rs2326009

Organism: Homo sapiens

Alleles: C>A

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0125 (3747/29964,GnomAD)
C==0127 (3698/29118,TOPMED)
C==0146 (733/5008,1000G)
C==0176 (678/3854,ALSPAC)
C==0189 (700/3708,TWINSUK)

Position: chr2:238085216 (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.238085216C>A
GRCh37.p13 chr 2	NC_000002.11:g.238993857C>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	C=0.083	A=0.917
1000Genomes	American	Sub	694	C=0.180	A=0.820
1000Genomes	East Asian	Sub	1008	C=0.029	A=0.971
1000Genomes	Europe	Sub	1006	C=0.162	A=0.838
1000Genomes	Global	Study-wide	5008	C=0.146	A=0.854
1000Genomes	South Asian	Sub	978	C=0.310	A=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.176	A=0.824
The Genome Aggregation Database	African	Sub	8722	C=0.102	A=0.898
The Genome Aggregation Database	American	Sub	836	C=0.170	A=0.830
The Genome Aggregation Database	East Asian	Sub	1622	C=0.025	A=0.975
The Genome Aggregation Database	Europe	Sub	18484	C=0.142	A=0.857
The Genome Aggregation Database	Global	Study-wide	29964	C=0.125	A=0.874
The Genome Aggregation Database	Other	Sub	300	C=0.100	A=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.127	A=0.873
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=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
rs2326009	8.9E-05	alcohol consumption	23743675

eQTL of rs2326009 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238993857	SCLY	ENSG00000132330.12	C>A	7.8532e-10	24327	Cerebellum
Chr2:238993857	SCLY	ENSG00000132330.12	C>A	2.8719e-4	24327	Frontal_Cortex_BA9
Chr2:238993857	SCLY	ENSG00000132330.12	C>A	1.0714e-8	24327	Cortex
Chr2:238993857	SCLY	ENSG00000132330.12	C>A	2.0850e-8	24327	Cerebellar_Hemisphere
Chr2:238993857	SCLY	ENSG00000132330.12	C>A	1.4177e-3	24327	Caudate_basal_ganglia
Chr2:238993857	SCLY	ENSG00000132330.12	C>A	7.2091e-4	24327	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	-43410
chr2	238951505	238951913	E067	-41944
chr2	238970839	238970899	E067	-22958
chr2	238990205	238990255	E067	-3602
chr2	238990452	238990751	E067	-3106
chr2	238970839	238970899	E068	-22958
chr2	239017313	239017876	E068	23456
chr2	238951505	238951913	E069	-41944
chr2	238970839	238970899	E069	-22958
chr2	238989790	238989866	E069	-3991
chr2	238989941	238990032	E069	-3825
chr2	238990205	238990255	E069	-3602
chr2	238970839	238970899	E070	-22958
chr2	238950342	238950447	E071	-43410
chr2	238951505	238951913	E071	-41944
chr2	238951961	238952020	E071	-41837
chr2	238970839	238970899	E071	-22958
chr2	238989247	238989354	E071	-4503
chr2	238989790	238989866	E071	-3991
chr2	238989941	238990032	E071	-3825
chr2	238990205	238990255	E071	-3602
chr2	238990452	238990751	E071	-3106
chr2	239007116	239007529	E071	13259
chr2	239017176	239017226	E071	23319
chr2	239017313	239017876	E071	23456
chr2	238950342	238950447	E072	-43410
chr2	238989790	238989866	E072	-3991
chr2	238989941	238990032	E072	-3825
chr2	238990205	238990255	E072	-3602
chr2	238990452	238990751	E072	-3106
chr2	239014417	239014467	E072	20560
chr2	239014951	239015001	E072	21094
chr2	238970839	238970899	E073	-22958
chr2	239014951	239015001	E073	21094
chr2	238950342	238950447	E074	-43410
chr2	238951505	238951913	E074	-41944
chr2	238989790	238989866	E074	-3991
chr2	238989941	238990032	E074	-3825
chr2	238990452	238990751	E074	-3106
chr2	239017313	239017876	E074	23456
chr2	238994008	238994058	E081	151
chr2	238994372	238994803	E081	515
chr2	238993565	238993671	E082	-186
chr2	238994008	238994058	E082	151

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-23250
chr2	238968700	238970607	E068	-23250
chr2	238968700	238970607	E069	-23250
chr2	238968700	238970607	E070	-23250
chr2	238968700	238970607	E071	-23250
chr2	238968700	238970607	E072	-23250
chr2	238968700	238970607	E073	-23250
chr2	238968700	238970607	E074	-23250
chr2	238968700	238970607	E081	-23250
chr2	238968700	238970607	E082	-23250