rs3823270

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

GMDS : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0010 (311/29998,GnomAD)
G=0011 (323/29118,TOPMED)
G=0033 (166/5008,1000G)
G=0009 (35/3854,ALSPAC)
G=0007 (25/3708,TWINSUK)

Position: chr6:1781739 (GRCh38.p7) (6p25.3)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 66 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 6	NC_000006.12:g.1781739A>G
GRCh37.p13 chr 6	NC_000006.11:g.1781973A>G

Gene: GMDS, GDP-mannose 4,6-dehydratase(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GMDS transcript variant 2	NM_001253846.1:c.	N/A	Intron Variant
GMDS transcript variant 1	NM_001500.3:c.	N/A	Intron Variant
GMDS transcript variant X1	XM_011514500.1:c.	N/A	Intron Variant
GMDS transcript variant X3	XM_011514502.2:c.	N/A	Intron Variant
GMDS transcript variant X10	XM_011514507.1:c.	N/A	Intron Variant
GMDS transcript variant X6	XM_017010752.1:c.	N/A	Intron Variant
GMDS transcript variant X4	XM_006715066.2:c.	N/A	Genic Downstream Transcript Variant
GMDS transcript variant X7	XM_011514503.2:c.	N/A	Genic Downstream Transcript Variant
GMDS transcript variant X8	XM_011514505.1:c.	N/A	Genic Downstream Transcript Variant
GMDS transcript variant X9	XM_011514506.1:c.	N/A	Genic Downstream Transcript Variant
GMDS transcript variant X2	XR_001743349.1:n.	N/A	Intron Variant
GMDS transcript variant X5	XR_001743350.1:n.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=1.000	G=0.000
1000Genomes	American	Sub	694	A=1.000	G=0.000
1000Genomes	East Asian	Sub	1008	A=0.926	G=0.074
1000Genomes	Europe	Sub	1006	A=0.993	G=0.007
1000Genomes	Global	Study-wide	5008	A=0.967	G=0.033
1000Genomes	South Asian	Sub	978	A=0.920	G=0.080
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.991	G=0.009
The Genome Aggregation Database	African	Sub	8734	A=0.998	G=0.002
The Genome Aggregation Database	American	Sub	838	A=1.000	G=0.000
The Genome Aggregation Database	East Asian	Sub	1618	A=0.931	G=0.069
The Genome Aggregation Database	Europe	Sub	18506	A=0.990	G=0.009
The Genome Aggregation Database	Global	Study-wide	29998	A=0.989	G=0.010
The Genome Aggregation Database	Other	Sub	302	A=1.000	G=0.000
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.988	G=0.011
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.993	G=0.007

PMID	Title	Author	Journal
19268276	Genome-wide association study of smoking initiation and current smoking.	Vink JM	Am J Hum Genet

P-Value

SNP ID	p-value	Traits	Study
rs3823270	0.00065	nicotine smoking	19268276

eQTL of rs3823270 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 rs3823270 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 )
chr6	1746144	1746434	E067	-35539
chr6	1778272	1778375	E067	-3598
chr6	1778381	1778436	E067	-3537
chr6	1778443	1778636	E067	-3337
chr6	1778637	1778763	E067	-3210
chr6	1746144	1746434	E068	-35539
chr6	1746474	1746524	E068	-35449
chr6	1767643	1768200	E068	-13773
chr6	1778381	1778436	E068	-3537
chr6	1778443	1778636	E068	-3337
chr6	1778637	1778763	E068	-3210
chr6	1778901	1779036	E068	-2937
chr6	1746144	1746434	E069	-35539
chr6	1746474	1746524	E069	-35449
chr6	1761637	1762434	E069	-19539
chr6	1737123	1737238	E070	-44735
chr6	1738694	1738753	E070	-43220
chr6	1738812	1738873	E070	-43100
chr6	1738932	1739156	E070	-42817
chr6	1739347	1739459	E070	-42514
chr6	1739671	1739742	E070	-42231
chr6	1739983	1740284	E070	-41689
chr6	1761133	1761193	E070	-20780
chr6	1761637	1762434	E070	-19539
chr6	1762497	1762973	E070	-19000
chr6	1771679	1771880	E070	-10093
chr6	1745779	1745829	E071	-36144
chr6	1746144	1746434	E071	-35539
chr6	1746474	1746524	E071	-35449
chr6	1761133	1761193	E071	-20780
chr6	1761637	1762434	E071	-19539
chr6	1778272	1778375	E071	-3598
chr6	1778381	1778436	E071	-3537
chr6	1778443	1778636	E071	-3337
chr6	1778637	1778763	E071	-3210
chr6	1746144	1746434	E072	-35539
chr6	1761637	1762434	E072	-19539
chr6	1762497	1762973	E072	-19000
chr6	1821876	1822647	E072	39903
chr6	1746144	1746434	E073	-35539
chr6	1778272	1778375	E073	-3598
chr6	1778381	1778436	E073	-3537
chr6	1778443	1778636	E073	-3337
chr6	1778637	1778763	E073	-3210
chr6	1778901	1779036	E073	-2937
chr6	1761637	1762434	E074	-19539
chr6	1767643	1768200	E074	-13773
chr6	1768215	1768300	E074	-13673
chr6	1768354	1768460	E074	-13513
chr6	1777723	1777801	E074	-4172
chr6	1778272	1778375	E074	-3598
chr6	1778381	1778436	E074	-3537
chr6	1778443	1778636	E074	-3337
chr6	1778637	1778763	E074	-3210
chr6	1778901	1779036	E074	-2937
chr6	1761637	1762434	E081	-19539
chr6	1762497	1762973	E081	-19000
chr6	1771679	1771880	E081	-10093
chr6	1798505	1798555	E081	16532
chr6	1798692	1798790	E081	16719
chr6	1798807	1798928	E081	16834
chr6	1798979	1799434	E081	17006
chr6	1806659	1806718	E081	24686
chr6	1777723	1777801	E082	-4172
chr6	1798807	1798928	E082	16834
chr6	1798979	1799434	E082	17006