rs2347896

Homo sapiens
C>A
CALD1 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
A=0114 (3441/29966,GnomAD)
A=0096 (2800/29118,TOPMED)
A=0079 (398/5008,1000G)
A=0156 (602/3854,ALSPAC)
A=0158 (585/3708,TWINSUK)
chr7:134780643 (GRCh38.p7) (7q33)
AD
GWASdb2
1   publication(s)
See rs on genome
4 Enhancers around
4 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 7NC_000007.14:g.134780643C>A
GRCh37.p13 chr 7NC_000007.13:g.134465394C>A
CALD1 RefSeqGeneNG_029186.1:g.6231C>A

Gene: CALD1, caldesmon 1(plus strand)

Molecule type Change Amino acid[Codon] SO Term
CALD1 transcript variant 2NM_004342.6:c.N/AIntron Variant
CALD1 transcript variant 1NM_033138.3:c.N/AIntron Variant
CALD1 transcript variant 3NM_033157.3:c.N/AIntron Variant
CALD1 transcript variant 4NM_033139.3:c.N/AGenic Upstream Transcript Variant
CALD1 transcript variant 5NM_033140.3:c.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X3XM_017012650.1:c.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X6XM_017012651.1:c.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X12XM_017012652.1:c.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X11XM_017012653.1:c.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X14XM_017012654.1:c.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X2XR_001744877.1:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X5XR_001744878.1:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X7XR_001744879.1:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X9XR_001744880.1:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X13XR_001744881.1:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X2XR_927535.2:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X4XR_927537.2:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X10XR_927541.2:n.N/AGenic Upstream Transcript Variant
CALD1 transcript variant X12XR_927542.2:n.N/AGenic Upstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322C=0.987A=0.013
1000GenomesAmericanSub694C=0.900A=0.100
1000GenomesEast AsianSub1008C=0.897A=0.103
1000GenomesEuropeSub1006C=0.864A=0.136
1000GenomesGlobalStudy-wide5008C=0.921A=0.079
1000GenomesSouth AsianSub978C=0.930A=0.070
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854C=0.844A=0.156
The Genome Aggregation DatabaseAfricanSub8730C=0.965A=0.035
The Genome Aggregation DatabaseAmericanSub836C=0.900A=0.100
The Genome Aggregation DatabaseEast AsianSub1618C=0.890A=0.110
The Genome Aggregation DatabaseEuropeSub18480C=0.846A=0.153
The Genome Aggregation DatabaseGlobalStudy-wide29966C=0.885A=0.114
The Genome Aggregation DatabaseOtherSub302C=0.890A=0.110
Trans-Omics for Precision MedicineGlobalStudy-wide29118C=0.903A=0.096
UK 10K study - TwinsTWIN COHORTStudy-wide3708C=0.842A=0.158
PMID Title Author Journal
21314694Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.Kendler KSAlcohol Clin Exp Res

P-Value

SNP ID p-value Traits Study
rs23478960.000503alcohol dependence21314694

eQTL of rs2347896 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 rs2347896 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 )
chr7134415465134415601E071-49793
chr7134415676134416055E071-49339
chr7134416087134416364E071-49030
chr7134501114134501599E07135720

Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr7134462675134466494E0680
chr7134462675134466494E0710
chr7134462675134466494E0720
chr7134462675134466494E0730