rs3788964

Homo sapiens
T>C
GCA : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0129 (3889/29952,GnomAD)
C=0108 (3169/29118,TOPMED)
C=0179 (895/5008,1000G)
C=0170 (657/3854,ALSPAC)
C=0167 (621/3708,TWINSUK)
chr2:162350970 (GRCh38.p7) (2q24.2)
ND
GWASdb2
6   publication(s)
See rs on genome
27 Enhancers around
81 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 2NC_000002.12:g.162350970T>C
GRCh37.p13 chr 2NC_000002.11:g.163207480T>C

Gene: GCA, grancalcin(plus strand)

Molecule type Change Amino acid[Codon] SO Term
GCA transcriptNM_012198.3:c.N/AIntron Variant
GCA transcript variant X4XM_005246446.2:c.N/AIntron Variant
GCA transcript variant X1XM_006712398.3:c.N/AIntron Variant
GCA transcript variant X2XM_006712400.3:c.N/AIntron Variant
GCA transcript variant X3XM_006712401.3:c.N/AIntron Variant
GCA transcript variant X5XM_011510926.2:c.N/AIntron Variant
GCA transcript variant X11XM_011510927.2:c.N/AIntron Variant
GCA transcript variant X5XM_017003764.1:c.N/AIntron Variant
GCA transcript variant X6XM_017003765.1:c.N/AIntron Variant
GCA transcript variant X7XM_017003766.1:c.N/AIntron Variant
GCA transcript variant X4XM_017003767.1:c.N/AIntron Variant
GCA transcript variant X10XM_017003768.1:c.N/AIntron Variant
GCA transcript variant X13XM_017003769.1:c.N/AIntron Variant
GCA transcript variant X6XM_011510928.2:c.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.992C=0.008
1000GenomesAmericanSub694T=0.890C=0.110
1000GenomesEast AsianSub1008T=0.638C=0.362
1000GenomesEuropeSub1006T=0.851C=0.149
1000GenomesGlobalStudy-wide5008T=0.821C=0.179
1000GenomesSouth AsianSub978T=0.700C=0.300
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.830C=0.170
The Genome Aggregation DatabaseAfricanSub8726T=0.969C=0.031
The Genome Aggregation DatabaseAmericanSub838T=0.900C=0.100
The Genome Aggregation DatabaseEast AsianSub1614T=0.684C=0.316
The Genome Aggregation DatabaseEuropeSub18472T=0.838C=0.161
The Genome Aggregation DatabaseGlobalStudy-wide29952T=0.870C=0.129
The Genome Aggregation DatabaseOtherSub302T=0.880C=0.120
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.891C=0.108
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.833C=0.167
PMID Title Author Journal
19956101Overview of the Rapid Response data.Brown WMGenes Immun
19268276Genome-wide association study of smoking initiation and current smoking.Vink JMAm J Hum Genet
19956106Analysis of 19 genes for association with type I diabetes in the Type I Diabetes Genetics Consortium families.Howson JMGenes Immun
18927125IFIH1 polymorphisms are significantly associated with type 1 diabetes and IFIH1 gene expression in peripheral blood mononuclear cells.Liu SHum Mol Genet
19956109The Type I Diabetes Genetics Consortium 'Rapid Response' family-based candidate gene study: strategy, genes selection, and main outcome.Julier CGenes Immun
18853133Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.Rafiq SDiabetologia

P-Value

SNP ID p-value Traits Study
rs37889640.000303nicotine smoking19268276

eQTL of rs3788964 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 rs3788964 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 )
chr2163226046163226382E06718566
chr2163172368163172412E068-35068
chr2163176493163176653E068-30827
chr2163176697163176760E068-30720
chr2163177839163177942E068-29538
chr2163178041163178131E068-29349
chr2163172368163172412E069-35068
chr2163176123163176422E069-31058
chr2163176493163176653E069-30827
chr2163176697163176760E069-30720
chr2163172368163172412E071-35068
chr2163176123163176422E071-31058
chr2163176493163176653E071-30827
chr2163176697163176760E071-30720
chr2163177062163177115E071-30365
chr2163177382163177504E071-29976
chr2163199777163199834E071-7646
chr2163227564163227848E07120084
chr2163227977163228027E07120497
chr2163176697163176760E072-30720
chr2163172368163172412E073-35068
chr2163199518163199606E073-7874
chr2163199777163199834E073-7646
chr2163177839163177942E074-29538
chr2163157571163158128E081-49352
chr2163256616163256727E08149136
chr2163230743163231044E08223263









Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr2163173568163173670E067-33810
chr2163173685163174071E067-33409
chr2163174116163174224E067-33256
chr2163174250163175964E067-31516
chr2163175966163176108E067-31372
chr2163199932163200012E067-7468
chr2163200040163201482E067-5998
chr2163201610163201691E067-5789
chr2163201708163201881E067-5599
chr2163201983163202037E067-5443
chr2163173568163173670E068-33810
chr2163173685163174071E068-33409
chr2163174116163174224E068-33256
chr2163174250163175964E068-31516
chr2163175966163176108E068-31372
chr2163199932163200012E068-7468
chr2163200040163201482E068-5998
chr2163201610163201691E068-5789
chr2163201708163201881E068-5599
chr2163201983163202037E068-5443
chr2163173685163174071E069-33409
chr2163174116163174224E069-33256
chr2163174250163175964E069-31516
chr2163175966163176108E069-31372
chr2163199932163200012E069-7468
chr2163200040163201482E069-5998
chr2163201610163201691E069-5789
chr2163201708163201881E069-5599
chr2163201983163202037E069-5443
chr2163174250163175964E070-31516
chr2163200040163201482E070-5998
chr2163201610163201691E070-5789
chr2163201708163201881E070-5599
chr2163201983163202037E070-5443
chr2163173568163173670E071-33810
chr2163173685163174071E071-33409
chr2163174116163174224E071-33256
chr2163174250163175964E071-31516
chr2163175966163176108E071-31372
chr2163199932163200012E071-7468
chr2163200040163201482E071-5998
chr2163201610163201691E071-5789
chr2163201708163201881E071-5599
chr2163201983163202037E071-5443
chr2163173685163174071E072-33409
chr2163174116163174224E072-33256
chr2163174250163175964E072-31516
chr2163175966163176108E072-31372
chr2163199932163200012E072-7468
chr2163200040163201482E072-5998
chr2163201610163201691E072-5789
chr2163201708163201881E072-5599
chr2163201983163202037E072-5443
chr2163173568163173670E073-33810
chr2163173685163174071E073-33409
chr2163174116163174224E073-33256
chr2163174250163175964E073-31516
chr2163199932163200012E073-7468
chr2163200040163201482E073-5998
chr2163201610163201691E073-5789
chr2163201708163201881E073-5599
chr2163201983163202037E073-5443
chr2163174116163174224E074-33256
chr2163174250163175964E074-31516
chr2163199932163200012E074-7468
chr2163200040163201482E074-5998
chr2163201610163201691E074-5789
chr2163201708163201881E074-5599
chr2163201983163202037E074-5443
chr2163174250163175964E081-31516
chr2163175966163176108E081-31372
chr2163199932163200012E081-7468
chr2163200040163201482E081-5998
chr2163201610163201691E081-5789
chr2163201708163201881E081-5599
chr2163174250163175964E082-31516
chr2163199932163200012E082-7468
chr2163200040163201482E082-5998
chr2163201610163201691E082-5789
chr2163201708163201881E082-5599
chr2163201983163202037E082-5443