rs6548153

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

TSSC1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0280 (8391/29916,GnomAD)
A=0324 (9439/29116,TOPMED)
A=0407 (2037/5008,1000G)
A=0140 (540/3854,ALSPAC)
A=0144 (534/3708,TWINSUK)

Position: chr2:3322274 (GRCh38.p7) (2p25.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 2 publication(s)

Genomic View: See rs on genome

Enhancer: 163 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.3322274C>A
GRCh37.p13 chr 2	NC_000002.11:g.3326045C>A

Gene: TSSC1, tumor suppressing subtransferable candidate 1(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TSSC1 transcript	NM_003310.2:c.	N/A	Intron Variant
TSSC1 transcript variant X1	XM_011510383.2:c.	N/A	Intron Variant
TSSC1 transcript variant X2	XM_011510384.2:c.	N/A	Intron Variant
EIPR1 transcript variant X2	XM_011510385.2:c.	N/A	Intron Variant
TSSC1 transcript variant X6	XM_011510387.2:c.	N/A	Intron Variant
TSSC1 transcript variant X4	XM_017004818.1:c.	N/A	Intron Variant
EIPR1 transcript variant X4	XM_006711893.2:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.471	A=0.529
1000Genomes	American	Sub	694	C=0.830	A=0.170
1000Genomes	East Asian	Sub	1008	C=0.376	A=0.624
1000Genomes	Europe	Sub	1006	C=0.817	A=0.183
1000Genomes	Global	Study-wide	5008	C=0.593	A=0.407
1000Genomes	South Asian	Sub	978	C=0.590	A=0.410
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.860	A=0.140
The Genome Aggregation Database	African	Sub	8696	C=0.508	A=0.492
The Genome Aggregation Database	American	Sub	836	C=0.810	A=0.190
The Genome Aggregation Database	East Asian	Sub	1614	C=0.341	A=0.659
The Genome Aggregation Database	Europe	Sub	18468	C=0.845	A=0.154
The Genome Aggregation Database	Global	Study-wide	29916	C=0.719	A=0.280
The Genome Aggregation Database	Other	Sub	302	C=0.840	A=0.160
Trans-Omics for Precision Medicine	Global	Study-wide	29116	C=0.675	A=0.324
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.856	A=0.144

PMID	Title	Author	Journal
26824906	No Evidence of a Common DNA Variant Profile Specific to World Class Endurance Athletes.	Rankinen T	PLoS One
22377092	ANAPC1 and SLCO3A1 are associated with nicotine dependence: meta-analysis of genome-wide association studies.	Wang KS	Drug Alcohol Depend

P-Value

SNP ID	p-value	Traits	Study
rs6548153	9.01E-05	nicotine dependence (smoking)	22377092

