SNP Detail Info-rs13025510

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ESPNL : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0128 (3846/29894,GnomAD)
A=0135 (3936/29118,TOPMED)
A=0153 (765/5008,1000G)
A=0174 (669/3854,ALSPAC)
A=0180 (667/3708,TWINSUK)

Position: chr2:238108499 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 35 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238108499G>A
GRCh37.p13 chr 2	NC_000002.11:g.239017140G>A

Molecule type	Change	Amino acid[Codon]	SO Term
ESPNL transcript variant 1	NM_194312.3:c.	N/A	Intron Variant
ESPNL transcript variant 2	NM_001308370.1:c.	N/A	Genic Upstream Transcript Variant
ESPNL transcript variant X1	XM_011511087.1:c.	N/A	Genic Upstream Transcript Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.892	A=0.108
1000Genomes	American	Sub	694	G=0.820	A=0.180
1000Genomes	East Asian	Sub	1008	G=0.971	A=0.029
1000Genomes	Europe	Sub	1006	G=0.848	A=0.152
1000Genomes	Global	Study-wide	5008	G=0.847	A=0.153
1000Genomes	South Asian	Sub	978	G=0.670	A=0.330
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.826	A=0.174
The Genome Aggregation Database	African	Sub	8700	G=0.878	A=0.122
The Genome Aggregation Database	American	Sub	836	G=0.820	A=0.180
The Genome Aggregation Database	East Asian	Sub	1610	G=0.976	A=0.024
The Genome Aggregation Database	Europe	Sub	18446	G=0.860	A=0.139
The Genome Aggregation Database	Global	Study-wide	29894	G=0.871	A=0.128
The Genome Aggregation Database	Other	Sub	302	G=0.900	A=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.864	A=0.135
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.820	A=0.180

PMID	Title	Author	Journal
23743675	A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks.	Kapoor M	Hum Genet

SNP ID	p-value	Traits	Study
rs13025510	0.000133	alcohol consumption	23743675

eQTL of rs13025510 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:239017140	SCLY	ENSG00000132330.12	G>A	7.8532e-10	47610	Cerebellum
Chr2:239017140	SCLY	ENSG00000132330.12	G>A	1.0714e-8	47610	Cortex
Chr2:239017140	SCLY	ENSG00000132330.12	G>A	2.0850e-8	47610	Cerebellar_Hemisphere
Chr2:239017140	KLHL30	ENSG00000168427.7	G>A	4.0997e-15	-30223	Cerebellar_Hemisphere
Chr2:239017140	SCLY	ENSG00000132330.12	G>A	7.2091e-4	47610	Anterior_cingulate_cortex

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0675928705908459	3.4305e-16

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238970839	238970899	E067	-46241
chr2	238990205	238990255	E067	-26885
chr2	238990452	238990751	E067	-26389
chr2	238970839	238970899	E068	-46241
chr2	239017313	239017876	E068	173
chr2	238970839	238970899	E069	-46241
chr2	238989790	238989866	E069	-27274
chr2	238989941	238990032	E069	-27108
chr2	238990205	238990255	E069	-26885
chr2	238970839	238970899	E070	-46241
chr2	238970839	238970899	E071	-46241
chr2	238989247	238989354	E071	-27786
chr2	238989790	238989866	E071	-27274
chr2	238989941	238990032	E071	-27108
chr2	238990205	238990255	E071	-26885
chr2	238990452	238990751	E071	-26389
chr2	239007116	239007529	E071	-9611
chr2	239017176	239017226	E071	36
chr2	239017313	239017876	E071	173
chr2	238989790	238989866	E072	-27274
chr2	238989941	238990032	E072	-27108
chr2	238990205	238990255	E072	-26885
chr2	238990452	238990751	E072	-26389
chr2	239014417	239014467	E072	-2673
chr2	239014951	239015001	E072	-2139
chr2	238970839	238970899	E073	-46241
chr2	239014951	239015001	E073	-2139
chr2	238989790	238989866	E074	-27274
chr2	238989941	238990032	E074	-27108
chr2	238990452	238990751	E074	-26389
chr2	239017313	239017876	E074	173
chr2	238994008	238994058	E081	-23082
chr2	238994372	238994803	E081	-22337
chr2	238993565	238993671	E082	-23469
chr2	238994008	238994058	E082	-23082

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-46533
chr2	238968700	238970607	E068	-46533
chr2	238968700	238970607	E069	-46533
chr2	238968700	238970607	E070	-46533
chr2	238968700	238970607	E071	-46533
chr2	238968700	238970607	E072	-46533
chr2	238968700	238970607	E073	-46533
chr2	238968700	238970607	E074	-46533
chr2	238968700	238970607	E081	-46533
chr2	238968700	238970607	E082	-46533

rs13025510