rs10203101

Organism: Homo sapiens

Alleles: C>T

Gene : Feature

UBE2F : Intron Variant
UBE2F-SCLY : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

C==0128 (3844/29990,GnomAD)
C==0134 (3912/29118,TOPMED)
C==0152 (760/5008,1000G)
C==0176 (680/3854,ALSPAC)
C==0191 (708/3708,TWINSUK)

Position: chr2:237994668 (GRCh38.p7) (2q37.3)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 119 Enhancers around

Promoter: 32 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 2	NC_000002.12:g.237994668C>T
GRCh37.p13 chr 2	NC_000002.11:g.238903310C>T

Gene: UBE2F, ubiquitin conjugating enzyme E2 F (putative)(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2F transcript variant 2	NM_001278305.1:c.	N/A	Intron Variant
UBE2F transcript variant 3	NM_001278306.1:c.	N/A	Intron Variant
UBE2F transcript variant 4	NM_001278307.1:c.	N/A	Intron Variant
UBE2F transcript variant 5	NM_001278308.1:c.	N/A	Intron Variant
UBE2F transcript variant 1	NM_080678.2:c.	N/A	Intron Variant
UBE2F transcript variant 6	NR_103498.1:n.	N/A	Intron Variant
UBE2F transcript variant 7	NR_103499.1:n.	N/A	Intron Variant
UBE2F transcript variant 8	NR_103500.1:n.	N/A	Intron Variant

Gene: UBE2F-SCLY, UBE2F-SCLY readthrough (NMD candidate)(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UBE2F-SCLY transcript	NR_037904.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	C=0.099	T=0.901
1000Genomes	American	Sub	694	C=0.180	T=0.820
1000Genomes	East Asian	Sub	1008	C=0.030	T=0.970
1000Genomes	Europe	Sub	1006	C=0.164	T=0.836
1000Genomes	Global	Study-wide	5008	C=0.152	T=0.848
1000Genomes	South Asian	Sub	978	C=0.310	T=0.690
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.176	T=0.824
The Genome Aggregation Database	African	Sub	8728	C=0.109	T=0.891
The Genome Aggregation Database	American	Sub	838	C=0.170	T=0.830
The Genome Aggregation Database	East Asian	Sub	1620	C=0.029	T=0.971
The Genome Aggregation Database	Europe	Sub	18502	C=0.144	T=0.855
The Genome Aggregation Database	Global	Study-wide	29990	C=0.128	T=0.871
The Genome Aggregation Database	Other	Sub	302	C=0.110	T=0.890
Trans-Omics for Precision Medicine	Global	Study-wide	29118	C=0.134	T=0.865
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.191	T=0.809

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

P-Value

SNP ID	p-value	Traits	Study
rs10203101	0.000148	alcohol consumption	23743675

eQTL of rs10203101 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr2:238903310	SCLY	ENSG00000132330.12	C>T	7.8532e-10	-66220	Cerebellum
Chr2:238903310	SCLY	ENSG00000132330.12	C>T	1.0714e-8	-66220	Cortex
Chr2:238903310	SCLY	ENSG00000132330.12	C>T	2.0850e-8	-66220	Cerebellar_Hemisphere
Chr2:238903310	SCLY	ENSG00000132330.12	C>T	1.4177e-3	-66220	Caudate_basal_ganglia
Chr2:238903310	SCLY	ENSG00000132330.12	C>T	2.3006e-3	-66220	Substantia_nigra
Chr2:238903310	SCLY	ENSG00000132330.12	C>T	7.2091e-4	-66220	Anterior_cingulate_cortex

meQTL of rs10203101 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
cg03558837	chr2:239029375	ESPNL	0.0646226347905888	2.4442e-14

