Variant report

Variant	rs17720639
Chromosome Location	chr5:58357931-58357932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10068543	0.89[JPT][hapmap]
rs13183985	0.89[JPT][hapmap]
rs17720871	0.82[EUR][1000 genomes]
rs17721311	0.80[EUR][1000 genomes]
rs17777280	0.81[EUR][1000 genomes]
rs17777617	0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs35244458	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62356680	0.81[EUR][1000 genomes]
rs62356683	0.81[EUR][1000 genomes]
rs62356684	0.81[EUR][1000 genomes]
rs6864156	0.88[JPT][hapmap]
rs6889456	0.89[JPT][hapmap]
rs7707541	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs950446	0.98[TSI][hapmap];0.81[EUR][1000 genomes]
rs986067	0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv830312	chr5:58191579-58382226	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv830313	chr5:58273724-58421098	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1032308	chr5:58312468-58371239	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17720639	KIF3A	trans	cerebellum	SCAN
rs17720639	RAB3C	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58336200-58375600	Weak transcription	Left Ventricle	heart
2	chr5:58336600-58358000	Weak transcription	Fetal Intestine Large	intestine
3	chr5:58336600-58358000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:58337400-58359000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:58338800-58359200	Weak transcription	Fetal Muscle Leg	muscle
6	chr5:58338800-58362000	Weak transcription	Gastric	stomach
7	chr5:58339000-58365200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:58340600-58359000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr5:58346000-58359000	Weak transcription	Stomach Mucosa	stomach
10	chr5:58347200-58359200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr5:58348200-58362000	Weak transcription	Psoas Muscle	Psoas
12	chr5:58349600-58360600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:58350400-58360200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr5:58350600-58360200	Weak transcription	Fetal Stomach	stomach
15	chr5:58351000-58359000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:58356400-58360800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr5:58356600-58360800	Enhancers	HepG2	liver
18	chr5:58357000-58358000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr5:58357200-58360400	Enhancers	Colon Smooth Muscle	Colon
20	chr5:58357400-58358000	Enhancers	NHEK	skin
21	chr5:58357400-58360600	Flanking Active TSS	A549	lung
22	chr5:58357600-58358600	Genic enhancers	Hela-S3	cervix
23	chr5:58357600-58358800	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr5:58357600-58362000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:58357800-58358200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr5:58357800-58358800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:58357800-58360200	Weak transcription	HMEC	breast

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