rs3131706

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0415 (12412/29894,GnomAD)
T==0453 (13208/29118,TOPMED)
T==0299 (1497/5008,1000G)
T==0430 (1658/3854,ALSPAC)
T==0427 (1583/3708,TWINSUK)

Position: chr1:39947426 (GRCh38.p7) (1p34.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 142 Enhancers around

Promoter: 22 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.39947426T>C
GRCh37.p13 chr 1	NC_000001.10:g.40413098T>C

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	T=0.456	C=0.544
1000Genomes	American	Sub	694	T=0.340	C=0.660
1000Genomes	East Asian	Sub	1008	T=0.015	C=0.985
1000Genomes	Europe	Sub	1006	T=0.432	C=0.568
1000Genomes	Global	Study-wide	5008	T=0.299	C=0.701
1000Genomes	South Asian	Sub	978	T=0.220	C=0.780
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.430	C=0.570
The Genome Aggregation Database	African	Sub	8686	T=0.486	C=0.514
The Genome Aggregation Database	American	Sub	838	T=0.320	C=0.680
The Genome Aggregation Database	East Asian	Sub	1622	T=0.018	C=0.982
The Genome Aggregation Database	Europe	Sub	18448	T=0.420	C=0.579
The Genome Aggregation Database	Global	Study-wide	29894	T=0.415	C=0.584
The Genome Aggregation Database	Other	Sub	300	T=0.470	C=0.530
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.453	C=0.546
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.427	C=0.573

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
rs3131706	0.000237	nicotine dependence	17158188

