SNP Detail Info-rs1407862

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.7032776G>A
GRCh37.p13 chr 9	NC_000009.11:g.7032776G>A

Gene: KDM4C, lysine demethylase 4C(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
KDM4C transcript variant 3	NM_001146695.1:c.	N/A	Intron Variant
KDM4C transcript variant 4	NM_001146696.1:c.	N/A	Intron Variant
KDM4C transcript variant 5	NM_001304339.1:c.	N/A	Intron Variant
KDM4C transcript variant 6	NM_001304340.1:c.	N/A	Intron Variant
KDM4C transcript variant 1	NM_015061.3:c.	N/A	Intron Variant
KDM4C transcript variant 7	NM_001304341.1:c.	N/A	Genic Downstream Transcript Variant
KDM4C transcript variant 8	NR_130707.1:n.	N/A	Genic Downstream Transcript Variant
KDM4C transcript variant X1	XM_006716741.2:c.	N/A	Intron Variant
KDM4C transcript variant X4	XM_011517811.2:c.	N/A	Intron Variant
KDM4C transcript variant X6	XM_011517812.2:c.	N/A	Intron Variant
KDM4C transcript variant X14	XM_011517816.2:c.	N/A	Intron Variant
KDM4C transcript variant X2	XM_017014498.1:c.	N/A	Intron Variant
KDM4C transcript variant X3	XM_017014499.1:c.	N/A	Intron Variant
KDM4C transcript variant X5	XM_017014500.1:c.	N/A	Intron Variant
KDM4C transcript variant X7	XM_017014501.1:c.	N/A	Intron Variant
KDM4C transcript variant X9	XM_017014502.1:c.	N/A	Intron Variant
KDM4C transcript variant X13	XM_017014503.1:c.	N/A	Intron Variant
KDM4C transcript variant X15	XM_017014504.1:c.	N/A	Intron Variant
KDM4C transcript variant X16	XM_017014505.1:c.	N/A	Intron Variant
KDM4C transcript variant X17	XM_017014506.1:c.	N/A	Intron Variant
KDM4C transcript variant X8	XR_001746252.1:n.	N/A	Intron Variant
KDM4C transcript variant X10	XR_001746253.1:n.	N/A	Intron Variant
KDM4C transcript variant X11	XR_001746254.1:n.	N/A	Intron Variant
KDM4C transcript variant X12	XR_001746255.1:n.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.488	A=0.512
1000Genomes	American	Sub	694	G=0.500	A=0.500
1000Genomes	East Asian	Sub	1008	G=0.534	A=0.466
1000Genomes	Europe	Sub	1006	G=0.579	A=0.421
1000Genomes	Global	Study-wide	5008	G=0.496	A=0.504
1000Genomes	South Asian	Sub	978	G=0.380	A=0.620
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.547	A=0.453
The Genome Aggregation Database	African	Sub	8698	G=0.488	A=0.512
The Genome Aggregation Database	American	Sub	838	G=0.480	A=0.520
The Genome Aggregation Database	East Asian	Sub	1610	G=0.560	A=0.440
The Genome Aggregation Database	Europe	Sub	18446	G=0.543	A=0.457
The Genome Aggregation Database	Global	Study-wide	29894	G=0.527	A=0.472
The Genome Aggregation Database	Other	Sub	302	G=0.640	A=0.360
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.527	A=0.472
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.538	A=0.462

PMID	Title	Author	Journal
22072270	Genome-wide association study identifies 5q21 and 9p24.1 (KDM4C) loci associated with alcohol withdrawal symptoms.	Wang KS	J Neural Transm (Vienna)

P-Value

SNP ID	p-value	Traits	Study
rs1407862	4.93E-05	alcohol withdrawal symptoms	22072270

eQTL of rs1407862 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 rs1407862 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 )
chr9	7052503	7053138	E068	19727
chr9	7056766	7057012	E068	23990
chr9	7057223	7057335	E068	24447
chr9	7057342	7057422	E068	24566
chr9	7057457	7058000	E068	24681
chr9	7058090	7058230	E068	25314
chr9	7058310	7058379	E068	25534
chr9	7058388	7058453	E068	25612
chr9	7058500	7058568	E068	25724
chr9	7052503	7053138	E069	19727
chr9	7053246	7053364	E069	20470
chr9	7053377	7053446	E069	20601
chr9	7053484	7053547	E069	20708
chr9	7057457	7058000	E069	24681
chr9	7058090	7058230	E069	25314
chr9	7078796	7079177	E069	46020
chr9	7082561	7082720	E069	49785
chr9	7037273	7037323	E070	4497
chr9	7082561	7082720	E072	49785
chr9	7052503	7053138	E073	19727
chr9	7053246	7053364	E073	20470
chr9	7053377	7053446	E073	20601
chr9	6999991	7000124	E074	-32652
chr9	7056387	7056589	E074	23611
chr9	7056766	7057012	E074	23990
chr9	7057457	7058000	E074	24681
chr9	7078796	7079177	E074	46020
chr9	7052503	7053138	E081	19727
chr9	7053246	7053364	E081	20470
chr9	7053377	7053446	E081	20601
chr9	7053246	7053364	E082	20470
chr9	7053377	7053446	E082	20601
chr9	7055053	7055161	E082	22277

rs1407862

Genomic Coordinates

Gene: KDM4C, lysine demethylase 4C(plus strand)

Population Frequency

P-Value

eQTL of rs1407862 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs1407862 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)