rs550338

Organism: Homo sapiens

Alleles: G>A

Gene : Feature

SOX5 : Intron Variant

p-value: Check p-value

Variation Type: SNV (Single Nucleotide Variation)

Frequency:

A=0300 (8989/29928,GnomAD)
A=0305 (8907/29118,TOPMED)
A=0467 (2340/5008,1000G)
A=0230 (888/3854,ALSPAC)
A=0224 (830/3708,TWINSUK)

Position: chr12:24359103 (GRCh38.p7) (12p12.1)

Phenotype: AD

Dataset:

GWASdb2

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 74 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.24359103G>A
GRCh37.p13 chr 12	NC_000012.11:g.24512037G>A
SOX5 RefSeqGene	NG_029612.1:g.208344C>T

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

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	G=0.697	A=0.303
1000Genomes	American	Sub	694	G=0.460	A=0.540
1000Genomes	East Asian	Sub	1008	G=0.235	A=0.765
1000Genomes	Europe	Sub	1006	G=0.764	A=0.236
1000Genomes	Global	Study-wide	5008	G=0.533	A=0.467
1000Genomes	South Asian	Sub	978	G=0.430	A=0.570
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.770	A=0.230
The Genome Aggregation Database	African	Sub	8712	G=0.707	A=0.293
The Genome Aggregation Database	American	Sub	836	G=0.420	A=0.580
The Genome Aggregation Database	East Asian	Sub	1614	G=0.198	A=0.802
The Genome Aggregation Database	Europe	Sub	18464	G=0.751	A=0.248
The Genome Aggregation Database	Global	Study-wide	29928	G=0.699	A=0.300
The Genome Aggregation Database	Other	Sub	302	G=0.760	A=0.240
Trans-Omics for Precision Medicine	Global	Study-wide	29118	G=0.694	A=0.305
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.776	A=0.224

PMID	Title	Author	Journal
20201924	Genome-wide association study of alcohol dependence implicates a region on chromosome 11.	Edenberg HJ	Alcohol Clin Exp Res

SNP ID	p-value	Traits	Study
rs550338	0.0000888	alcoholism	pha002893
rs550338	0.000089	alcohol dependence	20201924
rs550338	0.00022	alcohol dependence(early age of onset)	20201924

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

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	19244
chr12	24532388	24532781	E067	20351
chr12	24547114	24547468	E067	35077
chr12	24531281	24532359	E068	19244
chr12	24532388	24532781	E068	20351
chr12	24546082	24546432	E068	34045
chr12	24547114	24547468	E068	35077
chr12	24548101	24548151	E068	36064
chr12	24548471	24548609	E068	36434
chr12	24548612	24548785	E068	36575
chr12	24548887	24549032	E068	36850
chr12	24531281	24532359	E069	19244
chr12	24532847	24533544	E069	20810
chr12	24546082	24546432	E069	34045
chr12	24547114	24547468	E069	35077
chr12	24471344	24471426	E070	-40611
chr12	24471442	24471496	E070	-40541
chr12	24480952	24481093	E070	-30944
chr12	24481171	24481472	E070	-30565
chr12	24509545	24509601	E070	-2436
chr12	24515425	24515475	E070	3388
chr12	24515478	24515589	E070	3441
chr12	24516086	24516146	E070	4049
chr12	24516258	24516361	E070	4221
chr12	24516453	24516548	E070	4416
chr12	24520031	24520359	E070	7994
chr12	24530753	24531040	E070	18716
chr12	24531281	24532359	E070	19244
chr12	24532388	24532781	E070	20351
chr12	24532847	24533544	E070	20810
chr12	24548471	24548609	E070	36434
chr12	24548612	24548785	E070	36575
chr12	24531281	24532359	E071	19244
chr12	24532847	24533544	E071	20810
chr12	24548471	24548609	E071	36434
chr12	24548612	24548785	E071	36575
chr12	24547114	24547468	E072	35077
chr12	24548471	24548609	E073	36434
chr12	24548612	24548785	E073	36575
chr12	24548887	24549032	E073	36850
chr12	24546082	24546432	E074	34045
chr12	24548887	24549032	E074	36850
chr12	24549084	24549898	E074	37047
chr12	24478804	24479090	E081	-32947
chr12	24479104	24479154	E081	-32883
chr12	24479159	24479203	E081	-32834
chr12	24479672	24479722	E081	-32315
chr12	24531281	24532359	E081	19244
chr12	24532388	24532781	E081	20351
chr12	24532847	24533544	E081	20810
chr12	24533629	24533771	E081	21592
chr12	24533849	24533938	E081	21812
chr12	24533958	24534127	E081	21921
chr12	24534313	24534536	E081	22276
chr12	24534654	24534704	E081	22617
chr12	24545809	24545863	E081	33772
chr12	24545895	24546012	E081	33858
chr12	24546082	24546432	E081	34045
chr12	24547114	24547468	E081	35077
chr12	24548471	24548609	E081	36434
chr12	24548612	24548785	E081	36575
chr12	24548887	24549032	E081	36850
chr12	24549084	24549898	E081	37047
chr12	24531281	24532359	E082	19244
chr12	24532388	24532781	E082	20351
chr12	24532847	24533544	E082	20810
chr12	24533629	24533771	E082	21592
chr12	24533849	24533938	E082	21812
chr12	24533958	24534127	E082	21921
chr12	24534258	24534308	E082	22221
chr12	24534313	24534536	E082	22276
chr12	24545809	24545863	E082	33772
chr12	24545895	24546012	E082	33858
chr12	24548887	24549032	E082	36850

rs550338

Genomic Coordinates

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

Population Frequency

P-Value

eQTL of rs550338 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs550338 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)