rs6680211

Organism: Homo sapiens

Alleles: C>G

Gene : Feature

MAST2 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0452 (13498/29864,GnomAD)
G=0449 (13090/29118,TOPMED)
G=0497 (2491/5008,1000G)
G=0444 (1711/3854,ALSPAC)
G=0427 (1583/3708,TWINSUK)

Position: chr1:45849335 (GRCh38.p7) (1p34.1)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 39 Enhancers around

Promoter: 54 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 1	NC_000001.11:g.45849335C>G
GRCh37.p13 chr 1	NC_000001.10:g.46315007C>G

Gene: MAST2, microtubule associated serine/threonine kinase 2(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MAST2 transcript variant 2	NM_001319245.1:c.	N/A	Intron Variant
MAST2 transcript variant 3	NM_001324320.1:c.	N/A	Intron Variant
MAST2 transcript variant 1	NM_015112.2:c.	N/A	Intron Variant
MAST2 transcript variant 4	NM_001324321.1:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X1	XM_011541059.2:c.	N/A	Intron Variant
MAST2 transcript variant X2	XM_011541061.2:c.	N/A	Intron Variant
MAST2 transcript variant X3	XM_011541062.2:c.	N/A	Intron Variant
MAST2 transcript variant X4	XM_011541063.1:c.	N/A	Intron Variant
MAST2 transcript variant X5	XM_011541064.2:c.	N/A	Intron Variant
MAST2 transcript variant X6	XM_011541065.1:c.	N/A	Intron Variant
MAST2 transcript variant X16	XM_011541069.2:c.	N/A	Intron Variant
MAST2 transcript variant X8	XM_005270655.3:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X9	XM_005270656.4:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X13	XM_006710477.3:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X14	XM_011541067.2:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X15	XM_011541068.1:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X7	XM_017000752.1:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X10	XM_017000753.1:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X11	XM_017000754.1:c.	N/A	Genic Upstream Transcript Variant
MAST2 transcript variant X12	XM_017000755.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.549	G=0.451
1000Genomes	American	Sub	694	C=0.510	G=0.490
1000Genomes	East Asian	Sub	1008	C=0.314	G=0.686
1000Genomes	Europe	Sub	1006	C=0.552	G=0.448
1000Genomes	Global	Study-wide	5008	C=0.503	G=0.497
1000Genomes	South Asian	Sub	978	C=0.570	G=0.430
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.556	G=0.444
The Genome Aggregation Database	African	Sub	8680	C=0.564	G=0.436
The Genome Aggregation Database	American	Sub	834	C=0.490	G=0.510
The Genome Aggregation Database	East Asian	Sub	1610	C=0.376	G=0.624
The Genome Aggregation Database	Europe	Sub	18438	C=0.559	G=0.440
The Genome Aggregation Database	Global	Study-wide	29864	C=0.548	G=0.452
The Genome Aggregation Database	Other	Sub	302	C=0.490	G=0.510
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.550	G=0.449
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.573	G=0.427

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
rs6680211	0.000711	nicotine dependence	17158188

eQTL of rs6680211 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	0.0000e+0	349283	Cerebellum
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	2.8929e-22	349283	Frontal_Cortex_BA9
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	1.8000e-27	349283	Cortex
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	0.0000e+0	349283	Cerebellar_Hemisphere
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	2.0000e-28	349283	Caudate_basal_ganglia
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	0.0000e+0	349283	Putamen_basal_ganglia
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	2.6120e-19	349283	Anterior_cingulate_cortex
Chr1:46315007	CCDC163P	ENSG00000236624.4	C>G	2.2172e-24	349283	Nucleus_accumbens_basal_ganglia

meQTL of rs6680211 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg15605315	chr1:45957053	TESK2	0.0107985855007362	2.0528e-11
cg11803389	chr1:45965020	MMACHC\|CCDC163P	0.0398120670047323	5.9011e-11