Genomic View

Chromatin Interaction

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

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr2	238877816	238878038	E067	-25272
chr2	238878398	238878539	E067	-24771
chr2	238878551	238878601	E067	-24709
chr2	238878666	238878738	E067	-24572
chr2	238879158	238879263	E067	-24047
chr2	238886584	238886634	E067	-16676
chr2	238886907	238887414	E067	-15896
chr2	238888018	238888228	E067	-15082
chr2	238888415	238888465	E067	-14845
chr2	238888921	238888998	E067	-14312
chr2	238889558	238889737	E067	-13573
chr2	238889976	238890179	E067	-13131
chr2	238893121	238893238	E067	-10072
chr2	238904560	238904874	E067	1250
chr2	238904955	238905113	E067	1645
chr2	238917607	238917771	E067	14297
chr2	238931681	238931768	E067	28371
chr2	238950342	238950447	E067	47032
chr2	238951505	238951913	E067	48195
chr2	238877816	238878038	E068	-25272
chr2	238878398	238878539	E068	-24771
chr2	238878551	238878601	E068	-24709
chr2	238878666	238878738	E068	-24572
chr2	238879158	238879263	E068	-24047
chr2	238886584	238886634	E068	-16676
chr2	238886907	238887414	E068	-15896
chr2	238888018	238888228	E068	-15082
chr2	238888415	238888465	E068	-14845
chr2	238888921	238888998	E068	-14312
chr2	238889558	238889737	E068	-13573
chr2	238889976	238890179	E068	-13131
chr2	238892164	238892276	E068	-11034
chr2	238893121	238893238	E068	-10072
chr2	238877816	238878038	E069	-25272
chr2	238878398	238878539	E069	-24771
chr2	238878551	238878601	E069	-24709
chr2	238878666	238878738	E069	-24572
chr2	238886584	238886634	E069	-16676
chr2	238886907	238887414	E069	-15896
chr2	238888018	238888228	E069	-15082
chr2	238888921	238888998	E069	-14312
chr2	238889558	238889737	E069	-13573
chr2	238893121	238893238	E069	-10072
chr2	238904955	238905113	E069	1645
chr2	238918301	238918438	E069	14991
chr2	238919370	238919610	E069	16060
chr2	238919757	238919867	E069	16447
chr2	238928552	238929028	E069	25242
chr2	238951505	238951913	E069	48195
chr2	238886584	238886634	E070	-16676
chr2	238886907	238887414	E070	-15896
chr2	238888921	238888998	E070	-14312
chr2	238878666	238878738	E071	-24572
chr2	238879158	238879263	E071	-24047
chr2	238886011	238886062	E071	-17248
chr2	238886584	238886634	E071	-16676
chr2	238886907	238887414	E071	-15896
chr2	238888018	238888228	E071	-15082
chr2	238888415	238888465	E071	-14845
chr2	238888921	238888998	E071	-14312
chr2	238893121	238893238	E071	-10072
chr2	238917607	238917771	E071	14297
chr2	238917904	238917968	E071	14594
chr2	238918301	238918438	E071	14991
chr2	238919370	238919610	E071	16060
chr2	238919757	238919867	E071	16447
chr2	238950342	238950447	E071	47032
chr2	238951505	238951913	E071	48195
chr2	238951961	238952020	E071	48651
chr2	238867147	238867197	E072	-36113
chr2	238878551	238878601	E072	-24709
chr2	238886011	238886062	E072	-17248
chr2	238886584	238886634	E072	-16676
chr2	238886907	238887414	E072	-15896
chr2	238888018	238888228	E072	-15082
chr2	238888415	238888465	E072	-14845
chr2	238888921	238888998	E072	-14312
chr2	238889558	238889737	E072	-13573
chr2	238893121	238893238	E072	-10072
chr2	238917607	238917771	E072	14297
chr2	238950342	238950447	E072	47032
chr2	238878551	238878601	E073	-24709
chr2	238878666	238878738	E073	-24572
chr2	238886011	238886062	E073	-17248
chr2	238886584	238886634	E073	-16676
chr2	238886907	238887414	E073	-15896
chr2	238888018	238888228	E073	-15082
chr2	238888415	238888465	E073	-14845
chr2	238888921	238888998	E073	-14312
chr2	238889558	238889737	E073	-13573
chr2	238892164	238892276	E073	-11034
chr2	238893121	238893238	E073	-10072
chr2	238878551	238878601	E074	-24709
chr2	238878666	238878738	E074	-24572
chr2	238879158	238879263	E074	-24047
chr2	238880434	238880549	E074	-22761
chr2	238880894	238880969	E074	-22341
chr2	238884641	238884818	E074	-18492
chr2	238886011	238886062	E074	-17248
chr2	238886584	238886634	E074	-16676
chr2	238886907	238887414	E074	-15896
chr2	238888921	238888998	E074	-14312
chr2	238889558	238889737	E074	-13573
chr2	238889976	238890179	E074	-13131
chr2	238893121	238893238	E074	-10072
chr2	238904560	238904874	E074	1250
chr2	238904955	238905113	E074	1645
chr2	238915164	238915422	E074	11854
chr2	238917607	238917771	E074	14297
chr2	238917904	238917968	E074	14594
chr2	238918301	238918438	E074	14991
chr2	238919370	238919610	E074	16060
chr2	238919757	238919867	E074	16447
chr2	238931681	238931768	E074	28371
chr2	238950342	238950447	E074	47032
chr2	238951505	238951913	E074	48195
chr2	238877816	238878038	E081	-25272
chr2	238878398	238878539	E081	-24771
chr2	238886907	238887414	E082	-15896

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr2	238874796	238876104	E067	-27206
chr2	238876111	238876550	E067	-26760
chr2	238864688	238864740	E068	-38570
chr2	238864741	238864973	E068	-38337
chr2	238865051	238865134	E068	-38176
chr2	238865144	238865248	E068	-38062
chr2	238874796	238876104	E068	-27206
chr2	238876111	238876550	E068	-26760
chr2	238865051	238865134	E069	-38176
chr2	238865144	238865248	E069	-38062
chr2	238874796	238876104	E069	-27206
chr2	238876111	238876550	E069	-26760
chr2	238864741	238864973	E070	-38337
chr2	238874796	238876104	E070	-27206
chr2	238876111	238876550	E070	-26760
chr2	238874796	238876104	E071	-27206
chr2	238876111	238876550	E071	-26760
chr2	238874796	238876104	E072	-27206
chr2	238876111	238876550	E072	-26760
chr2	238865051	238865134	E073	-38176
chr2	238865144	238865248	E073	-38062
chr2	238874796	238876104	E073	-27206
chr2	238876111	238876550	E073	-26760
chr2	238874796	238876104	E074	-27206
chr2	238876111	238876550	E074	-26760
chr2	238876111	238876550	E081	-26760
chr2	238864688	238864740	E082	-38570
chr2	238864741	238864973	E082	-38337
chr2	238865051	238865134	E082	-38176
chr2	238865144	238865248	E082	-38062
chr2	238874796	238876104	E082	-27206
chr2	238876111	238876550	E082	-26760