rs2817475

Homo sapiens
C>T
SMYD3 : Intron Variant
LOC105373270 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
T=0216 (6477/29910,GnomAD)
T=0261 (7615/29116,TOPMED)
T=0186 (929/5008,1000G)
T=0147 (568/3854,ALSPAC)
T=0139 (515/3708,TWINSUK)
chr1:245798900 (GRCh38.p7) (1q44)
ND
GWASdb2
1   publication(s)
See rs on genome
31 Enhancers around
0 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 1NC_000001.11:g.245798900C>T
GRCh37.p13 chr 1NC_000001.10:g.245962202C>T

Gene: SMYD3, SET and MYND domain containing 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
SMYD3 transcript variant 1NM_001167740.1:c.N/AIntron Variant
SMYD3 transcript variant 2NM_022743.2:c.N/AIntron Variant
SMYD3 transcript variant X1XM_011544253.1:c.N/AIntron Variant
SMYD3 transcript variant X4XM_011544254.2:c.N/AIntron Variant
SMYD3 transcript variant X5XM_011544257.1:c.N/AIntron Variant
SMYD3 transcript variant X7XM_011544258.2:c.N/AIntron Variant
SMYD3 transcript variant X6XM_011544259.2:c.N/AIntron Variant
SMYD3 transcript variant X6XM_011544260.1:c.N/AIntron Variant
SMYD3 transcript variant X5XM_011544261.2:c.N/AIntron Variant
SMYD3 transcript variant X8XM_017002094.1:c.N/AIntron Variant
SMYD3 transcript variant X9XM_017002095.1:c.N/AIntron Variant

Gene: LOC105373270, uncharacterized LOC105373270(plus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105373270 transcript variant X3XR_001737771.1:n.N/AUpstream Transcript Variant
LOC105373270 transcript variant X1XR_001737770.1:n.N/AN/A
LOC105373270 transcript variant X2XR_949357.2:n.N/AN/A

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.541T=0.459
1000GenomesAmericanSub694C=0.890T=0.110
1000GenomesEast AsianSub1008C=0.998T=0.002
1000GenomesEuropeSub1006C=0.859T=0.141
1000GenomesGlobalStudy-wide5008C=0.814T=0.186
1000GenomesSouth AsianSub978C=0.890T=0.110
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.853T=0.147
Trans-Omics for Precision MedicineGlobalStudy-wide29116C=0.738T=0.261
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.861T=0.139
PMID Title Author Journal
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet

P-Value

SNP ID p-value Traits Study
rs28174750.000467nicotine smoking19268276

eQTL of rs2817475 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 rs2817475 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 )
chr1245934933245935818E068-26384
chr1245927132245927426E081-34776
chr1245927448245927596E081-34606
chr1245931960245932014E081-30188
chr1245934933245935818E081-26384
chr1245936637245937171E081-25031
chr1245937453245937786E081-24416
chr1245961649245961859E081-343
chr1245972782245972962E08110580
chr1245973253245973303E08111051
chr1245973620245973670E08111418
chr1245973680245974264E08111478
chr1245974316245974559E08112114
chr1245974621245974756E08112419
chr1245974815245974957E08112613
chr1245975362245975500E08113160
chr1245986188245987044E08123986
chr1245998754245999314E08136552
chr1245999491245999629E08137289
chr1245927132245927426E082-34776
chr1245927448245927596E082-34606
chr1245972782245972962E08210580
chr1245973253245973303E08211051
chr1245973620245973670E08211418
chr1245973680245974264E08211478
chr1245974621245974756E08212419
chr1245974815245974957E08212613
chr1245975362245975500E08213160
chr1245996803245996865E08234601
chr1245997397245997502E08235195
chr1245998754245999314E08236552