Variant report

Variant	rs243885
Chromosome Location	chr20:13051492-13051493
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	chr20:13046904..13049128-chr20:13050831..13053226,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1346937	0.92[ASN][1000 genomes]
rs1431431	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1431432	0.92[ASN][1000 genomes]
rs171501	0.83[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap]
rs187236	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254015	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2327690	0.82[CHB][hapmap]
rs243880	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs243886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs243887	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs243888	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs243889	0.83[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs243891	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2749391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848770	0.82[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.80[ASN][1000 genomes]
rs6078899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6131438	0.82[CHB][hapmap]
rs6134759	0.94[ASN][1000 genomes]
rs845729	0.83[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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
15	esv3425983	chr20:13046768-13461834	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13028400-13060200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr20:13030600-13074000	Weak transcription	Ovary	ovary
3	chr20:13039600-13065600	Weak transcription	Thymus	Thymus
4	chr20:13040600-13052400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr20:13042600-13076800	Weak transcription	Pancreas	Pancrea
6	chr20:13042800-13054200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr20:13046800-13054200	Weak transcription	Aorta	Aorta
8	chr20:13047200-13052400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:13047200-13054200	Weak transcription	Right Ventricle	heart
10	chr20:13049200-13058600	Strong transcription	Placenta	Placenta
11	chr20:13049400-13052400	Weak transcription	Liver	Liver
12	chr20:13049400-13074000	Weak transcription	Adipose Nuclei	Adipose
13	chr20:13049600-13056800	Strong transcription	HepG2	liver
14	chr20:13049600-13071000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr20:13049600-13121800	Weak transcription	Primary T cells from cord blood	blood
16	chr20:13049800-13054800	Weak transcription	Esophagus	oesophagus
17	chr20:13049800-13055000	Weak transcription	NHEK	skin
18	chr20:13049800-13055600	Strong transcription	Fetal Intestine Small	intestine
19	chr20:13049800-13060400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr20:13049800-13074200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr20:13049800-13074600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:13049800-13117600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr20:13050000-13053200	Weak transcription	Fetal Intestine Large	intestine
24	chr20:13050000-13054600	Weak transcription	Lung	lung
25	chr20:13050000-13062800	Weak transcription	Stomach Mucosa	stomach
26	chr20:13050400-13060400	Weak transcription	Left Ventricle	heart
27	chr20:13051400-13052600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links