Variant report

Variant	rs9879217
Chromosome Location	chr3:23427481-23427482
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11922562	1.00[AMR][1000 genomes]
rs17013009	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17013099	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17013329	0.88[YRI][hapmap]
rs28548892	1.00[AMR][1000 genomes]
rs28567933	1.00[AMR][1000 genomes]
rs28641973	1.00[AMR][1000 genomes]
rs57747253	1.00[AMR][1000 genomes]
rs58047209	1.00[AMR][1000 genomes]
rs58879825	1.00[AMR][1000 genomes]
rs60014070	1.00[AMR][1000 genomes]
rs61081559	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61500565	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61636332	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6768277	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6795043	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138415	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138436	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138449	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138480	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138490	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73138492	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73140509	1.00[AMR][1000 genomes]
rs73140514	1.00[AMR][1000 genomes]
rs73141810	1.00[AMR][1000 genomes]
rs73149654	1.00[AMR][1000 genomes]
rs73149686	1.00[AMR][1000 genomes]
rs73149689	1.00[AMR][1000 genomes]
rs7611624	1.00[AMR][1000 genomes]
rs7634565	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7646028	1.00[AMR][1000 genomes]
rs7652287	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9310716	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9681506	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9809364	0.88[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9810378	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9811442	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9819566	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9819788	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9821681	0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9829577	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9834737	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9842159	1.00[AMR][1000 genomes]
rs9845340	0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9852053	0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9861614	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs9866889	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9869171	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9878638	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9879132	0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv876624	chr3:23385877-23483536	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1012236	chr3:23408427-23469063	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1010032	chr3:23408985-23469063	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23409200-23431800	Weak transcription	Aorta	Aorta
2	chr3:23419200-23429000	Weak transcription	Brain Angular Gyrus	brain
3	chr3:23420000-23433600	Weak transcription	Primary T cells from cord blood	blood
4	chr3:23420400-23427600	Weak transcription	Primary B cells from cord blood	blood
5	chr3:23420600-23428200	Weak transcription	GM12878-XiMat	blood
6	chr3:23425400-23428000	Enhancers	Psoas Muscle	Psoas
7	chr3:23425400-23428000	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr3:23425800-23432200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:23426400-23428000	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:23426800-23428000	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr3:23426800-23428000	Enhancers	HSMMtube	muscle
12	chr3:23426800-23428600	Enhancers	Brain Substantia Nigra	brain
13	chr3:23426800-23430200	Enhancers	Fetal Heart	heart
14	chr3:23427000-23427800	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:23427000-23428000	Enhancers	Right Atrium	heart
16	chr3:23427000-23428200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:23427000-23429600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:23427000-23429600	Enhancers	Primary B cells from peripheral blood	blood
19	chr3:23427000-23445000	Weak transcription	Right Ventricle	heart
20	chr3:23427200-23428400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:23427200-23429800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr3:23427400-23428400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:23427400-23428600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:23427400-23429000	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:23427400-23430000	Enhancers	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links