rs7797803

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SDK1 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0289 (8645/29902,GnomAD)
G=0320 (9327/29118,TOPMED)
G=0330 (1654/5008,1000G)
G=0305 (1175/3854,ALSPAC)
G=0300 (1113/3708,TWINSUK)

Position: chr7:4181432 (GRCh38.p7) (7p22.2)

Phenotype: ND

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 72 Enhancers around

Promoter: 1 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 7	NC_000007.14:g.4181432A>G
GRCh37.p13 chr 7	NC_000007.13:g.4221064A>G

Gene: SDK1, sidekick cell adhesion molecule 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SDK1 transcript variant 2	NM_001079653.1:c.	N/A	Intron Variant
SDK1 transcript variant 1	NM_152744.3:c.	N/A	Intron Variant
SDK1 transcript variant X4	XM_011515188.1:c.	N/A	Intron Variant
SDK1 transcript variant X5	XM_011515189.1:c.	N/A	Intron Variant
SDK1 transcript variant X6	XM_011515190.1:c.	N/A	Intron Variant
SDK1 transcript variant X1	XM_017011837.1:c.	N/A	Intron Variant
SDK1 transcript variant X7	XM_017011838.1:c.	N/A	Genic Downstream Transcript Variant
SDK1 transcript variant X8	XM_017011839.1:c.	N/A	Genic Downstream Transcript Variant
SDK1 transcript variant X9	XM_017011840.1:c.	N/A	Genic Downstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.653	G=0.347
1000Genomes	American	Sub	694	A=0.720	G=0.280
1000Genomes	East Asian	Sub	1008	A=0.729	G=0.271
1000Genomes	Europe	Sub	1006	A=0.701	G=0.299
1000Genomes	Global	Study-wide	5008	A=0.670	G=0.330
1000Genomes	South Asian	Sub	978	A=0.560	G=0.440
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.695	G=0.305
The Genome Aggregation Database	African	Sub	8700	A=0.640	G=0.360
The Genome Aggregation Database	American	Sub	838	A=0.760	G=0.240
The Genome Aggregation Database	East Asian	Sub	1616	A=0.751	G=0.249
The Genome Aggregation Database	Europe	Sub	18446	A=0.738	G=0.261
The Genome Aggregation Database	Global	Study-wide	29902	A=0.710	G=0.289
The Genome Aggregation Database	Other	Sub	302	A=0.730	G=0.270
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.679	G=0.320
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.700	G=0.300

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
rs7797803	0.000146	nicotine smoking	19268276

eQTL of rs7797803 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 rs7797803 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg07249765	chr7:4244643	SDK1	-0.196210739130369	3.9902e-13
cg24441899	chr7:4244372	SDK1	-0.0573505202707726	9.4051e-11
cg02004499	chr7:4244250	SDK1	-0.102163366773887	4.9353e-9

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 )
chr7	4267830	4267880	E067	46766
chr7	4267957	4268007	E067	46893
chr7	4229568	4230056	E068	8504
chr7	4228491	4229225	E069	7427
chr7	4267830	4267880	E069	46766
chr7	4267957	4268007	E069	46893
chr7	4176463	4176517	E070	-44547
chr7	4176679	4176741	E070	-44323
chr7	4177116	4177166	E070	-43898
chr7	4177247	4177328	E070	-43736
chr7	4177383	4177491	E070	-43573
chr7	4185149	4185485	E070	-35579
chr7	4187733	4187853	E070	-33211
chr7	4187856	4187906	E070	-33158
chr7	4228491	4229225	E070	7427
chr7	4229568	4230056	E070	8504
chr7	4230174	4230272	E070	9110
chr7	4230293	4230471	E070	9229
chr7	4230684	4230724	E070	9620
chr7	4265448	4265502	E070	44384
chr7	4265512	4265562	E070	44448
chr7	4266093	4266460	E070	45029
chr7	4266599	4266649	E070	45535
chr7	4267830	4267880	E070	46766
chr7	4267957	4268007	E070	46893
chr7	4228491	4229225	E071	7427
chr7	4203290	4203385	E073	-17679
chr7	4228491	4229225	E074	7427
chr7	4173278	4173388	E081	-47676
chr7	4175258	4175488	E081	-45576
chr7	4175531	4175598	E081	-45466
chr7	4175612	4176419	E081	-44645
chr7	4176463	4176517	E081	-44547
chr7	4177771	4178062	E081	-43002
chr7	4179492	4180427	E081	-40637
chr7	4183468	4183651	E081	-37413
chr7	4183693	4184104	E081	-36960
chr7	4184125	4185110	E081	-35954
chr7	4185149	4185485	E081	-35579
chr7	4228491	4229225	E081	7427
chr7	4229568	4230056	E081	8504
chr7	4230174	4230272	E081	9110
chr7	4230293	4230471	E081	9229
chr7	4230684	4230724	E081	9620
chr7	4230865	4231020	E081	9801
chr7	4231265	4231315	E081	10201
chr7	4231353	4231433	E081	10289
chr7	4231516	4231674	E081	10452
chr7	4231723	4231967	E081	10659
chr7	4242519	4242631	E081	21455
chr7	4242815	4242997	E081	21751
chr7	4243089	4243139	E081	22025
chr7	4243204	4243541	E081	22140
chr7	4243798	4243906	E081	22734
chr7	4243954	4244412	E081	22890
chr7	4265448	4265502	E081	44384
chr7	4265512	4265562	E081	44448
chr7	4266093	4266460	E081	45029
chr7	4266599	4266649	E081	45535
chr7	4267830	4267880	E081	46766
chr7	4267957	4268007	E081	46893
chr7	4268079	4268142	E081	47015
chr7	4268539	4268661	E081	47475
chr7	4268858	4268936	E081	47794
chr7	4175258	4175488	E082	-45576
chr7	4229568	4230056	E082	8504
chr7	4230174	4230272	E082	9110
chr7	4230293	4230471	E082	9229
chr7	4243204	4243541	E082	22140
chr7	4243798	4243906	E082	22734
chr7	4266093	4266460	E082	45029
chr7	4266599	4266649	E082	45535

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr7	4244430	4244671	E070	23366