rs2249077

Organism: Homo sapiens

Alleles: T>C

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T==0127 (3817/29924,GnomAD)
T==0130 (3802/29118,TOPMED)
T==0149 (744/5008,1000G)
T==0176 (679/3854,ALSPAC)
T==0188 (698/3708,TWINSUK)

Position: chr2:238082344 (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.238082344T>C
GRCh37.p13 chr 2	NC_000002.11:g.238990985T>C

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	C=0.908
1000Genomes	American	Sub	694	T=0.180	C=0.820
1000Genomes	East Asian	Sub	1008	T=0.029	C=0.971
1000Genomes	Europe	Sub	1006	T=0.162	C=0.838
1000Genomes	Global	Study-wide	5008	T=0.149	C=0.851
1000Genomes	South Asian	Sub	978	T=0.310	C=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.176	C=0.824
The Genome Aggregation Database	African	Sub	8716	T=0.111	C=0.889
The Genome Aggregation Database	American	Sub	834	T=0.170	C=0.830
The Genome Aggregation Database	East Asian	Sub	1620	T=0.025	C=0.975
The Genome Aggregation Database	Europe	Sub	18452	T=0.142	C=0.857
The Genome Aggregation Database	Global	Study-wide	29924	T=0.127	C=0.872
The Genome Aggregation Database	Other	Sub	302	T=0.100	C=0.900
Trans-Omics for Precision Medicine	Global	Study-wide	29118	T=0.130	C=0.869
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.188	C=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
rs2249077	9.2E-05	alcohol consumption	23743675

eQTL of rs2249077 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238990985	SCLY	ENSG00000132330.12	T>C	7.8532e-10	21455	Cerebellum
Chr2:238990985	SCLY	ENSG00000132330.12	T>C	2.8719e-4	21455	Frontal_Cortex_BA9
Chr2:238990985	SCLY	ENSG00000132330.12	T>C	1.0714e-8	21455	Cortex
Chr2:238990985	SCLY	ENSG00000132330.12	T>C	2.0850e-8	21455	Cerebellar_Hemisphere
Chr2:238990985	SCLY	ENSG00000132330.12	T>C	1.4177e-3	21455	Caudate_basal_ganglia
Chr2:238990985	SCLY	ENSG00000132330.12	T>C	7.2091e-4	21455	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	-40538
chr2	238951505	238951913	E067	-39072
chr2	238970839	238970899	E067	-20086
chr2	238990205	238990255	E067	-730
chr2	238990452	238990751	E067	-234
chr2	238970839	238970899	E068	-20086
chr2	239017313	239017876	E068	26328
chr2	238951505	238951913	E069	-39072
chr2	238970839	238970899	E069	-20086
chr2	238989790	238989866	E069	-1119
chr2	238989941	238990032	E069	-953
chr2	238990205	238990255	E069	-730
chr2	238970839	238970899	E070	-20086
chr2	238950342	238950447	E071	-40538
chr2	238951505	238951913	E071	-39072
chr2	238951961	238952020	E071	-38965
chr2	238970839	238970899	E071	-20086
chr2	238989247	238989354	E071	-1631
chr2	238989790	238989866	E071	-1119
chr2	238989941	238990032	E071	-953
chr2	238990205	238990255	E071	-730
chr2	238990452	238990751	E071	-234
chr2	239007116	239007529	E071	16131
chr2	239017176	239017226	E071	26191
chr2	239017313	239017876	E071	26328
chr2	238950342	238950447	E072	-40538
chr2	238989790	238989866	E072	-1119
chr2	238989941	238990032	E072	-953
chr2	238990205	238990255	E072	-730
chr2	238990452	238990751	E072	-234
chr2	239014417	239014467	E072	23432
chr2	239014951	239015001	E072	23966
chr2	238970839	238970899	E073	-20086
chr2	239014951	239015001	E073	23966
chr2	238950342	238950447	E074	-40538
chr2	238951505	238951913	E074	-39072
chr2	238989790	238989866	E074	-1119
chr2	238989941	238990032	E074	-953
chr2	238990452	238990751	E074	-234
chr2	239017313	239017876	E074	26328
chr2	238994008	238994058	E081	3023
chr2	238994372	238994803	E081	3387
chr2	238993565	238993671	E082	2580
chr2	238994008	238994058	E082	3023

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-20378
chr2	238968700	238970607	E068	-20378
chr2	238968700	238970607	E069	-20378
chr2	238968700	238970607	E070	-20378
chr2	238968700	238970607	E071	-20378
chr2	238968700	238970607	E072	-20378
chr2	238968700	238970607	E073	-20378
chr2	238968700	238970607	E074	-20378
chr2	238968700	238970607	E081	-20378
chr2	238968700	238970607	E082	-20378