Variant report

Variant	rs41273553
Chromosome Location	chr3:100617532-100617533
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: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1036467	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10511181	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13060137	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs13072000	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13077353	0.92[EUR][1000 genomes]
rs13079002	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13080859	0.86[EUR][1000 genomes]
rs13088524	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13092605	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13099053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13100301	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17284842	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs17338506	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17398421	0.87[EUR][1000 genomes]
rs17398684	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2245266	0.98[EUR][1000 genomes]
rs2245473	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2245556	0.98[EUR][1000 genomes]
rs2576365	0.98[EUR][1000 genomes]
rs2576369	0.98[EUR][1000 genomes]
rs2576372	0.94[EUR][1000 genomes]
rs2576377	0.91[EUR][1000 genomes]
rs2576382	0.85[EUR][1000 genomes]
rs2576387	0.96[EUR][1000 genomes]
rs2576391	0.85[EUR][1000 genomes]
rs2595893	0.85[EUR][1000 genomes]
rs2595894	0.85[EUR][1000 genomes]
rs2713748	0.81[EUR][1000 genomes]
rs2713764	0.85[EUR][1000 genomes]
rs2713782	0.96[EUR][1000 genomes]
rs2713786	0.85[EUR][1000 genomes]
rs2713787	0.98[EUR][1000 genomes]
rs2713788	0.94[EUR][1000 genomes]
rs2713789	0.98[EUR][1000 genomes]
rs2713793	0.98[EUR][1000 genomes]
rs34275644	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34315591	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs34515751	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs34565718	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs34645172	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs34719725	0.87[EUR][1000 genomes]
rs34999788	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35090886	0.85[EUR][1000 genomes]
rs35509049	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35517882	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs35530876	0.87[EUR][1000 genomes]
rs35617051	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs35630894	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs35999953	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36156426	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs36165056	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36194526	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs4060963	0.98[EUR][1000 genomes]
rs41273557	0.80[EUR][1000 genomes]
rs4928096	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62273925	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62273927	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62273928	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62273930	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62273935	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62275197	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62275198	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62275199	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62275200	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs62275203	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62275204	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62277105	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66852780	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs67946790	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs67991823	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72928364	0.82[EUR][1000 genomes]
rs73137256	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73137276	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73143088	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7431835	0.96[EUR][1000 genomes]
rs9832195	0.98[EUR][1000 genomes]
rs9840644	0.94[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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100594400-100618200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:100599600-100645400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:100599800-100618200	Weak transcription	Fetal Lung	lung
4	chr3:100610400-100617600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:100610600-100619200	Weak transcription	Fetal Intestine Large	intestine
6	chr3:100612000-100622800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:100612200-100632200	Weak transcription	Fetal Stomach	stomach
8	chr3:100613000-100618200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:100613400-100618600	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:100616200-100618200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:100616800-100617600	Strong transcription	Fetal Muscle Leg	muscle
12	chr3:100616800-100617600	Enhancers	HUVEC	blood vessel
13	chr3:100616800-100617600	Strong transcription	NHDF-Ad	bronchial
14	chr3:100616800-100617600	Strong transcription	Osteobl	bone
15	chr3:100616800-100619400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:100617000-100617600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr3:100617000-100617600	Strong transcription	HSMM	muscle
18	chr3:100617000-100617800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:100617000-100617800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr3:100617000-100617800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:100617000-100617800	Strong transcription	HSMMtube	muscle
22	chr3:100617000-100618000	Enhancers	Stomach Mucosa	stomach
23	chr3:100617000-100619200	Enhancers	Duodenum Mucosa	Duodenum
24	chr3:100617000-100619400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr3:100617000-100621200	Enhancers	Hela-S3	cervix
26	chr3:100617200-100617600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr3:100617200-100618200	Flanking Active TSS	GM12878-XiMat	blood
28	chr3:100617200-100619000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:100617200-100621400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:100617200-100629400	Weak transcription	Ovary	ovary
31	chr3:100617400-100618000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr3:100617400-100618200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr3:100617400-100618600	Enhancers	NHEK	skin
34	chr3:100617400-100618800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:100617400-100619200	Enhancers	Primary hematopoietic stem cells	blood
36	chr3:100617400-100622000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links