SNP Detail Info-rs10956683

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 8	NC_000008.11:g.132819238G>A
GRCh37.p13 chr 8	NC_000008.10:g.133831483G>A

Gene: PHF20L1, PHD finger protein 20-like 1(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PHF20L1 transcript variant 4	NM_001277196.1:c.	N/A	Intron Variant
PHF20L1 transcript variant 1	NM_016018.4:c.	N/A	Intron Variant
PHF20L1 transcript variant 3	NM_198513.1:c.	N/A	Genic Downstream Transcript Variant
PHF20L1 transcript variant X3	XM_005250931.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X1	XM_011517075.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X2	XM_011517076.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X4	XM_011517077.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X5	XM_011517078.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X6	XM_011517079.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X8	XM_011517080.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X10	XM_011517081.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X18	XM_011517088.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X7	XM_017013509.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X9	XM_017013510.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X11	XM_017013511.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X12	XM_017013512.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X13	XM_017013513.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X14	XM_017013514.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X17	XM_017013515.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X20	XM_017013516.1:c.	N/A	Intron Variant
PHF20L1 transcript variant X21	XM_017013517.1:c.	N/A	Genic Downstream Transcript Variant
PHF20L1 transcript variant X15	XR_001745533.1:n.	N/A	Intron Variant
PHF20L1 transcript variant X16	XR_001745534.1:n.	N/A	Intron Variant
PHF20L1 transcript variant X17	XR_001745535.1:n.	N/A	Intron Variant
PHF20L1 transcript variant X19	XR_001745536.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.976	A=0.024
1000Genomes	American	Sub	694	G=0.850	A=0.150
1000Genomes	East Asian	Sub	1008	G=0.643	A=0.357
1000Genomes	Europe	Sub	1006	G=0.898	A=0.102
1000Genomes	Global	Study-wide	5008	G=0.855	A=0.145
1000Genomes	South Asian	Sub	978	G=0.870	A=0.130
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.904	A=0.096
The Genome Aggregation Database	African	Sub	8722	G=0.971	A=0.029
The Genome Aggregation Database	American	Sub	834	G=0.850	A=0.150
The Genome Aggregation Database	East Asian	Sub	1578	G=0.682	A=0.318
The Genome Aggregation Database	Europe	Sub	18444	G=0.913	A=0.086
The Genome Aggregation Database	Global	Study-wide	29878	G=0.915	A=0.084
The Genome Aggregation Database	Other	Sub	300	G=0.900	A=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.933	A=0.066
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.910	A=0.090

PMID	Title	Author	Journal
21314694	Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample.	Kendler KS	Alcohol Clin Exp Res

P-Value

SNP ID	p-value	Traits	Study
rs10956683	0.000422	alcohol dependence	21314694

eQTL of rs10956683 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
There is no eQTL annotation for this SNP

meQTL of rs10956683 in Fetal Brain

Probe ID	Position	Gene	beta	p-value
There is no meQTL annotation for this SNP

Enhancer Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance ( -/+ : Up/Downstream )
chr8	133804738	133805133	E067	-26350
chr8	133805227	133805406	E067	-26077
chr8	133797248	133797582	E068	-33901
chr8	133804738	133805133	E069	-26350
chr8	133805227	133805406	E069	-26077
chr8	133863600	133863806	E070	32117
chr8	133796954	133797131	E071	-34352
chr8	133797248	133797582	E071	-33901
chr8	133796954	133797131	E072	-34352
chr8	133805227	133805406	E072	-26077
chr8	133850563	133850613	E072	19080
chr8	133850623	133851153	E072	19140
chr8	133805227	133805406	E073	-26077
chr8	133880917	133880974	E081	49434
chr8	133881100	133881336	E081	49617
chr8	133879948	133880002	E082	48465
chr8	133880077	133880545	E082	48594
chr8	133880917	133880974	E082	49434
chr8	133881100	133881336	E082	49617

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr8	133786819	133788653	E067	-42830
chr8	133786819	133788653	E068	-42830
chr8	133786819	133788653	E069	-42830
chr8	133786819	133788653	E070	-42830
chr8	133786819	133788653	E071	-42830
chr8	133786819	133788653	E072	-42830
chr8	133786819	133788653	E073	-42830
chr8	133786819	133788653	E074	-42830
chr8	133786819	133788653	E081	-42830
chr8	133786819	133788653	E082	-42830

rs10956683

Genomic Coordinates

Gene: PHF20L1, PHD finger protein 20-like 1(plus strand)

Population Frequency

P-Value

eQTL of rs10956683 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs10956683 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)