rs2248623

Organism: Homo sapiens

Alleles: T>G

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0128 (3840/29986,GnomAD)
T==0131 (3821/29118,TOPMED)
T==0149 (744/5008,1000G)
T==0176 (678/3854,ALSPAC)
T==0188 (698/3708,TWINSUK)

Position: chr2:238086187 (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.238086187T>G
GRCh37.p13 chr 2	NC_000002.11:g.238994828T>G

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	T=0.092	G=0.908
1000Genomes	American	Sub	694	T=0.180	G=0.820
1000Genomes	East Asian	Sub	1008	T=0.029	G=0.971
1000Genomes	Europe	Sub	1006	T=0.162	G=0.838
1000Genomes	Global	Study-wide	5008	T=0.149	G=0.851
1000Genomes	South Asian	Sub	978	T=0.310	G=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.176	G=0.824
The Genome Aggregation Database	African	Sub	8732	T=0.112	G=0.888
The Genome Aggregation Database	American	Sub	838	T=0.170	G=0.830
The Genome Aggregation Database	East Asian	Sub	1620	T=0.025	G=0.975
The Genome Aggregation Database	Europe	Sub	18496	T=0.143	G=0.857
The Genome Aggregation Database	Global	Study-wide	29986	T=0.128	G=0.871
The Genome Aggregation Database	Other	Sub	300	T=0.100	G=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.131	G=0.868
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.188	G=0.812

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
rs2248623	0.000141	alcohol consumption	23743675

eQTL of rs2248623 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238994828	SCLY	ENSG00000132330.12	T>G	7.8532e-10	25298	Cerebellum
Chr2:238994828	SCLY	ENSG00000132330.12	T>G	2.8719e-4	25298	Frontal_Cortex_BA9
Chr2:238994828	SCLY	ENSG00000132330.12	T>G	1.0714e-8	25298	Cortex
Chr2:238994828	SCLY	ENSG00000132330.12	T>G	2.0850e-8	25298	Cerebellar_Hemisphere
Chr2:238994828	SCLY	ENSG00000132330.12	T>G	1.4177e-3	25298	Caudate_basal_ganglia
Chr2:238994828	SCLY	ENSG00000132330.12	T>G	7.2091e-4	25298	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	-44381
chr2	238951505	238951913	E067	-42915
chr2	238970839	238970899	E067	-23929
chr2	238990205	238990255	E067	-4573
chr2	238990452	238990751	E067	-4077
chr2	238970839	238970899	E068	-23929
chr2	239017313	239017876	E068	22485
chr2	238951505	238951913	E069	-42915
chr2	238970839	238970899	E069	-23929
chr2	238989790	238989866	E069	-4962
chr2	238989941	238990032	E069	-4796
chr2	238990205	238990255	E069	-4573
chr2	238970839	238970899	E070	-23929
chr2	238950342	238950447	E071	-44381
chr2	238951505	238951913	E071	-42915
chr2	238951961	238952020	E071	-42808
chr2	238970839	238970899	E071	-23929
chr2	238989247	238989354	E071	-5474
chr2	238989790	238989866	E071	-4962
chr2	238989941	238990032	E071	-4796
chr2	238990205	238990255	E071	-4573
chr2	238990452	238990751	E071	-4077
chr2	239007116	239007529	E071	12288
chr2	239017176	239017226	E071	22348
chr2	239017313	239017876	E071	22485
chr2	238950342	238950447	E072	-44381
chr2	238989790	238989866	E072	-4962
chr2	238989941	238990032	E072	-4796
chr2	238990205	238990255	E072	-4573
chr2	238990452	238990751	E072	-4077
chr2	239014417	239014467	E072	19589
chr2	239014951	239015001	E072	20123
chr2	238970839	238970899	E073	-23929
chr2	239014951	239015001	E073	20123
chr2	238950342	238950447	E074	-44381
chr2	238951505	238951913	E074	-42915
chr2	238989790	238989866	E074	-4962
chr2	238989941	238990032	E074	-4796
chr2	238990452	238990751	E074	-4077
chr2	239017313	239017876	E074	22485
chr2	238994008	238994058	E081	-770
chr2	238994372	238994803	E081	-25
chr2	238993565	238993671	E082	-1157
chr2	238994008	238994058	E082	-770

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-24221
chr2	238968700	238970607	E068	-24221
chr2	238968700	238970607	E069	-24221
chr2	238968700	238970607	E070	-24221
chr2	238968700	238970607	E071	-24221
chr2	238968700	238970607	E072	-24221
chr2	238968700	238970607	E073	-24221
chr2	238968700	238970607	E074	-24221
chr2	238968700	238970607	E081	-24221
chr2	238968700	238970607	E082	-24221