eQTL of rs6548153 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 rs6548153 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 )
chr2	3286942	3287003	E067	-39042
chr2	3287020	3287101	E067	-38944
chr2	3287161	3287392	E067	-38653
chr2	3287437	3287487	E067	-38558
chr2	3288474	3288570	E067	-37475
chr2	3292301	3292597	E067	-33448
chr2	3292709	3293177	E067	-32868
chr2	3293432	3293577	E067	-32468
chr2	3306786	3307043	E067	-19002
chr2	3361191	3361241	E067	35146
chr2	3361358	3361485	E067	35313
chr2	3287020	3287101	E068	-38944
chr2	3287161	3287392	E068	-38653
chr2	3290036	3290099	E068	-35946
chr2	3290477	3290528	E068	-35517
chr2	3290564	3290654	E068	-35391
chr2	3293432	3293577	E068	-32468
chr2	3360592	3360910	E068	34547
chr2	3361191	3361241	E068	35146
chr2	3361358	3361485	E068	35313
chr2	3286942	3287003	E069	-39042
chr2	3287020	3287101	E069	-38944
chr2	3287161	3287392	E069	-38653
chr2	3287437	3287487	E069	-38558
chr2	3290036	3290099	E069	-35946
chr2	3290477	3290528	E069	-35517
chr2	3290564	3290654	E069	-35391
chr2	3292301	3292597	E069	-33448
chr2	3292709	3293177	E069	-32868
chr2	3293432	3293577	E069	-32468
chr2	3294538	3294708	E069	-31337
chr2	3306786	3307043	E069	-19002
chr2	3307865	3307928	E069	-18117
chr2	3307956	3307996	E069	-18049
chr2	3352911	3353502	E069	26866
chr2	3284794	3284848	E070	-41197
chr2	3285098	3285176	E070	-40869
chr2	3286942	3287003	E070	-39042
chr2	3287020	3287101	E070	-38944
chr2	3287161	3287392	E070	-38653
chr2	3289066	3289113	E070	-36932
chr2	3289157	3289269	E070	-36776
chr2	3289313	3289363	E070	-36682
chr2	3290036	3290099	E070	-35946
chr2	3290477	3290528	E070	-35517
chr2	3290564	3290654	E070	-35391
chr2	3292301	3292597	E070	-33448
chr2	3293432	3293577	E070	-32468
chr2	3306235	3306291	E070	-19754
chr2	3306444	3306780	E070	-19265
chr2	3307865	3307928	E070	-18117
chr2	3307956	3307996	E070	-18049
chr2	3286942	3287003	E071	-39042
chr2	3287020	3287101	E071	-38944
chr2	3287161	3287392	E071	-38653
chr2	3288474	3288570	E071	-37475
chr2	3289066	3289113	E071	-36932
chr2	3289157	3289269	E071	-36776
chr2	3289313	3289363	E071	-36682
chr2	3290036	3290099	E071	-35946
chr2	3290477	3290528	E071	-35517
chr2	3290564	3290654	E071	-35391
chr2	3292709	3293177	E071	-32868
chr2	3293432	3293577	E071	-32468
chr2	3294538	3294708	E071	-31337
chr2	3306786	3307043	E071	-19002
chr2	3286942	3287003	E072	-39042
chr2	3287020	3287101	E072	-38944
chr2	3287161	3287392	E072	-38653
chr2	3290036	3290099	E072	-35946
chr2	3290477	3290528	E072	-35517
chr2	3290564	3290654	E072	-35391
chr2	3292301	3292597	E072	-33448
chr2	3292709	3293177	E072	-32868
chr2	3306786	3307043	E072	-19002
chr2	3307865	3307928	E072	-18117
chr2	3307956	3307996	E072	-18049
chr2	3366939	3367020	E072	40894
chr2	3292301	3292597	E073	-33448
chr2	3292709	3293177	E073	-32868
chr2	3293432	3293577	E073	-32468
chr2	3294538	3294708	E073	-31337
chr2	3296857	3297009	E073	-29036
chr2	3297097	3297193	E073	-28852
chr2	3297337	3297412	E073	-28633
chr2	3307171	3307838	E073	-18207
chr2	3307865	3307928	E073	-18117
chr2	3307956	3307996	E073	-18049
chr2	3352911	3353502	E073	26866
chr2	3285700	3286771	E074	-39274
chr2	3286942	3287003	E074	-39042
chr2	3287020	3287101	E074	-38944
chr2	3287161	3287392	E074	-38653
chr2	3290477	3290528	E074	-35517
chr2	3290564	3290654	E074	-35391
chr2	3292301	3292597	E074	-33448
chr2	3292709	3293177	E074	-32868
chr2	3293432	3293577	E074	-32468
chr2	3306786	3307043	E074	-19002
chr2	3307171	3307838	E074	-18207
chr2	3361191	3361241	E074	35146
chr2	3361358	3361485	E074	35313
chr2	3277200	3277329	E081	-48716
chr2	3284794	3284848	E081	-41197
chr2	3285098	3285176	E081	-40869
chr2	3285700	3286771	E081	-39274
chr2	3286942	3287003	E081	-39042
chr2	3287020	3287101	E081	-38944
chr2	3287161	3287392	E081	-38653
chr2	3287437	3287487	E081	-38558
chr2	3288474	3288570	E081	-37475
chr2	3289066	3289113	E081	-36932
chr2	3289157	3289269	E081	-36776
chr2	3289313	3289363	E081	-36682
chr2	3290036	3290099	E081	-35946
chr2	3290477	3290528	E081	-35517
chr2	3290564	3290654	E081	-35391
chr2	3292301	3292597	E081	-33448
chr2	3292709	3293177	E081	-32868
chr2	3293432	3293577	E081	-32468
chr2	3294538	3294708	E081	-31337
chr2	3295637	3295687	E081	-30358
chr2	3296336	3296569	E081	-29476
chr2	3296618	3296786	E081	-29259
chr2	3296857	3297009	E081	-29036
chr2	3297097	3297193	E081	-28852
chr2	3297337	3297412	E081	-28633
chr2	3297574	3297640	E081	-28405
chr2	3297928	3298037	E081	-28008
chr2	3303409	3303576	E081	-22469
chr2	3303689	3303789	E081	-22256
chr2	3304258	3304373	E081	-21672
chr2	3304522	3304626	E081	-21419
chr2	3306235	3306291	E081	-19754
chr2	3306444	3306780	E081	-19265
chr2	3306786	3307043	E081	-19002
chr2	3307171	3307838	E081	-18207
chr2	3307865	3307928	E081	-18117
chr2	3307956	3307996	E081	-18049
chr2	3317444	3317617	E081	-8428
chr2	3317797	3318106	E081	-7939
chr2	3318464	3318618	E081	-7427
chr2	3338111	3339171	E081	12066
chr2	3352911	3353502	E081	26866
chr2	3284794	3284848	E082	-41197
chr2	3285098	3285176	E082	-40869
chr2	3286942	3287003	E082	-39042
chr2	3287020	3287101	E082	-38944
chr2	3287161	3287392	E082	-38653
chr2	3287437	3287487	E082	-38558
chr2	3288474	3288570	E082	-37475
chr2	3289066	3289113	E082	-36932
chr2	3289157	3289269	E082	-36776
chr2	3289313	3289363	E082	-36682
chr2	3290036	3290099	E082	-35946
chr2	3292301	3292597	E082	-33448
chr2	3293432	3293577	E082	-32468
chr2	3294538	3294708	E082	-31337
chr2	3296336	3296569	E082	-29476
chr2	3306235	3306291	E082	-19754
chr2	3306444	3306780	E082	-19265
chr2	3306786	3307043	E082	-19002
chr2	3308110	3308169	E082	-17876