Variant report

Variant	rs6900233
Chromosome Location	chr6:142717283-142717284
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142716545..142718055-chr6:142718448..142720130,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10484733	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11155241	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11155242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759653	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12189838	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12190271	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197866	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198644	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1329705	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1329707	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17071756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928528	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294775	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs262117	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3817928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4304190	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570511	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6900087	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901807	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6903424	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6906468	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6912639	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6922607	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6925979	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73780219	0.98[ASN][1000 genomes]
rs73780221	0.98[ASN][1000 genomes]
rs7756434	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7757571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7765770	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7776356	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9321870	0.82[EUR][1000 genomes]
rs9373347	0.90[EUR][1000 genomes]
rs9403386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142698600-142733200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:142699800-142718600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr6:142699800-142719200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:142706200-142719600	Weak transcription	NHEK	skin
5	chr6:142708000-142734800	Weak transcription	Esophagus	oesophagus
6	chr6:142708200-142718600	Weak transcription	Placenta	Placenta
7	chr6:142708200-142719400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:142709200-142721000	Weak transcription	Fetal Intestine Small	intestine
9	chr6:142709400-142718800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:142710000-142721600	Weak transcription	NHLF	lung
11	chr6:142710200-142733400	Weak transcription	HSMM	muscle
12	chr6:142710600-142719600	Weak transcription	Small Intestine	intestine
13	chr6:142711400-142725000	Strong transcription	HepG2	liver
14	chr6:142711800-142725200	Strong transcription	Liver	Liver
15	chr6:142712200-142735000	Weak transcription	Fetal Brain Male	brain
16	chr6:142713600-142717600	Strong transcription	Fetal Lung	lung
17	chr6:142713800-142717400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:142713800-142718000	Strong transcription	A549	lung
19	chr6:142714200-142733200	Weak transcription	HMEC	breast
20	chr6:142714600-142718000	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr6:142714600-142718200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr6:142715200-142718400	Enhancers	HUVEC	blood vessel
23	chr6:142715600-142718200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:142715800-142717400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:142715800-142718200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:142715800-142718800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr6:142716000-142718000	Enhancers	Dnd41	blood
28	chr6:142716200-142717600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:142716400-142717400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
30	chr6:142716400-142717600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:142716400-142717600	Enhancers	Primary B cells from cord blood	blood
32	chr6:142716400-142717600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:142716400-142718000	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr6:142716600-142717400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr6:142716600-142717400	Enhancers	Thymus	Thymus
36	chr6:142716600-142717600	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr6:142716600-142717600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr6:142716600-142717600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr6:142716800-142717600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:142716800-142717600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:142716800-142719600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr6:142717000-142717600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr6:142717000-142717600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr6:142717200-142717400	Flanking Active TSS	GM12878-XiMat	blood
45	chr6:142717200-142717600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:142717200-142717600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:142717200-142717600	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr6:142717200-142717600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:142717200-142721600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links