SNP Detail Info-rs10975990

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.7026716G>A
GRCh37.p13 chr 9	NC_000009.11:g.7026716G>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=0.413	A=0.587
1000Genomes	American	Sub	694	G=0.460	A=0.540
1000Genomes	East Asian	Sub	1008	G=0.433	A=0.567
1000Genomes	Europe	Sub	1006	G=0.551	A=0.449
1000Genomes	Global	Study-wide	5008	G=0.424	A=0.576
1000Genomes	South Asian	Sub	978	G=0.280	A=0.720
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.511	A=0.489
The Genome Aggregation Database	African	Sub	8682	G=0.412	A=0.588
The Genome Aggregation Database	American	Sub	834	G=0.470	A=0.530
The Genome Aggregation Database	East Asian	Sub	1600	G=0.464	A=0.536
The Genome Aggregation Database	Europe	Sub	18432	G=0.499	A=0.500
The Genome Aggregation Database	Global	Study-wide	29850	G=0.472	A=0.527
The Genome Aggregation Database	Other	Sub	302	G=0.620	A=0.380
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.473	A=0.526
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.501	A=0.499

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)
25043041	Neuropsychosocial profiles of current and future adolescent alcohol misusers.	Whelan R	Nature

P-Value

SNP ID	p-value	Traits	Study
rs10975990	7.15E-06	alcohol withdrawal symptoms	22072270

eQTL of rs10975990 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 rs10975990 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	6978641	6978691	E067	-48025
chr9	6978754	6978915	E067	-47801
chr9	7052503	7053138	E068	25787
chr9	7056766	7057012	E068	30050
chr9	7057223	7057335	E068	30507
chr9	7057342	7057422	E068	30626
chr9	7057457	7058000	E068	30741
chr9	7058090	7058230	E068	31374
chr9	7058310	7058379	E068	31594
chr9	7058388	7058453	E068	31672
chr9	7058500	7058568	E068	31784
chr9	7052503	7053138	E069	25787
chr9	7053246	7053364	E069	26530
chr9	7053377	7053446	E069	26661
chr9	7053484	7053547	E069	26768
chr9	7057457	7058000	E069	30741
chr9	7058090	7058230	E069	31374
chr9	7037273	7037323	E070	10557
chr9	6978641	6978691	E071	-48025
chr9	6978754	6978915	E071	-47801
chr9	7052503	7053138	E073	25787
chr9	7053246	7053364	E073	26530
chr9	7053377	7053446	E073	26661
chr9	6999991	7000124	E074	-26592
chr9	7056387	7056589	E074	29671
chr9	7056766	7057012	E074	30050
chr9	7057457	7058000	E074	30741
chr9	7052503	7053138	E081	25787
chr9	7053246	7053364	E081	26530
chr9	7053377	7053446	E081	26661
chr9	7053246	7053364	E082	26530
chr9	7053377	7053446	E082	26661
chr9	7055053	7055161	E082	28337

rs10975990

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs10975990 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs10975990 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)