rs34049050

Organism: Homo sapiens

Alleles: A>G

Gene : Feature

SCLY : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

G=0126 (3803/29960,GnomAD)
G=0131 (3823/29118,TOPMED)
G=0148 (743/5008,1000G)
G=0175 (673/3854,ALSPAC)
G=0187 (692/3708,TWINSUK)

Position: chr2:238089940 (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.238089940A>G
GRCh37.p13 chr 2	NC_000002.11:g.238998581A>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	A=0.909	G=0.091
1000Genomes	American	Sub	694	A=0.820	G=0.180
1000Genomes	East Asian	Sub	1008	A=0.971	G=0.029
1000Genomes	Europe	Sub	1006	A=0.838	G=0.162
1000Genomes	Global	Study-wide	5008	A=0.852	G=0.148
1000Genomes	South Asian	Sub	978	A=0.690	G=0.310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.825	G=0.175
The Genome Aggregation Database	African	Sub	8726	A=0.892	G=0.108
The Genome Aggregation Database	American	Sub	838	A=0.830	G=0.170
The Genome Aggregation Database	East Asian	Sub	1622	A=0.975	G=0.025
The Genome Aggregation Database	Europe	Sub	18472	A=0.856	G=0.143
The Genome Aggregation Database	Global	Study-wide	29960	A=0.873	G=0.126
The Genome Aggregation Database	Other	Sub	302	A=0.900	G=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.868	G=0.131
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.813	G=0.187

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
rs34049050	0.000127	alcohol consumption	23743675

eQTL of rs34049050 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238998581	SCLY	ENSG00000132330.12	A>G	7.8532e-10	29051	Cerebellum
Chr2:238998581	SCLY	ENSG00000132330.12	A>G	2.8719e-4	29051	Frontal_Cortex_BA9
Chr2:238998581	SCLY	ENSG00000132330.12	A>G	1.0714e-8	29051	Cortex
Chr2:238998581	SCLY	ENSG00000132330.12	A>G	2.0850e-8	29051	Cerebellar_Hemisphere
Chr2:238998581	SCLY	ENSG00000132330.12	A>G	1.4177e-3	29051	Caudate_basal_ganglia
Chr2:238998581	SCLY	ENSG00000132330.12	A>G	7.2091e-4	29051	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	-48134
chr2	238951505	238951913	E067	-46668
chr2	238970839	238970899	E067	-27682
chr2	238990205	238990255	E067	-8326
chr2	238990452	238990751	E067	-7830
chr2	238970839	238970899	E068	-27682
chr2	239017313	239017876	E068	18732
chr2	238951505	238951913	E069	-46668
chr2	238970839	238970899	E069	-27682
chr2	238989790	238989866	E069	-8715
chr2	238989941	238990032	E069	-8549
chr2	238990205	238990255	E069	-8326
chr2	238970839	238970899	E070	-27682
chr2	238950342	238950447	E071	-48134
chr2	238951505	238951913	E071	-46668
chr2	238951961	238952020	E071	-46561
chr2	238970839	238970899	E071	-27682
chr2	238989247	238989354	E071	-9227
chr2	238989790	238989866	E071	-8715
chr2	238989941	238990032	E071	-8549
chr2	238990205	238990255	E071	-8326
chr2	238990452	238990751	E071	-7830
chr2	239007116	239007529	E071	8535
chr2	239017176	239017226	E071	18595
chr2	239017313	239017876	E071	18732
chr2	238950342	238950447	E072	-48134
chr2	238989790	238989866	E072	-8715
chr2	238989941	238990032	E072	-8549
chr2	238990205	238990255	E072	-8326
chr2	238990452	238990751	E072	-7830
chr2	239014417	239014467	E072	15836
chr2	239014951	239015001	E072	16370
chr2	238970839	238970899	E073	-27682
chr2	239014951	239015001	E073	16370
chr2	238950342	238950447	E074	-48134
chr2	238951505	238951913	E074	-46668
chr2	238989790	238989866	E074	-8715
chr2	238989941	238990032	E074	-8549
chr2	238990452	238990751	E074	-7830
chr2	239017313	239017876	E074	18732
chr2	238994008	238994058	E081	-4523
chr2	238994372	238994803	E081	-3778
chr2	238993565	238993671	E082	-4910
chr2	238994008	238994058	E082	-4523

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238968700	238970607	E067	-27974
chr2	238968700	238970607	E068	-27974
chr2	238968700	238970607	E069	-27974
chr2	238968700	238970607	E070	-27974
chr2	238968700	238970607	E071	-27974
chr2	238968700	238970607	E072	-27974
chr2	238968700	238970607	E073	-27974
chr2	238968700	238970607	E074	-27974
chr2	238968700	238970607	E081	-27974
chr2	238968700	238970607	E082	-27974