eQTL of rs3131706 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 rs3131706 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	40417787	40417849	E067	4689
chr1	40418111	40418765	E067	5013
chr1	40419544	40419606	E067	6446
chr1	40419677	40419819	E067	6579
chr1	40420008	40420109	E067	6910
chr1	40420112	40420162	E067	7014
chr1	40422763	40422824	E067	9665
chr1	40423041	40423213	E067	9943
chr1	40423416	40423551	E067	10318
chr1	40424233	40424404	E067	11135
chr1	40424474	40424569	E067	11376
chr1	40424629	40424707	E067	11531
chr1	40439061	40439685	E067	25963
chr1	40363800	40365113	E068	-47985
chr1	40365156	40365306	E068	-47792
chr1	40391993	40392442	E068	-20656
chr1	40392487	40392631	E068	-20467
chr1	40417787	40417849	E068	4689
chr1	40418111	40418765	E068	5013
chr1	40419544	40419606	E068	6446
chr1	40419677	40419819	E068	6579
chr1	40439061	40439685	E068	25963
chr1	40461559	40462039	E068	48461
chr1	40363800	40365113	E069	-47985
chr1	40387646	40387810	E069	-25288
chr1	40417787	40417849	E069	4689
chr1	40418111	40418765	E069	5013
chr1	40419544	40419606	E069	6446
chr1	40419677	40419819	E069	6579
chr1	40422763	40422824	E069	9665
chr1	40423041	40423213	E069	9943
chr1	40424233	40424404	E069	11135
chr1	40424474	40424569	E069	11376
chr1	40426089	40426761	E069	12991
chr1	40447524	40447999	E069	34426
chr1	40363373	40363506	E070	-49592
chr1	40363665	40363788	E070	-49310
chr1	40365609	40365732	E070	-47366
chr1	40420008	40420109	E070	6910
chr1	40420112	40420162	E070	7014
chr1	40422763	40422824	E070	9665
chr1	40423041	40423213	E070	9943
chr1	40423416	40423551	E070	10318
chr1	40426089	40426761	E070	12991
chr1	40453240	40453623	E070	40142
chr1	40453674	40453916	E070	40576
chr1	40363800	40365113	E071	-47985
chr1	40365156	40365306	E071	-47792
chr1	40365609	40365732	E071	-47366
chr1	40385234	40385596	E071	-27502
chr1	40391993	40392442	E071	-20656
chr1	40392487	40392631	E071	-20467
chr1	40392713	40392806	E071	-20292
chr1	40402810	40403212	E071	-9886
chr1	40418111	40418765	E071	5013
chr1	40419544	40419606	E071	6446
chr1	40419677	40419819	E071	6579
chr1	40423041	40423213	E071	9943
chr1	40423416	40423551	E071	10318
chr1	40424233	40424404	E071	11135
chr1	40424474	40424569	E071	11376
chr1	40426089	40426761	E071	12991
chr1	40439061	40439685	E071	25963
chr1	40453240	40453623	E071	40142
chr1	40453674	40453916	E071	40576
chr1	40363800	40365113	E072	-47985
chr1	40365156	40365306	E072	-47792
chr1	40365609	40365732	E072	-47366
chr1	40391993	40392442	E072	-20656
chr1	40392487	40392631	E072	-20467
chr1	40392713	40392806	E072	-20292
chr1	40417787	40417849	E072	4689
chr1	40418111	40418765	E072	5013
chr1	40419544	40419606	E072	6446
chr1	40419677	40419819	E072	6579
chr1	40420008	40420109	E072	6910
chr1	40420112	40420162	E072	7014
chr1	40422763	40422824	E072	9665
chr1	40423041	40423213	E072	9943
chr1	40423416	40423551	E072	10318
chr1	40424233	40424404	E072	11135
chr1	40424474	40424569	E072	11376
chr1	40425499	40425562	E072	12401
chr1	40425802	40425979	E072	12704
chr1	40426089	40426761	E072	12991
chr1	40365609	40365732	E073	-47366
chr1	40391403	40391722	E073	-21376
chr1	40391993	40392442	E073	-20656
chr1	40392487	40392631	E073	-20467
chr1	40392713	40392806	E073	-20292
chr1	40393229	40393548	E073	-19550
chr1	40417787	40417849	E073	4689
chr1	40419544	40419606	E073	6446
chr1	40419677	40419819	E073	6579
chr1	40420008	40420109	E073	6910
chr1	40420112	40420162	E073	7014
chr1	40424233	40424404	E073	11135
chr1	40424474	40424569	E073	11376
chr1	40424629	40424707	E073	11531
chr1	40425802	40425979	E073	12704
chr1	40426089	40426761	E073	12991
chr1	40439061	40439685	E073	25963
chr1	40365156	40365306	E074	-47792
chr1	40365609	40365732	E074	-47366
chr1	40391403	40391722	E074	-21376
chr1	40391993	40392442	E074	-20656
chr1	40417787	40417849	E074	4689
chr1	40418111	40418765	E074	5013
chr1	40419544	40419606	E074	6446
chr1	40419677	40419819	E074	6579
chr1	40420008	40420109	E074	6910
chr1	40420112	40420162	E074	7014
chr1	40426089	40426761	E074	12991
chr1	40439061	40439685	E074	25963
chr1	40461404	40461500	E074	48306
chr1	40461559	40462039	E074	48461
chr1	40363373	40363506	E081	-49592
chr1	40363665	40363788	E081	-49310
chr1	40363800	40365113	E081	-47985
chr1	40365156	40365306	E081	-47792
chr1	40365609	40365732	E081	-47366
chr1	40418111	40418765	E081	5013
chr1	40419544	40419606	E081	6446
chr1	40419677	40419819	E081	6579
chr1	40420008	40420109	E081	6910
chr1	40420112	40420162	E081	7014
chr1	40423041	40423213	E081	9943
chr1	40423416	40423551	E081	10318
chr1	40425802	40425979	E081	12704
chr1	40426089	40426761	E081	12991
chr1	40439061	40439685	E081	25963
chr1	40453674	40453916	E081	40576
chr1	40419544	40419606	E082	6446
chr1	40419677	40419819	E082	6579
chr1	40420008	40420109	E082	6910
chr1	40420112	40420162	E082	7014
chr1	40422763	40422824	E082	9665
chr1	40423041	40423213	E082	9943
chr1	40423416	40423551	E082	10318
chr1	40426089	40426761	E082	12991
chr1	40453240	40453623	E082	40142
chr1	40453674	40453916	E082	40576

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	40366173	40368557	E067	-44541
chr1	40420211	40421126	E067	7113
chr1	40366037	40366087	E068	-47011
chr1	40366173	40368557	E068	-44541
chr1	40420211	40421126	E068	7113
chr1	40366173	40368557	E069	-44541
chr1	40420211	40421126	E069	7113
chr1	40366037	40366087	E070	-47011
chr1	40366173	40368557	E070	-44541
chr1	40420211	40421126	E070	7113
chr1	40366173	40368557	E071	-44541
chr1	40420211	40421126	E071	7113
chr1	40366173	40368557	E072	-44541
chr1	40420211	40421126	E072	7113
chr1	40366173	40368557	E073	-44541
chr1	40366173	40368557	E074	-44541
chr1	40420211	40421126	E074	7113
chr1	40365816	40365866	E082	-47232
chr1	40365900	40365951	E082	-47147
chr1	40366037	40366087	E082	-47011
chr1	40366173	40368557	E082	-44541
chr1	40420211	40421126	E082	7113