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	46270930	46271151	E067	-43856
chr1	46328920	46329348	E067	13913
chr1	46337220	46337281	E067	22213
chr1	46337406	46337633	E067	22399
chr1	46357668	46358524	E067	42661
chr1	46337220	46337281	E068	22213
chr1	46337406	46337633	E068	22399
chr1	46357668	46358524	E068	42661
chr1	46328920	46329348	E069	13913
chr1	46330895	46330945	E069	15888
chr1	46331079	46331181	E069	16072
chr1	46333775	46333960	E069	18768
chr1	46337220	46337281	E069	22213
chr1	46337406	46337633	E069	22399
chr1	46327551	46327621	E070	12544
chr1	46328572	46328632	E070	13565
chr1	46328920	46329348	E070	13913
chr1	46333775	46333960	E070	18768
chr1	46268024	46268099	E071	-46908
chr1	46270930	46271151	E071	-43856
chr1	46330895	46330945	E071	15888
chr1	46331079	46331181	E071	16072
chr1	46337220	46337281	E071	22213
chr1	46337406	46337633	E071	22399
chr1	46328920	46329348	E072	13913
chr1	46333775	46333960	E072	18768
chr1	46337803	46338203	E072	22796
chr1	46357668	46358524	E072	42661
chr1	46328920	46329348	E073	13913
chr1	46330895	46330945	E073	15888
chr1	46331079	46331181	E073	16072
chr1	46357668	46358524	E073	42661
chr1	46268024	46268099	E074	-46908
chr1	46328920	46329348	E074	13913
chr1	46337220	46337281	E074	22213
chr1	46337406	46337633	E074	22399
chr1	46357668	46358524	E074	42661
chr1	46271808	46271863	E081	-43144
chr1	46333775	46333960	E081	18768

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr1	46268230	46269399	E067	-45608
chr1	46269691	46270757	E067	-44250
chr1	46329779	46329876	E067	14772
chr1	46329880	46330377	E067	14873
chr1	46330411	46330771	E067	15404
chr1	46331234	46331344	E067	16227
chr1	46268230	46269399	E068	-45608
chr1	46269691	46270757	E068	-44250
chr1	46329779	46329876	E068	14772
chr1	46329880	46330377	E068	14873
chr1	46330411	46330771	E068	15404
chr1	46268230	46269399	E069	-45608
chr1	46269691	46270757	E069	-44250
chr1	46329779	46329876	E069	14772
chr1	46329880	46330377	E069	14873
chr1	46330411	46330771	E069	15404
chr1	46268230	46269399	E070	-45608
chr1	46269691	46270757	E070	-44250
chr1	46329779	46329876	E070	14772
chr1	46329880	46330377	E070	14873
chr1	46330411	46330771	E070	15404
chr1	46331234	46331344	E070	16227
chr1	46268230	46269399	E071	-45608
chr1	46269691	46270757	E071	-44250
chr1	46329880	46330377	E071	14873
chr1	46330411	46330771	E071	15404
chr1	46268230	46269399	E072	-45608
chr1	46269691	46270757	E072	-44250
chr1	46329779	46329876	E072	14772
chr1	46329880	46330377	E072	14873
chr1	46330411	46330771	E072	15404
chr1	46331234	46331344	E072	16227
chr1	46268230	46269399	E073	-45608
chr1	46269691	46270757	E073	-44250
chr1	46329779	46329876	E073	14772
chr1	46329880	46330377	E073	14873
chr1	46330411	46330771	E073	15404
chr1	46268230	46269399	E074	-45608
chr1	46269691	46270757	E074	-44250
chr1	46329779	46329876	E074	14772
chr1	46329880	46330377	E074	14873
chr1	46330411	46330771	E074	15404
chr1	46268230	46269399	E081	-45608
chr1	46269691	46270757	E081	-44250
chr1	46329779	46329876	E081	14772
chr1	46329880	46330377	E081	14873
chr1	46330411	46330771	E081	15404
chr1	46331234	46331344	E081	16227
chr1	46268230	46269399	E082	-45608
chr1	46269691	46270757	E082	-44250
chr1	46329779	46329876	E082	14772
chr1	46329880	46330377	E082	14873
chr1	46330411	46330771	E082	15404
chr1	46331234	46331344	E082	16227