rs6438847

Homo sapiens
A>C
KALRN : Intron Variant
LOC105374076 : 2KB Upstream Variant
Check p-value
SNV (Single Nucleotide Variation)
C=0443 (12919/29118,TOPMED)
C=0422 (12269/29076,GnomAD)
A==0498 (2496/5008,1000G)
C=0326 (1258/3854,ALSPAC)
C=0327 (1214/3708,TWINSUK)
chr3:124578798 (GRCh38.p7) (3q21.2)
AD
GWASdb2
1   publication(s)
See rs on genome
69 Enhancers around
13 Promoters around

Genomic Coordinates

Sequence Name Change(s)
GRCh38.p7 chr 3NC_000003.12:g.124578798A>C
GRCh37.p13 chr 3NC_000003.11:g.124297645A>C
KALRN RefSeqGeneNG_012742.2:g.489088A>C

Gene: KALRN, kalirin, RhoGEF kinase(plus strand)

Molecule type Change Amino acid[Codon] SO Term
KALRN transcript variant 1NM_001024660.4:c.N/AIntron Variant
KALRN transcript variant 5NM_001322988.1:c.N/AIntron Variant
KALRN transcript variant 10NM_001322993.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 11NM_001322994.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 12NM_001322995.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 13NM_001322996.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 14NM_001322997.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 15NM_001322998.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 16NM_001322999.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 17NM_001323000.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 18NM_001323001.1:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 3NM_007064.4:c.N/AGenic Upstream Transcript Variant
KALRN transcript variant 6NM_001322989.1:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant 7NM_001322990.1:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant 8NM_001322991.1:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant 9NM_001322992.1:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant 2NM_003947.5:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant 4NR_028136.2:n.N/AGenic Downstream Transcript Variant
KALRN transcript variant X1XM_006713810.3:c.N/AIntron Variant
KALRN transcript variant X4XM_006713811.3:c.N/AIntron Variant
KALRN transcript variant X6XM_006713812.3:c.N/AIntron Variant
KALRN transcript variant X8XM_006713813.3:c.N/AIntron Variant
KALRN transcript variant X9XM_006713814.3:c.N/AIntron Variant
KALRN transcript variant X2XM_011513279.2:c.N/AIntron Variant
KALRN transcript variant X3XM_011513280.2:c.N/AIntron Variant
KALRN transcript variant X5XM_011513281.2:c.N/AIntron Variant
KALRN transcript variant X11XM_011513283.2:c.N/AIntron Variant
KALRN transcript variant X13XM_011513285.2:c.N/AIntron Variant
KALRN transcript variant X7XM_017007429.1:c.N/AIntron Variant
KALRN transcript variant X10XM_017007430.1:c.N/AIntron Variant
KALRN transcript variant X12XM_017007431.1:c.N/AIntron Variant
KALRN transcript variant X14XM_017007432.1:c.N/AIntron Variant
KALRN transcript variant X16XM_006713815.3:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant X16XM_017007433.1:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant X17XM_017007434.1:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant X18XM_017007435.1:c.N/AGenic Downstream Transcript Variant
KALRN transcript variant X20XR_001740356.1:n.N/AGenic Downstream Transcript Variant
KALRN transcript variant X21XR_001740357.1:n.N/AGenic Downstream Transcript Variant
KALRN transcript variant X22XR_001740358.1:n.N/AGenic Downstream Transcript Variant

Gene: LOC105374076, uncharacterized LOC105374076(minus strand): 2KB Upstream Variant

Molecule type Change Amino acid[Codon] SO Term
LOC105374076 transcriptXR_001740872.1:n.N/AUpstream Transcript Variant

