rs475488

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

None

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0159 (4772/29954,GnomAD)
A=0185 (5398/29116,TOPMED)
A=0213 (1068/5008,1000G)

Position: chr1:236658547 (GRCh38.p7) (1q43)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 67 Enhancers around

Promoter: 46 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.236658547G>A
GRCh37.p13 chr 1	NC_000001.10:g.236821847G>A

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.756	A=0.244
1000Genomes	American	Sub	694	G=0.710	A=0.290
1000Genomes	East Asian	Sub	1008	G=0.778	A=0.222
1000Genomes	Europe	Sub	1006	G=0.865	A=0.135
1000Genomes	Global	Study-wide	5008	G=0.787	A=0.213
1000Genomes	South Asian	Sub	978	G=0.810	A=0.190
The Genome Aggregation Database	African	Sub	8716	G=0.766	A=0.234
The Genome Aggregation Database	American	Sub	836	G=0.720	A=0.280
The Genome Aggregation Database	East Asian	Sub	1616	G=0.824	A=0.176
The Genome Aggregation Database	Europe	Sub	18486	G=0.884	A=0.115
The Genome Aggregation Database	Global	Study-wide	29954	G=0.840	A=0.159
The Genome Aggregation Database	Other	Sub	300	G=0.770	A=0.230
Trans-Omics for Precision Medicine	Global	Study-wide	29116	G=0.814	A=0.185

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
rs475488	0.00016	nicotine dependence	17407593

eQTL of rs475488 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 rs475488 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	236848575	236848665	E067	26728
chr1	236848756	236848861	E067	26909
chr1	236849027	236849116	E067	27180
chr1	236855586	236855790	E067	33739
chr1	236855873	236856382	E067	34026
chr1	236856614	236856719	E067	34767
chr1	236856983	236857615	E067	35136
chr1	236868345	236868426	E067	46498
chr1	236868720	236868947	E067	46873
chr1	236855586	236855790	E068	33739
chr1	236855873	236856382	E068	34026
chr1	236856614	236856719	E068	34767
chr1	236856983	236857615	E068	35136
chr1	236866027	236866712	E068	44180
chr1	236869601	236869869	E068	47754
chr1	236870028	236870207	E068	48181
chr1	236856614	236856719	E069	34767
chr1	236856983	236857615	E069	35136
chr1	236868720	236868947	E069	46873
chr1	236869094	236869385	E069	47247
chr1	236869601	236869869	E069	47754
chr1	236870028	236870207	E069	48181
chr1	236871429	236871518	E069	49582
chr1	236856983	236857615	E070	35136
chr1	236866027	236866712	E070	44180
chr1	236866776	236866868	E070	44929
chr1	236868720	236868947	E070	46873
chr1	236869094	236869385	E070	47247
chr1	236869601	236869869	E070	47754
chr1	236870028	236870207	E070	48181
chr1	236849027	236849116	E071	27180
chr1	236855586	236855790	E071	33739
chr1	236855873	236856382	E071	34026
chr1	236856614	236856719	E071	34767
chr1	236856983	236857615	E071	35136
chr1	236866027	236866712	E071	44180
chr1	236866776	236866868	E071	44929
chr1	236868720	236868947	E071	46873
chr1	236869094	236869385	E071	47247
chr1	236869601	236869869	E071	47754
chr1	236870028	236870207	E071	48181
chr1	236849027	236849116	E072	27180
chr1	236855586	236855790	E072	33739
chr1	236855873	236856382	E072	34026
chr1	236856614	236856719	E072	34767
chr1	236856983	236857615	E072	35136
chr1	236866027	236866712	E072	44180
chr1	236866776	236866868	E072	44929
chr1	236856614	236856719	E073	34767
chr1	236869094	236869385	E073	47247
chr1	236869601	236869869	E073	47754
chr1	236870028	236870207	E073	48181
chr1	236856614	236856719	E074	34767
chr1	236856983	236857615	E074	35136
chr1	236869094	236869385	E074	47247
chr1	236869601	236869869	E074	47754
chr1	236870028	236870207	E074	48181
chr1	236870650	236870700	E074	48803
chr1	236870739	236870808	E074	48892
chr1	236844581	236844726	E081	22734
chr1	236848756	236848861	E081	26909
chr1	236849027	236849116	E081	27180
chr1	236855873	236856382	E081	34026
chr1	236856614	236856719	E081	34767
chr1	236866776	236866868	E081	44929
chr1	236866027	236866712	E082	44180
chr1	236866776	236866868	E082	44929

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	236849279	236850209	E067	27432
chr1	236850211	236850951	E067	28364
chr1	236851241	236851330	E067	29394
chr1	236851383	236851503	E067	29536
chr1	236849279	236850209	E068	27432
chr1	236850211	236850951	E068	28364
chr1	236851241	236851330	E068	29394
chr1	236851383	236851503	E068	29536
chr1	236851673	236851754	E068	29826
chr1	236851805	236852433	E068	29958
chr1	236852696	236852812	E068	30849
chr1	236852873	236853320	E068	31026
chr1	236853398	236853809	E068	31551
chr1	236853863	236853930	E068	32016
chr1	236853966	236854034	E068	32119
chr1	236854114	236854185	E068	32267
chr1	236849279	236850209	E069	27432
chr1	236850211	236850951	E069	28364
chr1	236851241	236851330	E069	29394
chr1	236851383	236851503	E069	29536
chr1	236851673	236851754	E069	29826
chr1	236851805	236852433	E069	29958
chr1	236849279	236850209	E070	27432
chr1	236850211	236850951	E070	28364
chr1	236851241	236851330	E070	29394
chr1	236851383	236851503	E070	29536
chr1	236849279	236850209	E071	27432
chr1	236850211	236850951	E071	28364
chr1	236851241	236851330	E071	29394
chr1	236851383	236851503	E071	29536
chr1	236851673	236851754	E071	29826
chr1	236851805	236852433	E071	29958
chr1	236849279	236850209	E072	27432
chr1	236850211	236850951	E072	28364
chr1	236851241	236851330	E072	29394
chr1	236851383	236851503	E072	29536
chr1	236849279	236850209	E073	27432
chr1	236850211	236850951	E073	28364
chr1	236849279	236850209	E074	27432
chr1	236850211	236850951	E074	28364
chr1	236849279	236850209	E082	27432
chr1	236850211	236850951	E082	28364
chr1	236851241	236851330	E082	29394
chr1	236851383	236851503	E082	29536
chr1	236851673	236851754	E082	29826
chr1	236851805	236852433	E082	29958