rs7309268

Organism: Homo sapiens

Alleles: G>T

Gene : Feature

SOX5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

T=0067 (2017/29982,GnomAD)
T=0068 (1981/29118,TOPMED)
T=0035 (176/5008,1000G)
T=0072 (278/3854,ALSPAC)
T=0072 (266/3708,TWINSUK)

Position: chr12:24407310 (GRCh38.p7) (12p12.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 87 Enhancers around

Promoter: 0 Promoter around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 12	NC_000012.12:g.24407310G>T
GRCh37.p13 chr 12	NC_000012.11:g.24560244G>T
SOX5 RefSeqGene	NG_029612.1:g.160137C>A

Gene: SOX5, SRY-box 5(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SOX5 transcript variant 4	NM_001261414.1:c.	N/A	Intron Variant
SOX5 transcript variant 2	NM_152989.3:c.	N/A	Intron Variant
SOX5 transcript variant 5	NM_001261415.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant 1	NM_006940.4:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant 3	NM_178010.2:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X13	XM_011520834.2:c.	N/A	Intron Variant
SOX5 transcript variant X12	XM_011520835.2:c.	N/A	Intron Variant
SOX5 transcript variant X5	XM_017019890.1:c.	N/A	Intron Variant
SOX5 transcript variant X6	XM_017019891.1:c.	N/A	Intron Variant
SOX5 transcript variant X8	XM_017019892.1:c.	N/A	Intron Variant
SOX5 transcript variant X19	XM_017019893.1:c.	N/A	Intron Variant
SOX5 transcript variant X23	XM_017019896.1:c.	N/A	Intron Variant
SOX5 transcript variant X27	XM_017019897.1:c.	N/A	Intron Variant
SOX5 transcript variant X31	XM_017019898.1:c.	N/A	Intron Variant
SOX5 transcript variant X32	XM_017019899.1:c.	N/A	Intron Variant
SOX5 transcript variant X16	XM_011520831.2:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X3	XM_011520832.2:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X4	XM_011520833.2:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X22	XM_011520837.2:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X26	XM_011520838.2:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X37	XM_011520842.2:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X1	XM_017019888.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X2	XM_017019889.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X20	XM_017019894.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X21	XM_017019895.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X33	XM_017019900.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X34	XM_017019901.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X35	XM_017019902.1:c.	N/A	Genic Upstream Transcript Variant
SOX5 transcript variant X36	XM_017019903.1:c.	N/A	Genic Upstream Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.964	T=0.036
1000Genomes	American	Sub	694	G=0.960	T=0.040
1000Genomes	East Asian	Sub	1008	G=1.000	T=0.000
1000Genomes	Europe	Sub	1006	G=0.913	T=0.087
1000Genomes	Global	Study-wide	5008	G=0.965	T=0.035
1000Genomes	South Asian	Sub	978	G=0.990	T=0.010
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.928	T=0.072
The Genome Aggregation Database	African	Sub	8728	G=0.959	T=0.041
The Genome Aggregation Database	American	Sub	838	G=0.970	T=0.030
The Genome Aggregation Database	East Asian	Sub	1622	G=1.000	T=0.000
The Genome Aggregation Database	Europe	Sub	18492	G=0.913	T=0.086
The Genome Aggregation Database	Global	Study-wide	29982	G=0.932	T=0.067
The Genome Aggregation Database	Other	Sub	302	G=0.900	T=0.100
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.932	T=0.068
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.928	T=0.072

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
rs7309268	0.000964	alcohol dependence	21314694

eQTL of rs7309268 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 rs7309268 in Fetal Brain

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

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 )
chr12	24531281	24532359	E067	-27885
chr12	24532388	24532781	E067	-27463
chr12	24547114	24547468	E067	-12776
chr12	24531281	24532359	E068	-27885
chr12	24532388	24532781	E068	-27463
chr12	24546082	24546432	E068	-13812
chr12	24547114	24547468	E068	-12776
chr12	24548101	24548151	E068	-12093
chr12	24548471	24548609	E068	-11635
chr12	24548612	24548785	E068	-11459
chr12	24548887	24549032	E068	-11212
chr12	24597524	24597625	E068	37280
chr12	24597772	24598129	E068	37528
chr12	24531281	24532359	E069	-27885
chr12	24532847	24533544	E069	-26700
chr12	24546082	24546432	E069	-13812
chr12	24547114	24547468	E069	-12776
chr12	24515425	24515475	E070	-44769
chr12	24515478	24515589	E070	-44655
chr12	24516086	24516146	E070	-44098
chr12	24516258	24516361	E070	-43883
chr12	24516453	24516548	E070	-43696
chr12	24520031	24520359	E070	-39885
chr12	24530753	24531040	E070	-29204
chr12	24531281	24532359	E070	-27885
chr12	24532388	24532781	E070	-27463
chr12	24532847	24533544	E070	-26700
chr12	24548471	24548609	E070	-11635
chr12	24548612	24548785	E070	-11459
chr12	24595507	24595606	E070	35263
chr12	24595676	24595818	E070	35432
chr12	24597524	24597625	E070	37280
chr12	24531281	24532359	E071	-27885
chr12	24532847	24533544	E071	-26700
chr12	24548471	24548609	E071	-11635
chr12	24548612	24548785	E071	-11459
chr12	24547114	24547468	E072	-12776
chr12	24548471	24548609	E073	-11635
chr12	24548612	24548785	E073	-11459
chr12	24548887	24549032	E073	-11212
chr12	24546082	24546432	E074	-13812
chr12	24548887	24549032	E074	-11212
chr12	24549084	24549898	E074	-10346
chr12	24567370	24567958	E074	7126
chr12	24531281	24532359	E081	-27885
chr12	24532388	24532781	E081	-27463
chr12	24532847	24533544	E081	-26700
chr12	24533629	24533771	E081	-26473
chr12	24533849	24533938	E081	-26306
chr12	24533958	24534127	E081	-26117
chr12	24534313	24534536	E081	-25708
chr12	24534654	24534704	E081	-25540
chr12	24545809	24545863	E081	-14381
chr12	24545895	24546012	E081	-14232
chr12	24546082	24546432	E081	-13812
chr12	24547114	24547468	E081	-12776
chr12	24548471	24548609	E081	-11635
chr12	24548612	24548785	E081	-11459
chr12	24548887	24549032	E081	-11212
chr12	24549084	24549898	E081	-10346
chr12	24567370	24567958	E081	7126
chr12	24577079	24577166	E081	16835
chr12	24577399	24578018	E081	17155
chr12	24578036	24578151	E081	17792
chr12	24580332	24580436	E081	20088
chr12	24580489	24580774	E081	20245
chr12	24581036	24581139	E081	20792
chr12	24581179	24581229	E081	20935
chr12	24581353	24581403	E081	21109
chr12	24581721	24581896	E081	21477
chr12	24531281	24532359	E082	-27885
chr12	24532388	24532781	E082	-27463
chr12	24532847	24533544	E082	-26700
chr12	24533629	24533771	E082	-26473
chr12	24533849	24533938	E082	-26306
chr12	24533958	24534127	E082	-26117
chr12	24534258	24534308	E082	-25936
chr12	24534313	24534536	E082	-25708
chr12	24545809	24545863	E082	-14381
chr12	24545895	24546012	E082	-14232
chr12	24548887	24549032	E082	-11212
chr12	24576594	24576669	E082	16350
chr12	24576700	24576773	E082	16456
chr12	24577079	24577166	E082	16835
chr12	24577399	24578018	E082	17155
chr12	24578036	24578151	E082	17792
chr12	24578315	24578405	E082	18071