SNP Detail Info-rs555540

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 3	NC_000003.12:g.124448118G>A
GRCh38.p7 chr 3	NC_000003.12:g.124448118G>T
GRCh37.p13 chr 3	NC_000003.11:g.124166965G>A
GRCh37.p13 chr 3	NC_000003.11:g.124166965G>T
KALRN RefSeqGene	NG_012742.2:g.358408G>A
KALRN RefSeqGene	NG_012742.2:g.358408G>T

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

Molecule type	Change	Amino acid[Codon]	SO Term
KALRN transcript variant 1	NM_001024660.4:c.	N/A	Intron Variant
KALRN transcript variant 5	NM_001322988.1:c.	N/A	Intron Variant
KALRN transcript variant 6	NM_001322989.1:c.	N/A	Intron Variant
KALRN transcript variant 7	NM_001322990.1:c.	N/A	Intron Variant
KALRN transcript variant 8	NM_001322991.1:c.	N/A	Intron Variant
KALRN transcript variant 9	NM_001322992.1:c.	N/A	Intron Variant
KALRN transcript variant 2	NM_003947.5:c.	N/A	Intron Variant
KALRN transcript variant 10	NM_001322993.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 11	NM_001322994.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 12	NM_001322995.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 13	NM_001322996.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 14	NM_001322997.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 15	NM_001322998.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 16	NM_001322999.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 17	NM_001323000.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 18	NM_001323001.1:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 3	NM_007064.4:c.	N/A	Genic Upstream Transcript Variant
KALRN transcript variant 4	NR_028136.2:n.	N/A	Genic Downstream Transcript Variant
KALRN transcript variant X1	XM_006713810.3:c.	N/A	Intron Variant
KALRN transcript variant X4	XM_006713811.3:c.	N/A	Intron Variant
KALRN transcript variant X6	XM_006713812.3:c.	N/A	Intron Variant
KALRN transcript variant X8	XM_006713813.3:c.	N/A	Intron Variant
KALRN transcript variant X9	XM_006713814.3:c.	N/A	Intron Variant
KALRN transcript variant X16	XM_006713815.3:c.	N/A	Intron Variant
KALRN transcript variant X2	XM_011513279.2:c.	N/A	Intron Variant
KALRN transcript variant X3	XM_011513280.2:c.	N/A	Intron Variant
KALRN transcript variant X5	XM_011513281.2:c.	N/A	Intron Variant
KALRN transcript variant X11	XM_011513283.2:c.	N/A	Intron Variant
KALRN transcript variant X13	XM_011513285.2:c.	N/A	Intron Variant
KALRN transcript variant X7	XM_017007429.1:c.	N/A	Intron Variant
KALRN transcript variant X10	XM_017007430.1:c.	N/A	Intron Variant
KALRN transcript variant X12	XM_017007431.1:c.	N/A	Intron Variant
KALRN transcript variant X14	XM_017007432.1:c.	N/A	Intron Variant
KALRN transcript variant X16	XM_017007433.1:c.	N/A	Intron Variant
KALRN transcript variant X17	XM_017007434.1:c.	N/A	Intron Variant
KALRN transcript variant X18	XM_017007435.1:c.	N/A	Intron Variant
KALRN transcript variant X20	XR_001740356.1:n.	N/A	Intron Variant
KALRN transcript variant X21	XR_001740357.1:n.	N/A	Intron Variant
KALRN transcript variant X22	XR_001740358.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.725	T=0.275
1000Genomes	American	Sub	694	G=0.760	T=0.240
1000Genomes	East Asian	Sub	1008	G=0.809	T=0.191
1000Genomes	Europe	Sub	1006	G=0.690	T=0.310
1000Genomes	Global	Study-wide	5008	G=0.722	T=0.278
1000Genomes	South Asian	Sub	978	G=0.630	T=0.370
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.673	T=0.327
The Genome Aggregation Database	African	Sub	8682	G=0.724	A=0.000
The Genome Aggregation Database	American	Sub	836	G=0.770	A=0.00,
The Genome Aggregation Database	East Asian	Sub	1614	G=0.843	A=0.000
The Genome Aggregation Database	Europe	Sub	18456	G=0.652	A=0.000
The Genome Aggregation Database	Global	Study-wide	29890	G=0.687	A=0.000
The Genome Aggregation Database	Other	Sub	302	G=0.650	A=0.00,
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.710	T=0.289
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.666	T=0.334

PMID	Title	Author	Journal
24277619	ALDH2 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 EE	Am J Med Genet B Neuropsychiatr Genet

P-Value

SNP ID	p-value	Traits	Study
rs555540	0.00017	alcohol consumption (maxi-drinks)	24277619

eQTL of rs555540 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr3:124166965	ADCY5	ENSG00000173175.10	G>T	2.7436e-3	998360	Cerebellum

meQTL of rs555540 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

rs555540

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs555540 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs555540 in Fetal Brain

Genomic View

Chromatin Interaction