Variant report

Variant	rs2245266
Chromosome Location	chr3:100618773-100618774
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100616771..100619471-chr3:100625186..100627247,2	MCF-7	breast:
2	chr3:100611635..100615364-chr3:100616570..100618813,3	K562	blood:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1036467	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs10511181	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs13060137	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs13072000	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13077353	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs13079002	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13080859	0.84[EUR][1000 genomes]
rs13088524	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs13092605	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13099053	0.98[EUR][1000 genomes]
rs13100301	0.91[EUR][1000 genomes]
rs17284842	0.87[CEU][hapmap];0.91[EUR][1000 genomes]
rs17338506	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17398421	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs17398684	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2245473	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2245556	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576365	1.00[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576369	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2576372	0.96[EUR][1000 genomes]
rs2576377	0.81[CEU][hapmap];0.92[EUR][1000 genomes]
rs2576382	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2576387	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2576391	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2595893	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2595894	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs2713748	0.83[EUR][1000 genomes]
rs2713764	0.87[EUR][1000 genomes]
rs2713782	1.00[CEU][hapmap];0.82[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2713786	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2713787	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2713788	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2713789	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2713793	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34275644	0.87[EUR][1000 genomes]
rs34315591	0.89[EUR][1000 genomes]
rs34515751	0.87[EUR][1000 genomes]
rs34565718	0.91[EUR][1000 genomes]
rs34719725	0.85[EUR][1000 genomes]
rs34999788	0.95[EUR][1000 genomes]
rs35090886	0.87[EUR][1000 genomes]
rs35509049	0.85[EUR][1000 genomes]
rs35517882	0.81[EUR][1000 genomes]
rs35530876	0.85[EUR][1000 genomes]
rs35617051	0.84[EUR][1000 genomes]
rs35630894	0.85[EUR][1000 genomes]
rs35999953	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36156426	0.91[EUR][1000 genomes]
rs36165056	1.00[EUR][1000 genomes]
rs36194526	0.87[EUR][1000 genomes]
rs4060963	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41273553	0.98[EUR][1000 genomes]
rs4928096	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62273925	0.94[EUR][1000 genomes]
rs62273927	0.91[EUR][1000 genomes]
rs62273928	0.91[EUR][1000 genomes]
rs62273930	0.87[EUR][1000 genomes]
rs62273935	0.85[EUR][1000 genomes]
rs62275197	0.85[EUR][1000 genomes]
rs62275198	0.85[EUR][1000 genomes]
rs62275199	0.83[EUR][1000 genomes]
rs62275200	0.83[EUR][1000 genomes]
rs62277105	0.88[EUR][1000 genomes]
rs67946790	0.85[EUR][1000 genomes]
rs67991823	0.94[EUR][1000 genomes]
rs72928364	0.84[EUR][1000 genomes]
rs73137256	0.88[EUR][1000 genomes]
rs73137276	0.91[EUR][1000 genomes]
rs73143088	0.85[EUR][1000 genomes]
rs7431835	0.87[CEU][hapmap];0.94[EUR][1000 genomes]
rs9832195	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9840644	0.96[EUR][1000 genomes]

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	nsv514163	chr3:100547342-100670846	Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2757881	chr3:100613387-100776497	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759163	chr3:100613387-100776497	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr3:100610600-100619200	Weak transcription	Fetal Intestine Large	intestine
3	chr3:100612000-100622800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr3:100612200-100632200	Weak transcription	Fetal Stomach	stomach
5	chr3:100616800-100619400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr3:100617000-100619200	Enhancers	Duodenum Mucosa	Duodenum
7	chr3:100617000-100619400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr3:100617000-100621200	Enhancers	Hela-S3	cervix
9	chr3:100617200-100619000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr3:100617200-100621400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr3:100617200-100629400	Weak transcription	Ovary	ovary
12	chr3:100617400-100618800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:100617400-100619200	Enhancers	Primary hematopoietic stem cells	blood
14	chr3:100617400-100622000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:100617600-100619000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:100617600-100619200	Genic enhancers	NHDF-Ad	bronchial
17	chr3:100617600-100619600	Genic enhancers	Osteobl	bone
18	chr3:100617600-100620200	Flanking Active TSS	HUVEC	blood vessel
19	chr3:100617600-100622000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:100617600-100641000	Weak transcription	Fetal Muscle Leg	muscle
21	chr3:100617800-100619000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:100617800-100619800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:100617800-100620000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:100617800-100641000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:100618000-100619000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr3:100618000-100619000	Enhancers	HSMM	muscle
27	chr3:100618000-100619000	Weak transcription	NHLF	lung
28	chr3:100618200-100619000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr3:100618200-100619000	Enhancers	Brain Anterior Caudate	brain
30	chr3:100618200-100619400	Enhancers	Fetal Lung	lung
31	chr3:100618200-100620400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:100618400-100618800	Enhancers	HSMMtube	muscle
33	chr3:100618400-100619000	Enhancers	Stomach Mucosa	stomach
34	chr3:100618600-100619000	Enhancers	Colon Smooth Muscle	Colon
35	chr3:100618600-100619200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:100618600-100619200	Flanking Active TSS	GM12878-XiMat	blood
37	chr3:100618600-100621200	Weak transcription	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links