0.385
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.634	A=0.366

PMID	Title	Author	Journal
17158188	Novel genes identified in a high-density genome wide association study for nicotine dependence.	Bierut LJ	Hum Mol Genet

P-Value

SNP ID	p-value	Traits	Study
rs506598	0.000429	nicotine dependence	17158188

eQTL of rs506598 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 rs506598 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 )
chr5	80270275	80270330	E067	-45340
chr5	80270533	80270613	E067	-45057
chr5	80270961	80271260	E067	-44410
chr5	80282792	80282855	E067	-32815
chr5	80283173	80283298	E067	-32372
chr5	80283337	80283438	E067	-32232
chr5	80284339	80284389	E067	-31281
chr5	80284410	80284645	E067	-31025
chr5	80285703	80285860	E067	-29810
chr5	80286128	80287179	E067	-28491
chr5	80299691	80300088	E067	-15582
chr5	80300350	80300422	E067	-15248
chr5	80312899	80313000	E067	-2670
chr5	80313090	80313141	E067	-2529
chr5	80319443	80319680	E067	3773
chr5	80339517	80339786	E067	23847
chr5	80268904	80269055	E068	-46615
chr5	80269152	80269225	E068	-46445
chr5	80270275	80270330	E068	-45340
chr5	80270533	80270613	E068	-45057
chr5	80270961	80271260	E068	-44410
chr5	80282792	80282855	E068	-32815
chr5	80283173	80283298	E068	-32372
chr5	80293934	80294015	E068	-21655
chr5	80312899	80313000	E068	-2670
chr5	80313090	80313141	E068	-2529
chr5	80319443	80319680	E068	3773
chr5	80319894	80319954	E068	4224
chr5	80341374	80341446	E068	25704
chr5	80343669	80343749	E068	27999
chr5	80343867	80344025	E068	28197
chr5	80268904	80269055	E069	-46615
chr5	80269152	80269225	E069	-46445
chr5	80270275	80270330	E069	-45340
chr5	80270533	80270613	E069	-45057
chr5	80270961	80271260	E069	-44410
chr5	80277258	80277308	E069	-38362
chr5	80282792	80282855	E069	-32815
chr5	80283173	80283298	E069	-32372
chr5	80283337	80283438	E069	-32232
chr5	80284339	80284389	E069	-31281
chr5	80284410	80284645	E069	-31025
chr5	80285703	80285860	E069	-29810
chr5	80286128	80287179	E069	-28491
chr5	80293934	80294015	E069	-21655
chr5	80299691	80300088	E069	-15582
chr5	80300350	80300422	E069	-15248
chr5	80312899	80313000	E069	-2670
chr5	80313090	80313141	E069	-2529
chr5	80316450	80316921	E069	780
chr5	80317371	80317603	E069	1701
chr5	80317765	80319342	E069	2095
chr5	80319443	80319680	E069	3773
chr5	80319894	80319954	E069	4224
chr5	80343669	80343749	E069	27999
chr5	80343867	80344025	E069	28197
chr5	80345410	80345594	E069	29740
chr5	80361177	80361597	E069	45507
chr5	80270275	80270330	E071	-45340
chr5	80270533	80270613	E071	-45057
chr5	80270961	80271260	E071	-44410
chr5	80282792	80282855	E071	-32815
chr5	80283173	80283298	E071	-32372
chr5	80283337	80283438	E071	-32232
chr5	80284339	80284389	E071	-31281
chr5	80285703	80285860	E071	-29810
chr5	80286128	80287179	E071	-28491
chr5	80288041	80288203	E071	-27467
chr5	80299691	80300088	E071	-15582
chr5	80300350	80300422	E071	-15248
chr5	80312899	80313000	E071	-2670
chr5	80313090	80313141	E071	-2529
chr5	80316450	80316921	E071	780
chr5	80317371	80317603	E071	1701
chr5	80317765	80319342	E071	2095
chr5	80319443	80319680	E071	3773
chr5	80319894	80319954	E071	4224
chr5	80320607	80320842	E071	4937
chr5	80341374	80341446	E071	25704
chr5	80343669	80343749	E071	27999
chr5	80343867	80344025	E071	28197
chr5	80345828	80345888	E071	30158
chr5	80270275	80270330	E072	-45340
chr5	80270533	80270613	E072	-45057
chr5	80282792	80282855	E072	-32815
chr5	80283173	80283298	E072	-32372
chr5	80283337	80283438	E072	-32232
chr5	80284339	80284389	E072	-31281
chr5	80284410	80284645	E072	-31025
chr5	80285703	80285860	E072	-29810
chr5	80286128	80287179	E072	-28491
chr5	80299691	80300088	E072	-15582
chr5	80300350	80300422	E072	-15248
chr5	80319443	80319680	E072	3773
chr5	80319894	80319954	E072	4224
chr5	80343669	80343749	E072	27999
chr5	80343867	80344025	E072	28197
chr5	80345828	80345888	E072	30158
chr5	80359991	80360108	E072	44321
chr5	80360153	80360207	E072	44483
chr5	80360448	80360682	E072	44778
chr5	80361177	80361597	E072	45507
chr5	80272966	80273072	E073	-42598
chr5	80283173	80283298	E073	-32372
chr5	80283337	80283438	E073	-32232
chr5	80288041	80288203	E073	-27467
chr5	80300350	80300422	E073	-15248
chr5	80313090	80313141	E073	-2529
chr5	80343669	80343749	E073	27999
chr5	80361177	80361597	E073	45507
chr5	80268904	80269055	E074	-46615
chr5	80269152	80269225	E074	-46445
chr5	80270275	80270330	E074	-45340
chr5	80270533	80270613	E074	-45057
chr5	80270961	80271260	E074	-44410
chr5	80281570	80281656	E074	-34014
chr5	80281708	80281804	E074	-33866
chr5	80282792	80282855	E074	-32815
chr5	80283173	80283298	E074	-32372
chr5	80283337	80283438	E074	-32232
chr5	80284339	80284389	E074	-31281
chr5	80284410	80284645	E074	-31025
chr5	80285703	80285860	E074	-29810
chr5	80286128	80287179	E074	-28491
chr5	80288041	80288203	E074	-27467
chr5	80297763	80298098	E074	-17572
chr5	80299691	80300088	E074	-15582
chr5	80300350	80300422	E074	-15248
chr5	80312064	80312131	E074	-3539
chr5	80312899	80313000	E074	-2670
chr5	80313090	80313141	E074	-2529
chr5	80314493	80314658	E074	-1012
chr5	80315187	80315434	E074	-236
chr5	80316450	80316921	E074	780
chr5	80317371	80317603	E074	1701
chr5	80317765	80319342	E074	2095
chr5	80319443	80319680	E074	3773
chr5	80339517	80339786	E074	23847
chr5	80341374	80341446	E074	25704
chr5	80343669	80343749	E074	27999
chr5	80343867	80344025	E074	28197
chr5	80345410	80345594	E074	29740
chr5	80345828	80345888	E074	30158
chr5	80359991	80360108	E074	44321
chr5	80360153	80360207	E074	44483
chr5	80360448	80360682	E074	44778
chr5	80361177	80361597	E074	45507