rs2262426

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G==0127 (3811/29878,GnomAD)
G==0129 (3776/29118,TOPMED)
G==0149 (745/5008,1000G)
G==0176 (679/3854,ALSPAC)
G==0189 (699/3708,TWINSUK)

Position: chr2:238075856 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 44 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238075856G>A
GRCh37.p13 chr 2	NC_000002.11:g.238984497G>A

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

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2F-SCLY transcript	NR_037904.1:n.	N/A	Intron Variant

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.092	A=0.908
1000Genomes	American	Sub	694	G=0.180	A=0.820
1000Genomes	East Asian	Sub	1008	G=0.029	A=0.971
1000Genomes	Europe	Sub	1006	G=0.162	A=0.838
1000Genomes	Global	Study-wide	5008	G=0.149	A=0.851
1000Genomes	South Asian	Sub	978	G=0.310	A=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.176	A=0.824
The Genome Aggregation Database	African	Sub	8720	G=0.110	A=0.890
The Genome Aggregation Database	American	Sub	838	G=0.170	A=0.830
The Genome Aggregation Database	East Asian	Sub	1620	G=0.025	A=0.975
The Genome Aggregation Database	Europe	Sub	18400	G=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29878	G=0.127	A=0.872
The Genome Aggregation Database	Other	Sub	300	G=0.100	A=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.129	A=0.870
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.189	A=0.811

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
rs2262426	0.000133	alcohol consumption	23743675

eQTL of rs2262426 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238984497	SCLY	ENSG00000132330.12	G>A	7.8532e-10	14967	Cerebellum
Chr2:238984497	SCLY	ENSG00000132330.12	G>A	2.8719e-4	14967	Frontal_Cortex_BA9
Chr2:238984497	SCLY	ENSG00000132330.12	G>A	1.0714e-8	14967	Cortex
Chr2:238984497	SCLY	ENSG00000132330.12	G>A	2.0850e-8	14967	Cerebellar_Hemisphere
Chr2:238984497	SCLY	ENSG00000132330.12	G>A	1.4177e-3	14967	Caudate_basal_ganglia
Chr2:238984497	SCLY	ENSG00000132330.12	G>A	2.3006e-3	14967	Substantia_nigra
Chr2:238984497	SCLY	ENSG00000132330.12	G>A	7.2091e-4	14967	Anterior_cingulate_cortex

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0646226347905888	2.4442e-14

There is no significant Hi-C chromatin interaction data for this SNP.

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238950342	238950447	E067	-34050
chr2	238951505	238951913	E067	-32584
chr2	238970839	238970899	E067	-13598
chr2	238990205	238990255	E067	5708
chr2	238990452	238990751	E067	5955
chr2	238970839	238970899	E068	-13598
chr2	239017313	239017876	E068	32816
chr2	238951505	238951913	E069	-32584
chr2	238970839	238970899	E069	-13598
chr2	238989790	238989866	E069	5293
chr2	238989941	238990032	E069	5444
chr2	238990205	238990255	E069	5708
chr2	238970839	238970899	E070	-13598
chr2	238950342	238950447	E071	-34050
chr2	238951505	238951913	E071	-32584
chr2	238951961	238952020	E071	-32477
chr2	238970839	238970899	E071	-13598
chr2	238989247	238989354	E071	4750
chr2	238989790	238989866	E071	5293
chr2	238989941	238990032	E071	5444
chr2	238990205	238990255	E071	5708
chr2	238990452	238990751	E071	5955
chr2	239007116	239007529	E071	22619
chr2	239017176	239017226	E071	32679
chr2	239017313	239017876	E071	32816
chr2	238950342	238950447	E072	-34050
chr2	238989790	238989866	E072	5293
chr2	238989941	238990032	E072	5444
chr2	238990205	238990255	E072	5708
chr2	238990452	238990751	E072	5955
chr2	239014417	239014467	E072	29920
chr2	239014951	239015001	E072	30454
chr2	238970839	238970899	E073	-13598
chr2	239014951	239015001	E073	30454
chr2	238950342	238950447	E074	-34050
chr2	238951505	238951913	E074	-32584
chr2	238989790	238989866	E074	5293
chr2	238989941	238990032	E074	5444
chr2	238990452	238990751	E074	5955
chr2	239017313	239017876	E074	32816
chr2	238994008	238994058	E081	9511
chr2	238994372	238994803	E081	9875
chr2	238993565	238993671	E082	9068
chr2	238994008	238994058	E082	9511

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-13890
chr2	238968700	238970607	E068	-13890
chr2	238968700	238970607	E069	-13890
chr2	238968700	238970607	E070	-13890
chr2	238968700	238970607	E071	-13890
chr2	238968700	238970607	E072	-13890
chr2	238968700	238970607	E073	-13890
chr2	238968700	238970607	E074	-13890
chr2	238968700	238970607	E081	-13890
chr2	238968700	238970607	E082	-13890