rs2264166

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==0143 (4309/29958,GnomAD)
C==0154 (4507/29118,TOPMED)
C==0167 (834/5008,1000G)
C==0176 (679/3854,ALSPAC)
C==0189 (700/3708,TWINSUK)

Position: chr2:238072660 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 46 Enhancers around

Promoter: 10 Promoters around

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.238072660C>A
GRCh37.p13 chr 2	NC_000002.11:g.238981301C>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=0.156	A=0.844
1000Genomes	American	Sub	694	C=0.190	A=0.810
1000Genomes	East Asian	Sub	1008	C=0.029	A=0.971
1000Genomes	Europe	Sub	1006	C=0.163	A=0.837
1000Genomes	Global	Study-wide	5008	C=0.167	A=0.833
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	8718	C=0.166	A=0.834
The Genome Aggregation Database	American	Sub	836	C=0.180	A=0.820
The Genome Aggregation Database	East Asian	Sub	1620	C=0.025	A=0.975
The Genome Aggregation Database	Europe	Sub	18482	C=0.143	A=0.856
The Genome Aggregation Database	Global	Study-wide	29958	C=0.143	A=0.856
The Genome Aggregation Database	Other	Sub	302	C=0.100	A=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.154	A=0.845
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
rs2264166	0.000104	alcohol consumption	23743675

eQTL of rs2264166 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238981301	SCLY	ENSG00000132330.12	C>A	7.8532e-10	11771	Cerebellum
Chr2:238981301	SCLY	ENSG00000132330.12	C>A	2.8719e-4	11771	Frontal_Cortex_BA9
Chr2:238981301	SCLY	ENSG00000132330.12	C>A	1.0714e-8	11771	Cortex
Chr2:238981301	SCLY	ENSG00000132330.12	C>A	2.0850e-8	11771	Cerebellar_Hemisphere
Chr2:238981301	SCLY	ENSG00000132330.12	C>A	1.4177e-3	11771	Caudate_basal_ganglia
Chr2:238981301	SCLY	ENSG00000132330.12	C>A	7.2091e-4	11771	Anterior_cingulate_cortex

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0645599800790513	1.4233e-14

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

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238931681	238931768	E067	-49533
chr2	238950342	238950447	E067	-30854
chr2	238951505	238951913	E067	-29388
chr2	238970839	238970899	E067	-10402
chr2	238990205	238990255	E067	8904
chr2	238990452	238990751	E067	9151
chr2	238970839	238970899	E068	-10402
chr2	239017313	239017876	E068	36012
chr2	238951505	238951913	E069	-29388
chr2	238970839	238970899	E069	-10402
chr2	238989790	238989866	E069	8489
chr2	238989941	238990032	E069	8640
chr2	238990205	238990255	E069	8904
chr2	238970839	238970899	E070	-10402
chr2	238950342	238950447	E071	-30854
chr2	238951505	238951913	E071	-29388
chr2	238951961	238952020	E071	-29281
chr2	238970839	238970899	E071	-10402
chr2	238989247	238989354	E071	7946
chr2	238989790	238989866	E071	8489
chr2	238989941	238990032	E071	8640
chr2	238990205	238990255	E071	8904
chr2	238990452	238990751	E071	9151
chr2	239007116	239007529	E071	25815
chr2	239017176	239017226	E071	35875
chr2	239017313	239017876	E071	36012
chr2	238950342	238950447	E072	-30854
chr2	238989790	238989866	E072	8489
chr2	238989941	238990032	E072	8640
chr2	238990205	238990255	E072	8904
chr2	238990452	238990751	E072	9151
chr2	239014417	239014467	E072	33116
chr2	239014951	239015001	E072	33650
chr2	238970839	238970899	E073	-10402
chr2	239014951	239015001	E073	33650
chr2	238931681	238931768	E074	-49533
chr2	238950342	238950447	E074	-30854
chr2	238951505	238951913	E074	-29388
chr2	238989790	238989866	E074	8489
chr2	238989941	238990032	E074	8640
chr2	238990452	238990751	E074	9151
chr2	239017313	239017876	E074	36012
chr2	238994008	238994058	E081	12707
chr2	238994372	238994803	E081	13071
chr2	238993565	238993671	E082	12264
chr2	238994008	238994058	E082	12707

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-10694
chr2	238968700	238970607	E068	-10694
chr2	238968700	238970607	E069	-10694
chr2	238968700	238970607	E070	-10694
chr2	238968700	238970607	E071	-10694
chr2	238968700	238970607	E072	-10694
chr2	238968700	238970607	E073	-10694
chr2	238968700	238970607	E074	-10694
chr2	238968700	238970607	E081	-10694
chr2	238968700	238970607	E082	-10694