Variant report

Variant	rs9840859
Chromosome Location	chr3:47704222-47704223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11130141	1.00[MEX][hapmap]
rs12496190	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12633923	1.00[MEX][hapmap]
rs1464615	1.00[MEX][hapmap]
rs1471711	1.00[MEX][hapmap]
rs1568690	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs2047558	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4858796	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4858839	1.00[MEX][hapmap];1.00[YRI][hapmap]
rs4858850	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs6442073	0.95[AFR][1000 genomes]
rs6777379	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6778157	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6779582	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6787014	1.00[MEX][hapmap];1.00[YRI][hapmap]
rs9812315	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9812957	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9826123	1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9841020	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs9871162	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs9871805	0.82[AFR][1000 genomes]
rs9881599	1.00[MEX][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	nsv1003072	chr3:47673628-47869154	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv590232	chr3:47681881-47765547	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv876758	chr3:47681881-47842234	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
4	nsv967013	chr3:47704199-47705557	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47654400-47707600	Weak transcription	Stomach Mucosa	stomach
2	chr3:47655800-47765600	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:47656600-47790800	Strong transcription	Fetal Thymus	thymus
4	chr3:47661400-47711400	Weak transcription	Colonic Mucosa	Colon
5	chr3:47672000-47718600	Weak transcription	Right Ventricle	heart
6	chr3:47673600-47719200	Weak transcription	Small Intestine	intestine
7	chr3:47674200-47705000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:47677200-47707400	Weak transcription	HMEC	breast
9	chr3:47677200-47715400	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:47677200-47720000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:47677400-47711600	Weak transcription	Brain Substantia Nigra	brain
12	chr3:47677800-47704600	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:47677800-47712000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:47678000-47717800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr3:47684200-47711800	Weak transcription	Ovary	ovary
16	chr3:47684600-47705200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr3:47684800-47705200	Weak transcription	Aorta	Aorta
18	chr3:47684800-47718400	Weak transcription	Spleen	Spleen
19	chr3:47688200-47705200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:47688200-47763400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:47688600-47710600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:47688600-47718000	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:47689800-47711800	Weak transcription	Left Ventricle	heart
24	chr3:47689800-47714200	Weak transcription	Psoas Muscle	Psoas
25	chr3:47692800-47719200	Weak transcription	Gastric	stomach
26	chr3:47693800-47705000	Weak transcription	Pancreas	Pancrea
27	chr3:47694400-47745800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr3:47695000-47704400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr3:47695000-47705600	Strong transcription	Liver	Liver
30	chr3:47695000-47713800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr3:47695200-47737200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr3:47697000-47709200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:47697800-47706400	Strong transcription	Duodenum Mucosa	Duodenum
34	chr3:47698200-47709200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:47698400-47731400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:47698600-47705600	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr3:47699000-47705400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:47699000-47712600	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:47699400-47705000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:47699800-47705400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:47700200-47705200	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:47700200-47715200	Weak transcription	Fetal Brain Male	brain
43	chr3:47700200-47757000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:47700400-47707600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:47700400-47710600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:47700400-47710600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:47700400-47715400	Weak transcription	Fetal Heart	heart
48	chr3:47700600-47705000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:47700600-47705400	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr3:47700600-47710200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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