SNP Detail Info-rs41264151

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

UBE2F-SCLY : Non Coding Transcript Variant
SCLY : 3 Prime UTR Variant
ESPNL : 2KB Upstream Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0135 (4038/29872,GnomAD)
A=0143 (4175/29118,TOPMED)
A=0158 (792/5008,1000G)
A=0180 (694/3854,ALSPAC)
A=0190 (704/3708,TWINSUK)

Position: chr2:238098994 (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.238098994G>A
GRCh37.p13 chr 2	NC_000002.11:g.239007635G>A

Gene: SCLY, selenocysteine lyase(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SCLY transcript	NM_016510.5:c.	N/A	3 Prime UTR Variant

Gene: ESPNL, espin-like(plus strand): 2KB Upstream Variant

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

Gene: UBE2F-SCLY, UBE2F-SCLY readthrough (NMD candidate)(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2F-SCLY transcript	NR_037904.1:n.255...NR_037904.1:n.2553G>A	G>A	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.877	A=0.123
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=0.835	A=0.165
1000Genomes	Global	Study-wide	5008	G=0.842	A=0.158
1000Genomes	South Asian	Sub	978	G=0.690	A=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.820	A=0.180
The Genome Aggregation Database	African	Sub	8700	G=0.868	A=0.132
The Genome Aggregation Database	American	Sub	838	G=0.820	A=0.180
The Genome Aggregation Database	East Asian	Sub	1618	G=0.976	A=0.024
The Genome Aggregation Database	Europe	Sub	18414	G=0.854	A=0.145
The Genome Aggregation Database	Global	Study-wide	29872	G=0.864	A=0.135
The Genome Aggregation Database	Other	Sub	302	G=0.890	A=0.110
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.856	A=0.143
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.810	A=0.190

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
rs41264151	0.000121	alcohol consumption	23743675

eQTL of rs41264151 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:239007635	SCLY	ENSG00000132330.12	G>A	7.8532e-10	38105	Cerebellum
Chr2:239007635	SCLY	ENSG00000132330.12	G>A	1.0714e-8	38105	Cortex
Chr2:239007635	SCLY	ENSG00000132330.12	G>A	2.0850e-8	38105	Cerebellar_Hemisphere
Chr2:239007635	SCLY	ENSG00000132330.12	G>A	7.2091e-4	38105	Anterior_cingulate_cortex

meQTL of rs41264151 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0630940305512061	4.3635e-14

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238970839	238970899	E067	-36736
chr2	238990205	238990255	E067	-17380
chr2	238990452	238990751	E067	-16884
chr2	238970839	238970899	E068	-36736
chr2	239017313	239017876	E068	9678
chr2	238970839	238970899	E069	-36736
chr2	238989790	238989866	E069	-17769
chr2	238989941	238990032	E069	-17603
chr2	238990205	238990255	E069	-17380
chr2	238970839	238970899	E070	-36736
chr2	238970839	238970899	E071	-36736
chr2	238989247	238989354	E071	-18281
chr2	238989790	238989866	E071	-17769
chr2	238989941	238990032	E071	-17603
chr2	238990205	238990255	E071	-17380
chr2	238990452	238990751	E071	-16884
chr2	239007116	239007529	E071	-106
chr2	239017176	239017226	E071	9541
chr2	239017313	239017876	E071	9678
chr2	238989790	238989866	E072	-17769
chr2	238989941	238990032	E072	-17603
chr2	238990205	238990255	E072	-17380
chr2	238990452	238990751	E072	-16884
chr2	239014417	239014467	E072	6782
chr2	239014951	239015001	E072	7316
chr2	238970839	238970899	E073	-36736
chr2	239014951	239015001	E073	7316
chr2	238989790	238989866	E074	-17769
chr2	238989941	238990032	E074	-17603
chr2	238990452	238990751	E074	-16884
chr2	239017313	239017876	E074	9678
chr2	238994008	238994058	E081	-13577
chr2	238994372	238994803	E081	-12832
chr2	238993565	238993671	E082	-13964
chr2	238994008	238994058	E082	-13577

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-37028
chr2	238968700	238970607	E068	-37028
chr2	238968700	238970607	E069	-37028
chr2	238968700	238970607	E070	-37028
chr2	238968700	238970607	E071	-37028
chr2	238968700	238970607	E072	-37028
chr2	238968700	238970607	E073	-37028
chr2	238968700	238970607	E074	-37028
chr2	238968700	238970607	E081	-37028
chr2	238968700	238970607	E082	-37028

rs41264151