rs2409665

Organism: Homo sapiens

Alleles: G>C

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C=0385 (11527/29904,GnomAD)
C=0385 (11220/29118,TOPMED)
C=0311 (1559/5008,1000G)
C=0423 (1629/3854,ALSPAC)
C=0433 (1604/3708,TWINSUK)

Position: chr8:10878723 (GRCh38.p7) (8p23.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 70 Enhancers around

Promoter: 19 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.10878723G>C
GRCh37.p13 chr 8	NC_000008.10:g.10736233G>C

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.601	C=0.399
1000Genomes	American	Sub	694	G=0.710	C=0.290
1000Genomes	East Asian	Sub	1008	G=0.994	C=0.006
1000Genomes	Europe	Sub	1006	G=0.583	C=0.417
1000Genomes	Global	Study-wide	5008	G=0.689	C=0.311
1000Genomes	South Asian	Sub	978	G=0.580	C=0.420
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.577	C=0.423
The Genome Aggregation Database	African	Sub	8690	G=0.612	C=0.388
The Genome Aggregation Database	American	Sub	838	G=0.790	C=0.210
The Genome Aggregation Database	East Asian	Sub	1618	G=0.986	C=0.014
The Genome Aggregation Database	Europe	Sub	18456	G=0.577	C=0.422
The Genome Aggregation Database	Global	Study-wide	29904	G=0.614	C=0.385
The Genome Aggregation Database	Other	Sub	302	G=0.500	C=0.500
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.614	C=0.385
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.567	C=0.433

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
rs2409665	0.000209	nicotine dependence	17158188

eQTL of rs2409665 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr8:10736233	AF131215.2	ENSG00000255310.2	G>C	3.8096e-5	-231003	Cerebellar_Hemisphere
Chr8:10736233	AF131216.5	ENSG00000255020.1	G>C	8.9174e-7	-468778	Cerebellar_Hemisphere

meQTL of rs2409665 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 )
chr8	10703501	10703571	E067	-32662
chr8	10713338	10713615	E067	-22618
chr8	10713751	10714290	E067	-21943
chr8	10785596	10785676	E067	49363
chr8	10712478	10713055	E068	-23178
chr8	10713338	10713615	E068	-22618
chr8	10713751	10714290	E068	-21943
chr8	10785371	10785532	E068	49138
chr8	10785596	10785676	E068	49363
chr8	10695989	10696089	E069	-40144
chr8	10712478	10713055	E069	-23178
chr8	10713338	10713615	E069	-22618
chr8	10713751	10714290	E069	-21943
chr8	10715134	10715367	E069	-20866
chr8	10695989	10696089	E070	-40144
chr8	10785596	10785676	E070	49363
chr8	10695989	10696089	E071	-40144
chr8	10713751	10714290	E071	-21943
chr8	10695989	10696089	E072	-40144
chr8	10712478	10713055	E072	-23178
chr8	10713338	10713615	E072	-22618
chr8	10713751	10714290	E072	-21943
chr8	10762415	10762465	E072	26182
chr8	10762477	10762554	E072	26244
chr8	10762813	10762952	E072	26580
chr8	10785596	10785676	E072	49363
chr8	10695989	10696089	E073	-40144
chr8	10712478	10713055	E073	-23178
chr8	10713338	10713615	E073	-22618
chr8	10785596	10785676	E073	49363
chr8	10695989	10696089	E074	-40144
chr8	10713751	10714290	E074	-21943
chr8	10714588	10714652	E074	-21581
chr8	10704309	10704349	E081	-31884
chr8	10704596	10704646	E081	-31587
chr8	10704689	10704739	E081	-31494
chr8	10710098	10710259	E081	-25974
chr8	10710414	10710470	E081	-25763
chr8	10710540	10710590	E081	-25643
chr8	10711085	10711199	E081	-25034
chr8	10711322	10711482	E081	-24751
chr8	10711539	10712215	E081	-24018
chr8	10712478	10713055	E081	-23178
chr8	10713338	10713615	E081	-22618
chr8	10714905	10714955	E081	-21278
chr8	10735221	10735277	E081	-956
chr8	10735450	10735509	E081	-724
chr8	10735552	10735731	E081	-502
chr8	10735823	10735883	E081	-350
chr8	10735899	10735949	E081	-284
chr8	10736464	10737238	E081	231
chr8	10750160	10750846	E081	13927
chr8	10762813	10762952	E081	26580
chr8	10763222	10763477	E081	26989
chr8	10763495	10763633	E081	27262
chr8	10767140	10767190	E081	30907
chr8	10767587	10767637	E081	31354
chr8	10768134	10768184	E081	31901
chr8	10768273	10768537	E081	32040
chr8	10768610	10768660	E081	32377
chr8	10694671	10695000	E082	-41233
chr8	10703369	10703438	E082	-32795
chr8	10703501	10703571	E082	-32662
chr8	10703634	10703929	E082	-32304
chr8	10711085	10711199	E082	-25034
chr8	10711322	10711482	E082	-24751
chr8	10711539	10712215	E082	-24018
chr8	10712478	10713055	E082	-23178
chr8	10713338	10713615	E082	-22618
chr8	10784652	10784692	E082	48419

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr8	10696347	10697890	E067	-38343
chr8	10707830	10708701	E067	-27532
chr8	10696347	10697890	E068	-38343
chr8	10707830	10708701	E068	-27532
chr8	10696347	10697890	E069	-38343
chr8	10707830	10708701	E069	-27532
chr8	10696347	10697890	E070	-38343
chr8	10696347	10697890	E071	-38343
chr8	10707830	10708701	E071	-27532
chr8	10708806	10708868	E071	-27365
chr8	10709069	10709950	E071	-26283
chr8	10696347	10697890	E072	-38343
chr8	10707830	10708701	E072	-27532
chr8	10696347	10697890	E073	-38343
chr8	10707830	10708701	E073	-27532
chr8	10696347	10697890	E074	-38343
chr8	10707830	10708701	E074	-27532
chr8	10696347	10697890	E081	-38343
chr8	10696347	10697890	E082	-38343