rs2394340

Homo sapiens
T>C
LRRTM3 : Non Coding Transcript Variant
CTNNA3 : Intron Variant
Check p-value
SNV (Single Nucleotide Variation)
T==0446 (13278/29766,GnomAD)
T==0403 (11737/29118,TOPMED)
T==0468 (2342/5008,1000G)
C=0455 (1754/3854,ALSPAC)
C=0454 (1684/3708,TWINSUK)
chr10:67101514 (GRCh38.p7) (10q21.3)
AD
GWASdb2
1   publication(s)
See rs on genome
52 Enhancers around
1 Promoter around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 10NC_000010.11:g.67101514T>C
GRCh37.p13 chr 10NC_000010.10:g.68861272T>C
CTNNA3 RefSeqGeneNG_034072.1:g.599678A>G

Gene: CTNNA3, catenin alpha 3(minus strand)

Molecule type Change Amino acid[Codon] SO Term
CTNNA3 transcript variant 2NM_001127384.2:c.N/AIntron Variant
CTNNA3 transcript variant 1NM_013266.3:c.N/AIntron Variant
CTNNA3 transcript variant 3NM_001291133.1:c.N/AGenic Downstream Transcript Variant
CTNNA3 transcript variant X1XM_017016151.1:c.N/AIntron Variant
CTNNA3 transcript variant X2XM_017016152.1:c.N/AIntron Variant
CTNNA3 transcript variant X3XM_017016153.1:c.N/AIntron Variant
CTNNA3 transcript variant X4XM_017016154.1:c.N/AIntron Variant
CTNNA3 transcript variant X5XM_017016155.1:c.N/AIntron Variant
CTNNA3 transcript variant X6XM_017016156.1:c.N/AIntron Variant
CTNNA3 transcript variant X7XM_017016157.1:c.N/AGenic Upstream Transcript Variant
CTNNA3 transcript variant X8XM_017016158.1:c.N/AGenic Downstream Transcript Variant

Gene: LRRTM3, leucine rich repeat transmembrane neuronal 3(plus strand)

Molecule type Change Amino acid[Codon] SO Term
LRRTM3 transcript variant 1NM_178011.4:c.N/A3 Prime UTR Variant
LRRTM3 transcript variant 2NR_111909.1:n.405...NR_111909.1:n.4058T>CT>CNon Coding Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322T=0.185C=0.815
1000GenomesAmericanSub694T=0.580C=0.420
1000GenomesEast AsianSub1008T=0.610C=0.390
1000GenomesEuropeSub1006T=0.498C=0.502
1000GenomesGlobalStudy-wide5008T=0.468C=0.532
1000GenomesSouth AsianSub978T=0.590C=0.410
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854T=0.545C=0.455
The Genome Aggregation DatabaseAfricanSub8706T=0.218C=0.782
The Genome Aggregation DatabaseAmericanSub828T=0.600C=0.400
The Genome Aggregation DatabaseEast AsianSub1580T=0.601C=0.399
The Genome Aggregation DatabaseEuropeSub18350T=0.534C=0.465
The Genome Aggregation DatabaseGlobalStudy-wide29766T=0.446C=0.553
The Genome Aggregation DatabaseOtherSub302T=0.390C=0.610
Trans-Omics for Precision MedicineGlobalStudy-wide29118T=0.403C=0.596
UK 10K study - TwinsTWIN COHORTStudy-wide3708T=0.546C=0.454
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
rs23943400.000803alcohol dependence21314694

eQTL of rs2394340 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 rs2394340 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 )
chr106883902368839122E067-22150
chr106884604968846487E067-14785
chr106884664568847115E067-14157
chr106884751868847568E067-13704
chr106884764968847699E067-13573
chr106884797068848042E067-13230
chr106884815868848275E067-12997
chr106885789868858189E067-3083
chr106885823068858299E067-2973
chr106885836168858481E067-2791
chr106885852968858808E067-2464
chr106884664568847115E068-14157
chr106884797068848042E068-13230
chr106884815868848275E068-12997
chr106885823068858299E068-2973
chr106885836168858481E068-2791
chr106885852968858808E068-2464
chr106888283268882946E06821560
chr106884604968846487E069-14785
chr106884664568847115E069-14157
chr106885640268856452E069-4820
chr106885647268856522E069-4750
chr106885836168858481E069-2791
chr106885852968858808E069-2464
chr106888283268882946E06921560
chr106884151668841613E071-19659
chr106884764968847699E071-13573
chr106884797068848042E071-13230
chr106885836168858481E071-2791
chr106885852968858808E071-2464
chr106888283268882946E07121560
chr106885836168858481E072-2791
chr106885852968858808E072-2464
chr106884604968846487E073-14785
chr106884664568847115E073-14157
chr106884604968846487E074-14785
chr106884664568847115E074-14157
chr106884751868847568E074-13704
chr106884764968847699E074-13573
chr106884797068848042E074-13230
chr106885747368857606E074-3666
chr106885769668857801E074-3471
chr106885789868858189E074-3083
chr106885823068858299E074-2973
chr106885836168858481E074-2791
chr106885852968858808E074-2464
chr106887918568879225E07417913
chr106887946468879667E07418192
chr106887982468879874E07418552
chr106888020868880299E07418936
chr106888283268882946E07421560
chr106888306768883124E07421795







Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr106891116868911228E07449896