SNP Detail Info-rs878134

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

ESPNL : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0167 (16614/99410,ExAC)
T=0124 (3727/29932,GnomAD)
T=0127 (3711/29118,TOPMED)
G==0139 (1813/12982,GO-ESP)
T=0146 (731/5008,1000G)
T=0176 (678/3854,ALSPAC)
T=0185 (685/3708,TWINSUK)

Position: chr2:238107999 (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

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238107999G>T
GRCh37.p13 chr 2	NC_000002.11:g.239016640G>T

Gene: ESPNL, espin-like(plus strand)

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

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.918	T=0.082
1000Genomes	American	Sub	694	G=0.820	T=0.180
1000Genomes	East Asian	Sub	1008	G=0.971	T=0.029
1000Genomes	Europe	Sub	1006	G=0.846	T=0.154
1000Genomes	Global	Study-wide	5008	G=0.854	T=0.146
1000Genomes	South Asian	Sub	978	G=0.680	T=0.320
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.824	T=0.176
The Exome Aggregation Consortium	American	Sub	18352	G=0.837	T=0.163
The Exome Aggregation Consortium	Asian	Sub	19420	G=0.810	T=0.189
The Exome Aggregation Consortium	Europe	Sub	60964	G=0.838	T=0.161
The Exome Aggregation Consortium	Global	Study-wide	99410	G=0.832	T=0.167
The Exome Aggregation Consortium	Other	Sub	674	G=0.840	T=0.160
The Genome Aggregation Database	African	Sub	8712	G=0.896	T=0.104
The Genome Aggregation Database	American	Sub	838	G=0.820	T=0.180
The Genome Aggregation Database	East Asian	Sub	1620	G=0.977	T=0.023
The Genome Aggregation Database	Europe	Sub	18460	G=0.858	T=0.141
The Genome Aggregation Database	Global	Study-wide	29932	G=0.875	T=0.124
The Genome Aggregation Database	Other	Sub	302	G=0.900	T=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.872	T=0.127
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.815	T=0.185

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

P-Value

SNP ID	p-value	Traits	Study
rs878134	0.000128	alcohol consumption	23743675

eQTL of rs878134 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:239016640	SCLY	ENSG00000132330.12	G>T	7.8532e-10	47110	Cerebellum
Chr2:239016640	SCLY	ENSG00000132330.12	G>T	1.0714e-8	47110	Cortex
Chr2:239016640	SCLY	ENSG00000132330.12	G>T	2.0850e-8	47110	Cerebellar_Hemisphere
Chr2:239016640	KLHL30	ENSG00000168427.7	G>T	4.0997e-15	-30723	Cerebellar_Hemisphere
Chr2:239016640	SCLY	ENSG00000132330.12	G>T	7.2091e-4	47110	Anterior_cingulate_cortex

meQTL of rs878134 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0725761156294358	4.3080e-18

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238970839	238970899	E067	-45741
chr2	238990205	238990255	E067	-26385
chr2	238990452	238990751	E067	-25889
chr2	238970839	238970899	E068	-45741
chr2	239017313	239017876	E068	673
chr2	238970839	238970899	E069	-45741
chr2	238989790	238989866	E069	-26774
chr2	238989941	238990032	E069	-26608
chr2	238990205	238990255	E069	-26385
chr2	238970839	238970899	E070	-45741
chr2	238970839	238970899	E071	-45741
chr2	238989247	238989354	E071	-27286
chr2	238989790	238989866	E071	-26774
chr2	238989941	238990032	E071	-26608
chr2	238990205	238990255	E071	-26385
chr2	238990452	238990751	E071	-25889
chr2	239007116	239007529	E071	-9111
chr2	239017176	239017226	E071	536
chr2	239017313	239017876	E071	673
chr2	238989790	238989866	E072	-26774
chr2	238989941	238990032	E072	-26608
chr2	238990205	238990255	E072	-26385
chr2	238990452	238990751	E072	-25889
chr2	239014417	239014467	E072	-2173
chr2	239014951	239015001	E072	-1639
chr2	238970839	238970899	E073	-45741
chr2	239014951	239015001	E073	-1639
chr2	238989790	238989866	E074	-26774
chr2	238989941	238990032	E074	-26608
chr2	238990452	238990751	E074	-25889
chr2	239017313	239017876	E074	673
chr2	238994008	238994058	E081	-22582
chr2	238994372	238994803	E081	-21837
chr2	238993565	238993671	E082	-22969
chr2	238994008	238994058	E082	-22582

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-46033
chr2	238968700	238970607	E068	-46033
chr2	238968700	238970607	E069	-46033
chr2	238968700	238970607	E070	-46033
chr2	238968700	238970607	E071	-46033
chr2	238968700	238970607	E072	-46033
chr2	238968700	238970607	E073	-46033
chr2	238968700	238970607	E074	-46033
chr2	238968700	238970607	E081	-46033
chr2	238968700	238970607	E082	-46033

rs878134