SNP Detail Info-rs878133

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

ESPNL : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0090 (2704/29920,GnomAD)
A=0083 (2444/29118,TOPMED)
A=0083 (414/5008,1000G)
A=0162 (623/3854,ALSPAC)
A=0164 (609/3708,TWINSUK)

Position: chr2:238108292 (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.238108292G>A
GRCh37.p13 chr 2	NC_000002.11:g.239016933G>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=0.995	A=0.005
1000Genomes	American	Sub	694	G=0.840	A=0.160
1000Genomes	East Asian	Sub	1008	G=0.998	A=0.002
1000Genomes	Europe	Sub	1006	G=0.859	A=0.141
1000Genomes	Global	Study-wide	5008	G=0.917	A=0.083
1000Genomes	South Asian	Sub	978	G=0.840	A=0.160
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.838	A=0.162
The Genome Aggregation Database	African	Sub	8716	G=0.972	A=0.028
The Genome Aggregation Database	American	Sub	836	G=0.830	A=0.170
The Genome Aggregation Database	East Asian	Sub	1622	G=0.999	A=0.001
The Genome Aggregation Database	Europe	Sub	18444	G=0.875	A=0.124
The Genome Aggregation Database	Global	Study-wide	29920	G=0.909	A=0.090
The Genome Aggregation Database	Other	Sub	302	G=0.950	A=0.050
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.916	A=0.083
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.836	A=0.164

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
rs878133	0.000128	alcohol consumption	23743675

eQTL of rs878133 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:239016933	SCLY	ENSG00000132330.12	G>A	7.8532e-10	47403	Cerebellum
Chr2:239016933	SCLY	ENSG00000132330.12	G>A	1.0714e-8	47403	Cortex
Chr2:239016933	SCLY	ENSG00000132330.12	G>A	2.0850e-8	47403	Cerebellar_Hemisphere
Chr2:239016933	KLHL30	ENSG00000168427.7	G>A	4.0997e-15	-30430	Cerebellar_Hemisphere
Chr2:239016933	SCLY	ENSG00000132330.12	G>A	7.2091e-4	47403	Anterior_cingulate_cortex

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0704957723809585	6.6236e-14

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238970839	238970899	E067	-46034
chr2	238990205	238990255	E067	-26678
chr2	238990452	238990751	E067	-26182
chr2	238970839	238970899	E068	-46034
chr2	239017313	239017876	E068	380
chr2	238970839	238970899	E069	-46034
chr2	238989790	238989866	E069	-27067
chr2	238989941	238990032	E069	-26901
chr2	238990205	238990255	E069	-26678
chr2	238970839	238970899	E070	-46034
chr2	238970839	238970899	E071	-46034
chr2	238989247	238989354	E071	-27579
chr2	238989790	238989866	E071	-27067
chr2	238989941	238990032	E071	-26901
chr2	238990205	238990255	E071	-26678
chr2	238990452	238990751	E071	-26182
chr2	239007116	239007529	E071	-9404
chr2	239017176	239017226	E071	243
chr2	239017313	239017876	E071	380
chr2	238989790	238989866	E072	-27067
chr2	238989941	238990032	E072	-26901
chr2	238990205	238990255	E072	-26678
chr2	238990452	238990751	E072	-26182
chr2	239014417	239014467	E072	-2466
chr2	239014951	239015001	E072	-1932
chr2	238970839	238970899	E073	-46034
chr2	239014951	239015001	E073	-1932
chr2	238989790	238989866	E074	-27067
chr2	238989941	238990032	E074	-26901
chr2	238990452	238990751	E074	-26182
chr2	239017313	239017876	E074	380
chr2	238994008	238994058	E081	-22875
chr2	238994372	238994803	E081	-22130
chr2	238993565	238993671	E082	-23262
chr2	238994008	238994058	E082	-22875

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-46326
chr2	238968700	238970607	E068	-46326
chr2	238968700	238970607	E069	-46326
chr2	238968700	238970607	E070	-46326
chr2	238968700	238970607	E071	-46326
chr2	238968700	238970607	E072	-46326
chr2	238968700	238970607	E073	-46326
chr2	238968700	238970607	E074	-46326
chr2	238968700	238970607	E081	-46326
chr2	238968700	238970607	E082	-46326

rs878133