rs36057641

Organism: Homo sapiens

Alleles: delAA / delA

Gene : Feature

BBS4 : Intron Variant

p-value: Check p-value

Variation Type: Indel (Insertion and Deletion)

Frequency:

(A)14==0048 (239/5008,1000G)

Position: chr15:72730279-72730292 (GRCh38.p7) (15q24.1)

Phenotype: AD

Dataset:

Publications: 1 publication(s)

Genomic View: See rs on genome

Enhancer: 80 Enhancers around

Promoter: 7 Promoters around

Variant Details Frequency Publications p-values eSNP meSNP

Genomic Coordinates

Sequence Name	Change(s)
GRCh38.p7 chr 15	NC_000015.10:g.72730291_72730292delAA
GRCh38.p7 chr 15	NC_000015.10:g.72730292delA
GRCh37.p13 chr 15	NC_000015.9:g.73022632_73022633delAA
GRCh37.p13 chr 15	NC_000015.9:g.73022633delA
BBS4 RefSeqGene	NG_009416.2:g.49107_49108delAA
BBS4 RefSeqGene	NG_009416.2:g.49108delA

Gene: BBS4, Bardet-Biedl syndrome 4(plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
BBS4 transcript variant 2	NM_001252678.1:c.	N/A	Intron Variant
BBS4 transcript variant 5	NM_001320665.1:c.	N/A	Intron Variant
BBS4 transcript variant 1	NM_033028.4:c.	N/A	Intron Variant
BBS4 transcript variant 3	NR_045565.1:n.	N/A	Intron Variant
BBS4 transcript variant 4	NR_045566.1:n.	N/A	Intron Variant
BBS4 transcript variant X2	XM_011521848.1:c.	N/A	Intron Variant
BBS4 transcript variant X3	XM_011521849.1:c.	N/A	Intron Variant
BBS4 transcript variant X7	XM_011521851.1:c.	N/A	Intron Variant
BBS4 transcript variant X1	XM_017022450.1:c.	N/A	Intron Variant
BBS4 transcript variant X4	XM_017022451.1:c.	N/A	Intron Variant
BBS4 transcript variant X4	XM_017022452.1:c.	N/A	Intron Variant
BBS4 transcript variant X5	XM_017022453.1:c.	N/A	Intron Variant
BBS4 transcript variant X6	XM_017022454.1:c.	N/A	Intron Variant

Population Frequency

Study	Population	Group	Sample #	Ref Allele	Alt Allele
1000Genomes	African	Sub	1322	(A)14=0.166	delA=0.834
1000Genomes	American	Sub	694	(A)14=0.020	delA=0.980
1000Genomes	East Asian	Sub	1008	(A)14=0.003	delA=0.997
1000Genomes	Europe	Sub	1006	(A)14=0.002	delA=0.998
1000Genomes	Global	Study-wide	5008	(A)14=0.048	delA=0.952
1000Genomes	South Asian	Sub	978	(A)14=0.000	delA=1.000

PMID	Title	Author	Journal
29071344	Genetic Risk Variants Associated With Comorbid Alcohol Dependence and Major Depression.	Zhou H	JAMA Psychiatry

P-Value

SNP ID	p-value	Traits	Study

eQTL of rs36057641 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 rs36057641 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 )
chr15	60428060	60428238	E067	-19600
chr15	60428255	60428317	E067	-19521
chr15	60428320	60428471	E067	-19367
chr15	60427434	60427484	E068	-20354
chr15	60427659	60427709	E068	-20129
chr15	60428060	60428238	E068	-19600
chr15	60428255	60428317	E068	-19521
chr15	60428320	60428471	E068	-19367
chr15	60411428	60411534	E069	-36304
chr15	60411582	60411678	E069	-36160
chr15	60412296	60412664	E069	-35174
chr15	60412722	60413044	E069	-34794
chr15	60420788	60421453	E069	-26385
chr15	60421455	60421735	E069	-26103
chr15	60421798	60421886	E069	-25952
chr15	60427659	60427709	E069	-20129
chr15	60428060	60428238	E069	-19600
chr15	60428255	60428317	E069	-19521
chr15	60428320	60428471	E069	-19367
chr15	60471748	60471838	E069	23910
chr15	60407945	60408488	E070	-39350
chr15	60411428	60411534	E070	-36304
chr15	60411582	60411678	E070	-36160
chr15	60411742	60411822	E070	-36016
chr15	60454537	60454775	E070	6699
chr15	60454877	60455070	E070	7039
chr15	60455242	60455440	E070	7404
chr15	60411742	60411822	E071	-36016
chr15	60412185	60412276	E071	-35562
chr15	60412296	60412664	E071	-35174
chr15	60412722	60413044	E071	-34794
chr15	60420788	60421453	E071	-26385
chr15	60421455	60421735	E071	-26103
chr15	60421798	60421886	E071	-25952
chr15	60427434	60427484	E071	-20354
chr15	60427659	60427709	E071	-20129
chr15	60428060	60428238	E071	-19600
chr15	60428255	60428317	E071	-19521
chr15	60428320	60428471	E071	-19367
chr15	60429174	60429273	E071	-18565
chr15	60429284	60429346	E071	-18492
chr15	60496049	60496323	E071	48211
chr15	60411428	60411534	E072	-36304
chr15	60411582	60411678	E072	-36160
chr15	60411742	60411822	E072	-36016
chr15	60420788	60421453	E072	-26385
chr15	60421455	60421735	E072	-26103
chr15	60421798	60421886	E072	-25952
chr15	60428060	60428238	E072	-19600
chr15	60428255	60428317	E072	-19521
chr15	60428320	60428471	E072	-19367
chr15	60412722	60413044	E073	-34794
chr15	60411428	60411534	E074	-36304
chr15	60411582	60411678	E074	-36160
chr15	60411742	60411822	E074	-36016
chr15	60412185	60412276	E074	-35562
chr15	60412296	60412664	E074	-35174
chr15	60412722	60413044	E074	-34794
chr15	60418844	60418898	E074	-28940
chr15	60419019	60419074	E074	-28764
chr15	60420788	60421453	E074	-26385
chr15	60421455	60421735	E074	-26103
chr15	60421798	60421886	E074	-25952
chr15	60427434	60427484	E074	-20354
chr15	60427659	60427709	E074	-20129
chr15	60429174	60429273	E074	-18565
chr15	60429284	60429346	E074	-18492
chr15	60429733	60429903	E074	-17935
chr15	60429965	60430330	E074	-17508
chr15	60454537	60454775	E074	6699
chr15	60454877	60455070	E074	7039
chr15	60455242	60455440	E074	7404
chr15	60412185	60412276	E081	-35562
chr15	60496049	60496323	E081	48211
chr15	60496595	60497223	E081	48757
chr15	60497285	60497429	E081	49447
chr15	60411428	60411534	E082	-36304
chr15	60411582	60411678	E082	-36160
chr15	60411742	60411822	E082	-36016
chr15	60496049	60496323	E082	48211

Promoter Annotation (GRCh37.p13)

Chromosome	Start	End	Region	Distance(-/+:Up/Downstream)
chr15	60419143	60420748	E067	-27090
chr15	60419143	60420748	E068	-27090
chr15	60419143	60420748	E069	-27090
chr15	60419143	60420748	E071	-27090
chr15	60419143	60420748	E072	-27090
chr15	60419143	60420748	E073	-27090
chr15	60419143	60420748	E074	-27090