SNP Detail Info-rs10758821

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 9	NC_000009.12:g.7030268G>T
GRCh37.p13 chr 9	NC_000009.11:g.7030268G>T

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=0.618	T=0.382
1000Genomes	American	Sub	694	G=0.510	T=0.490
1000Genomes	East Asian	Sub	1008	G=0.539	T=0.461
1000Genomes	Europe	Sub	1006	G=0.582	T=0.418
1000Genomes	Global	Study-wide	5008	G=0.535	T=0.465
1000Genomes	South Asian	Sub	978	G=0.390	T=0.610
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.549	T=0.451
The Genome Aggregation Database	African	Sub	8688	G=0.595	T=0.405
The Genome Aggregation Database	American	Sub	830	G=0.490	T=0.510
The Genome Aggregation Database	East Asian	Sub	1602	G=0.561	T=0.439
The Genome Aggregation Database	Europe	Sub	18448	G=0.549	T=0.450
The Genome Aggregation Database	Global	Study-wide	29870	G=0.562	T=0.437
The Genome Aggregation Database	Other	Sub	302	G=0.640	T=0.360
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.578	T=0.421
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.539	T=0.461

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
rs10758821	2.79E-05	alcohol withdrawal symptoms	22072270

eQTL of rs10758821 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 rs10758821 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	22235
chr9	7056766	7057012	E068	26498
chr9	7057223	7057335	E068	26955
chr9	7057342	7057422	E068	27074
chr9	7057457	7058000	E068	27189
chr9	7058090	7058230	E068	27822
chr9	7058310	7058379	E068	28042
chr9	7058388	7058453	E068	28120
chr9	7058500	7058568	E068	28232
chr9	7052503	7053138	E069	22235
chr9	7053246	7053364	E069	22978
chr9	7053377	7053446	E069	23109
chr9	7053484	7053547	E069	23216
chr9	7057457	7058000	E069	27189
chr9	7058090	7058230	E069	27822
chr9	7078796	7079177	E069	48528
chr9	7037273	7037323	E070	7005
chr9	7052503	7053138	E073	22235
chr9	7053246	7053364	E073	22978
chr9	7053377	7053446	E073	23109
chr9	6999991	7000124	E074	-30144
chr9	7056387	7056589	E074	26119
chr9	7056766	7057012	E074	26498
chr9	7057457	7058000	E074	27189
chr9	7078796	7079177	E074	48528
chr9	7052503	7053138	E081	22235
chr9	7053246	7053364	E081	22978
chr9	7053377	7053446	E081	23109
chr9	7053246	7053364	E082	22978
chr9	7053377	7053446	E082	23109
chr9	7055053	7055161	E082	24785

rs10758821

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs10758821 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs10758821 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)