Variant report

Variant	rs11698429
Chromosome Location	chr20:13009926-13009927
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	chr20:13002186..13004190-chr20:13008427..13010353,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12479968	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12481402	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1367743	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs17190775	0.84[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes]
rs17190782	0.92[EUR][1000 genomes]
rs17190927	1.00[ASW][hapmap]
rs2236124	1.00[ASW][hapmap]
rs2327446	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs243887	0.82[TSI][hapmap]
rs3761894	0.92[EUR][1000 genomes]
rs3761896	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs3859619	0.92[EUR][1000 genomes]
rs4813104	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55646676	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6033574	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6041799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6074543	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs6074544	0.92[EUR][1000 genomes]
rs6074545	0.92[EUR][1000 genomes]
rs6074548	0.94[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs6074564	1.00[ASW][hapmap]
rs6078875	0.92[EUR][1000 genomes]
rs6078877	0.92[EUR][1000 genomes]
rs6078890	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6078891	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6078895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6078899	0.85[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057219	chr20:12729479-13338337	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv912684	chr20:12734299-13311983	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1067036	chr20:12737436-13338337	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv3488304	chr20:12738054-13341279	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3488305	chr20:12738054-13341279	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv518184	chr20:12743808-13344672	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv1063587	chr20:12756524-13330103	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv544185	chr20:12756524-13330103	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv916296	chr20:12756605-13329940	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv1067720	chr20:12756725-13329963	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv532513	chr20:12756725-13329963	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	nsv1064901	chr20:12773504-13318421	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv833923	chr20:12904689-13064426	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv833924	chr20:12997093-13189239	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13003400-13015400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr20:13003600-13010400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:13003600-13010400	Strong transcription	HepG2	liver
4	chr20:13003800-13010400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:13003800-13014600	Weak transcription	Esophagus	oesophagus
6	chr20:13003800-13026400	Weak transcription	Aorta	Aorta
7	chr20:13003800-13049600	Weak transcription	Lung	lung
8	chr20:13004000-13010000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr20:13004000-13013000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:13004000-13027200	Weak transcription	Pancreas	Pancrea
11	chr20:13004000-13029200	Weak transcription	Ovary	ovary
12	chr20:13005000-13010600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr20:13005400-13012800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr20:13005800-13010600	Enhancers	HMEC	breast
15	chr20:13006600-13014000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr20:13007000-13010400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr20:13007200-13010400	Enhancers	NHEK	skin
18	chr20:13007400-13011800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr20:13007400-13012000	Enhancers	HSMM	muscle
20	chr20:13007600-13011600	Enhancers	HSMMtube	muscle
21	chr20:13007800-13012400	Enhancers	Placenta Amnion	Placenta Amnion
22	chr20:13007800-13014200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr20:13007800-13016200	Weak transcription	Left Ventricle	heart
24	chr20:13008000-13011800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr20:13008200-13010200	Weak transcription	Fetal Intestine Small	intestine
26	chr20:13008200-13011000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr20:13008400-13010400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr20:13008400-13013000	Weak transcription	Liver	Liver
29	chr20:13008400-13014600	Genic enhancers	Placenta	Placenta
30	chr20:13008600-13010000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr20:13008600-13010400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:13008600-13010400	Enhancers	Osteobl	bone
33	chr20:13008600-13011000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr20:13008600-13011400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr20:13008600-13011400	Enhancers	NHLF	lung
36	chr20:13008600-13011600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr20:13008600-13011600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr20:13008600-13011600	Enhancers	NH-A	brain
39	chr20:13008800-13010400	Weak transcription	Fetal Intestine Large	intestine
40	chr20:13009200-13010400	Enhancers	Hela-S3	cervix
41	chr20:13009200-13011600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr20:13009400-13010800	Enhancers	Adipose Nuclei	Adipose
43	chr20:13009400-13011000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr20:13009400-13011400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr20:13009400-13011400	Enhancers	HUVEC	blood vessel
46	chr20:13009400-13011600	Enhancers	NHDF-Ad	bronchial
47	chr20:13009400-13012000	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr20:13009600-13010400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr20:13009600-13010400	Enhancers	A549	lung
50	chr20:13009600-13011400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links