Population Frequency

Study Population Group Sample # Ref Allele Alt Allele
1000GenomesAfricanSub1322A=0.402C=0.598
1000GenomesAmericanSub694A=0.540C=0.460
1000GenomesEast AsianSub1008A=0.195C=0.805
1000GenomesEuropeSub1006A=0.652C=0.348
1000GenomesGlobalStudy-wide5008A=0.498C=0.502
1000GenomesSouth AsianSub978A=0.750C=0.250
The Avon Longitudinal Study of Parents and ChildrenPARENT AND CHILD COHORTStudy-wide3854A=0.674C=0.326
The Genome Aggregation DatabaseAfricanSub8494A=0.462C=0.538
The Genome Aggregation DatabaseAmericanSub814A=0.530C=0.470
The Genome Aggregation DatabaseEast AsianSub1604A=0.215C=0.785
The Genome Aggregation DatabaseEuropeSub17866A=0.664C=0.335
The Genome Aggregation DatabaseGlobalStudy-wide29076A=0.578C=0.422
The Genome Aggregation DatabaseOtherSub298A=0.760C=0.240
Trans-Omics for Precision MedicineGlobalStudy-wide29118A=0.556C=0.443
UK 10K study - TwinsTWIN COHORTStudy-wide3708A=0.673C=0.327
PMID Title Author Journal
24277619ALDH2 is associated to alcohol dependence and is the major genetic determinant of "daily maximum drinks" in a GWAS study of an isolated rural Chinese sample.Quillen EEAm J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID p-value Traits Study
rs64388470.000302alcohol dependence24277619

eQTL of rs6438847 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 rs6438847 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 )
chr3124248791124248972E067-48673
chr3124277738124279355E067-18290
chr3124283700124284244E067-13401
chr3124311442124312141E06713797
chr3124248791124248972E068-48673
chr3124276328124276972E068-20673
chr3124277550124277600E068-20045
chr3124277738124279355E068-18290
chr3124283700124284244E068-13401
chr3124284432124284689E068-12956
chr3124311442124312141E06813797
chr3124312273124312327E06814628
chr3124312455124312518E06814810
chr3124318134124318923E06820489
chr3124318975124319278E06821330
chr3124319281124319381E06821636
chr3124319712124319937E06822067
chr3124248791124248972E069-48673
chr3124249033124249268E069-48377
chr3124277550124277600E069-20045
chr3124277738124279355E069-18290
chr3124283700124284244E069-13401
chr3124274695124274804E070-22841
chr3124274954124275233E070-22412
chr3124275972124276022E070-21623
chr3124276328124276972E070-20673
chr3124277550124277600E070-20045
chr3124277738124279355E070-18290
chr3124281272124281494E070-16151
chr3124248791124248972E071-48673
chr3124269219124269584E071-28061
chr3124277738124279355E071-18290
chr3124311442124312141E07113797
chr3124312455124312518E07114810
chr3124269219124269584E072-28061
chr3124276328124276972E072-20673
chr3124277550124277600E072-20045
chr3124277738124279355E072-18290
chr3124280460124280514E072-17131
chr3124280899124280954E072-16691
chr3124281272124281494E072-16151
chr3124283700124284244E072-13401
chr3124269219124269584E073-28061
chr3124277738124279355E073-18290
chr3124283700124284244E073-13401
chr3124284432124284689E073-12956
chr3124316233124316383E07318588
chr3124317016124317098E07319371
chr3124248791124248972E074-48673
chr3124249033124249268E074-48377
chr3124277738124279355E074-18290
chr3124319281124319381E07421636
chr3124275972124276022E081-21623
chr3124276328124276972E081-20673
chr3124277550124277600E081-20045
chr3124277738124279355E081-18290
chr3124279598124279856E081-17789
chr3124280460124280514E081-17131
chr3124280899124280954E081-16691
chr3124283700124284244E081-13401
chr3124275972124276022E082-21623
chr3124276328124276972E082-20673
chr3124277550124277600E082-20045
chr3124277738124279355E082-18290
chr3124280211124280261E082-17384
chr3124280460124280514E082-17131
chr3124280899124280954E082-16691
chr3124281272124281494E082-16151
chr3124283700124284244E082-13401










Promoter Annotation (GRCh37.p13)

Chromosome Start End Region Distance(-/+:Up/Downstream)
chr3124303180124304241E0675535
chr3124304270124304358E0676625
chr3124303180124304241E0685535
chr3124304270124304358E0686625
chr3124304270124304358E0696625
chr3124304270124304358E0716625
chr3124303180124304241E0725535
chr3124304270124304358E0726625
chr3124303180124304241E0735535
chr3124304270124304358E0736625
chr3124303180124304241E0745535
chr3124303180124304241E0825535
chr3124304270124304358E0826625