SNP Detail Info-rs3759871

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.44651559A>G
GRCh37.p13 chr 15	NC_000015.9:g.44943757A>G
SPG11 RefSeqGene	NG_008885.1:g.17120T>C

Gene: SPG11, spastic paraplegia 11 (autosomal recessive)(minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SPG11 transcript variant 1	NM_025137.3:c.138...NM_025137.3:c.1388T>C	F [TTT]> S [TCT]	Coding Sequence Variant
spatacsin isoform 1	NP_079413.3:p.Phe...NP_079413.3:p.Phe463Ser	F [Phe]> S [Ser]	Missense Variant
SPG11 transcript variant 2	NM_001160227.1:c....NM_001160227.1:c.1388T>C	F [TTT]> S [TCT]	Coding Sequence Variant
spatacsin isoform 2	NP_001153699.1:p....NP_001153699.1:p.Phe463Ser	F [Phe]> S [Ser]	Missense Variant
SPG11 transcript variant X6	XM_017022636.1:c.	N/A	Genic Upstream Transcript Variant
SPG11 transcript variant X2	XM_006720700.1:c....XM_006720700.1:c.1388T>C	F [TTT]> S [TCT]	Coding Sequence Variant
spatacsin isoform X2	XP_006720763.1:p....XP_006720763.1:p.Phe463Ser	F [Phe]> S [Ser]	Missense Variant
SPG11 transcript variant X1	XM_017022634.1:c....XM_017022634.1:c.1388T>C	F [TTT]> S [TCT]	Coding Sequence Variant
spatacsin isoform X1	XP_016878123.1:p....XP_016878123.1:p.Phe463Ser	F [Phe]> S [Ser]	Missense Variant
SPG11 transcript variant X3	XM_017022635.1:c....XM_017022635.1:c.1388T>C	F [TTT]> S [TCT]	Coding Sequence Variant
spatacsin isoform X3	XP_016878124.1:p....XP_016878124.1:p.Phe463Ser	F [Phe]> S [Ser]	Missense Variant
SPG11 transcript variant X4	XM_006720701.3:c....XM_006720701.3:c.1388T>C	F [TTT]> S [TCT]	Coding Sequence Variant
spatacsin isoform X4	XP_006720764.1:p....XP_006720764.1:p.Phe463Ser	F [Phe]> S [Ser]	Missense Variant
SPG11 transcript variant X5	XR_931917.2:n.141...XR_931917.2:n.1419T>C	T>C	Non Coding Transcript Variant
SPG11 transcript variant X7	XR_001751402.1:n....XR_001751402.1:n.1419T>C	T>C	Non Coding Transcript Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	A=0.477	G=0.523
1000Genomes	American	Sub	694	A=0.410	G=0.590
1000Genomes	East Asian	Sub	1008	A=0.535	G=0.465
1000Genomes	Europe	Sub	1006	A=0.549	G=0.451
1000Genomes	Global	Study-wide	5008	A=0.525	G=0.475
1000Genomes	South Asian	Sub	978	A=0.640	G=0.360
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.565	G=0.435
The Exome Aggregation Consortium	American	Sub	21968	A=0.451	G=0.548
The Exome Aggregation Consortium	Asian	Sub	25124	A=0.595	G=0.404
The Exome Aggregation Consortium	Europe	Sub	73318	A=0.537	G=0.462
The Exome Aggregation Consortium	Global	Study-wide	121318	A=0.534	G=0.465
The Exome Aggregation Consortium	Other	Sub	908	A=0.540	G=0.460
The Genome Aggregation Database	African	Sub	8702	A=0.477	G=0.523
The Genome Aggregation Database	American	Sub	838	A=0.430	G=0.570
The Genome Aggregation Database	East Asian	Sub	1616	A=0.558	G=0.442
The Genome Aggregation Database	Europe	Sub	18470	A=0.533	G=0.466
The Genome Aggregation Database	Global	Study-wide	29928	A=0.515	G=0.484
The Genome Aggregation Database	Other	Sub	302	A=0.530	G=0.470
Trans-Omics for Precision Medicine	Global	Study-wide	29118	A=0.496	G=0.503
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.563	G=0.437

PMID	Title	Author	Journal
21703634	A meta-analysis of two genome-wide association studies identifies 3 new loci for alcohol dependence.	Wang KS	J Psychiatr Res
20301389	Spastic Paraplegia 11	Stevanin G	-

P-Value

SNP ID	p-value	Traits	Study
rs3759871	2.46E-05	alcohol dependence	21703634

eQTL of rs3759871 in Brain tissues (GTEx Analysis Release V7)

Position (v37)	eGene	GeneID	Variant	p-value	TSS	Tissue
Chr15:44943757	AC011330.5	ENSG00000249839.1	A>G	1.8363e-6	967220	Caudate_basal_ganglia

meQTL of rs3759871 in Fetal Brain

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

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr15	44954100	44956826	E067	10343
chr15	44954100	44956826	E068	10343
chr15	44954100	44956826	E069	10343
chr15	44954100	44956826	E070	10343
chr15	44954100	44956826	E071	10343
chr15	44954100	44956826	E072	10343
chr15	44954100	44956826	E073	10343
chr15	44954100	44956826	E074	10343
chr15	44954100	44956826	E081	10343
chr15	44954100	44956826	E082	10343

rs3759871

Genomic Coordinates

Gene: SPG11, spastic paraplegia 11 (autosomal recessive)(minus strand)

Population Frequency

P-Value

eQTL of rs3759871 in Brain tissues (GTEx Analysis Release V7)

meQTL of rs3759871 in Fetal Brain

Genomic View

Chromatin Interaction

Enhancer Annotation (GRCh37.p13)

Promoter Annotation (GRCh37.p13)