rs592557

Organism: Homo sapiens

Alleles: C>A / C>T

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0314 (9402/29944,GnomAD)
T=0300 (8737/29116,TOPMED)
T=0254 (1274/5008,1000G)
T=0380 (1465/3854,ALSPAC)
T=0378 (1402/3708,TWINSUK)

Position: chr1:232354204 (GRCh38.p7) (1q42.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 99 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.232354204C>A
GRCh38.p7 chr 1	NC_000001.11:g.232354204C>T
GRCh37.p13 chr 1	NC_000001.10:g.232489950C>A
GRCh37.p13 chr 1	NC_000001.10:g.232489950C>T

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.829	T=0.171
1000Genomes	American	Sub	694	C=0.740	T=0.260
1000Genomes	East Asian	Sub	1008	C=0.853	T=0.147
1000Genomes	Europe	Sub	1006	C=0.630	T=0.370
1000Genomes	Global	Study-wide	5008	C=0.746	T=0.254
1000Genomes	South Asian	Sub	978	C=0.650	T=0.350
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.620	T=0.380
The Genome Aggregation Database	African	Sub	8710	C=0.779	T=0.221
The Genome Aggregation Database	American	Sub	836	C=0.720	T=0.280
The Genome Aggregation Database	East Asian	Sub	1620	C=0.843	T=0.157
The Genome Aggregation Database	Europe	Sub	18476	C=0.627	T=0.373
The Genome Aggregation Database	Global	Study-wide	29944	C=0.686	T=0.314
The Genome Aggregation Database	Other	Sub	302	C=0.690	T=0.310
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.699	T=0.300
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.622	T=0.378

PMID	Title	Author	Journal
17407593	Molecular genetics of nicotine dependence and abstinence: whole genome association using 520,000 SNPs.	Uhl GR	BMC Genet

P-Value

SNP ID	p-value	Traits	Study
rs592557	0.0004	nicotine dependence	17407593

eQTL of rs592557 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 rs592557 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	41807775	41808086	E067	41214
chr1	41751581	41751642	E068	-14919
chr1	41751668	41751718	E068	-14843
chr1	41751759	41751832	E068	-14729
chr1	41752257	41752452	E068	-14109
chr1	41785585	41785787	E068	19024
chr1	41786217	41786395	E068	19656
chr1	41785585	41785787	E069	19024
chr1	41785798	41786151	E069	19237
chr1	41740481	41740831	E070	-25730
chr1	41740927	41741020	E070	-25541
chr1	41748403	41748454	E070	-18107
chr1	41748467	41748644	E070	-17917
chr1	41748730	41748843	E070	-17718
chr1	41749125	41749176	E070	-17385
chr1	41749229	41749357	E070	-17204
chr1	41749399	41749512	E070	-17049
chr1	41751278	41751328	E070	-15233
chr1	41751581	41751642	E070	-14919
chr1	41751668	41751718	E070	-14843
chr1	41751759	41751832	E070	-14729
chr1	41752257	41752452	E070	-14109
chr1	41752837	41752985	E070	-13576
chr1	41779130	41779717	E070	12569
chr1	41779892	41780012	E070	13331
chr1	41780215	41780540	E070	13654
chr1	41781359	41781793	E070	14798
chr1	41781996	41782129	E070	15435
chr1	41784887	41785136	E070	18326
chr1	41785169	41785326	E070	18608
chr1	41785585	41785787	E070	19024
chr1	41785798	41786151	E070	19237
chr1	41786217	41786395	E070	19656
chr1	41786615	41786951	E070	20054
chr1	41796597	41796790	E070	30036
chr1	41797002	41797150	E070	30441
chr1	41807775	41808086	E070	41214
chr1	41733751	41734477	E071	-32084
chr1	41740481	41740831	E071	-25730
chr1	41740927	41741020	E071	-25541
chr1	41748467	41748644	E071	-17917
chr1	41748730	41748843	E071	-17718
chr1	41807775	41808086	E072	41214
chr1	41733751	41734477	E073	-32084
chr1	41738366	41738518	E081	-28043
chr1	41740481	41740831	E081	-25730
chr1	41740927	41741020	E081	-25541
chr1	41751278	41751328	E081	-15233
chr1	41751581	41751642	E081	-14919
chr1	41751668	41751718	E081	-14843
chr1	41751759	41751832	E081	-14729
chr1	41752257	41752452	E081	-14109
chr1	41752837	41752985	E081	-13576
chr1	41756933	41757024	E081	-9537
chr1	41757222	41757300	E081	-9261
chr1	41759612	41759807	E081	-6754
chr1	41760009	41760090	E081	-6471
chr1	41760318	41760586	E081	-5975
chr1	41780215	41780540	E081	13654
chr1	41780578	41780807	E081	14017
chr1	41780816	41780929	E081	14255
chr1	41780949	41781152	E081	14388
chr1	41781203	41781310	E081	14642
chr1	41781359	41781793	E081	14798
chr1	41781996	41782129	E081	15435
chr1	41785169	41785326	E081	18608
chr1	41785585	41785787	E081	19024
chr1	41785798	41786151	E081	19237
chr1	41786217	41786395	E081	19656
chr1	41786615	41786951	E081	20054
chr1	41807775	41808086	E081	41214
chr1	41733751	41734477	E082	-32084
chr1	41734627	41734734	E082	-31827
chr1	41734913	41734990	E082	-31571
chr1	41735145	41735189	E082	-31372
chr1	41748403	41748454	E082	-18107
chr1	41748467	41748644	E082	-17917
chr1	41748730	41748843	E082	-17718
chr1	41751581	41751642	E082	-14919
chr1	41751668	41751718	E082	-14843
chr1	41751759	41751832	E082	-14729
chr1	41752257	41752452	E082	-14109
chr1	41752837	41752985	E082	-13576
chr1	41756933	41757024	E082	-9537
chr1	41757222	41757300	E082	-9261
chr1	41757503	41757742	E082	-8819
chr1	41759612	41759807	E082	-6754
chr1	41780215	41780540	E082	13654
chr1	41780578	41780807	E082	14017
chr1	41780816	41780929	E082	14255
chr1	41780949	41781152	E082	14388
chr1	41781203	41781310	E082	14642
chr1	41781359	41781793	E082	14798
chr1	41781996	41782129	E082	15435
chr1	41785798	41786151	E082	19237
chr1	41786217	41786395	E082	19656
chr1	41786615	41786951	E082	20054
chr1	41807477	41807537	E082	40916
chr1	41807775	41808086	E082	41214