Variant report

Variant	rs6041870
Chromosome Location	chr20:13092482-13092483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1014311	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1014379	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4375935	0.95[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs4428077	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4814203	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs6033621	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6041859	1.00[CEU][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes]
rs6041860	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs6041863	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6041878	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6041879	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6109718	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs720147	0.81[EUR][1000 genomes]
rs734261	1.00[ASW][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs743092	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs879697	0.95[EUR][1000 genomes]
rs879698	0.95[EUR][1000 genomes]
rs882301	0.81[AMR][1000 genomes];0.96[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	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
14	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:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:13049600-13121800	Weak transcription	Primary T cells from cord blood	blood
2	chr20:13049800-13117600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:13055800-13092600	Weak transcription	Aorta	Aorta
4	chr20:13071600-13108000	Weak transcription	Left Ventricle	heart
5	chr20:13072600-13100400	Weak transcription	Fetal Stomach	stomach
6	chr20:13073400-13101400	Weak transcription	Fetal Muscle Leg	muscle
7	chr20:13075400-13096400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr20:13075800-13092800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr20:13080800-13102400	Weak transcription	Thymus	Thymus
10	chr20:13083600-13095800	Weak transcription	Esophagus	oesophagus
11	chr20:13083600-13114600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr20:13086200-13094600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr20:13086200-13107600	Weak transcription	NHEK	skin
14	chr20:13086600-13123200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr20:13087000-13100400	Weak transcription	Fetal Lung	lung
16	chr20:13087000-13108200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr20:13087200-13101600	Strong transcription	Placenta	Placenta
18	chr20:13087800-13107200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr20:13088800-13103000	Strong transcription	Fetal Intestine Large	intestine
20	chr20:13090000-13094600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr20:13090000-13094800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr20:13090800-13093200	Strong transcription	Ovary	ovary
23	chr20:13090800-13093800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:13090800-13094800	Strong transcription	Fetal Intestine Small	intestine
25	chr20:13091000-13093600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr20:13091000-13094200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr20:13091200-13092800	Enhancers	Liver	Liver
28	chr20:13091800-13092800	Genic enhancers	HepG2	liver
29	chr20:13091800-13093600	Strong transcription	Adipose Nuclei	Adipose
30	chr20:13091800-13127800	Weak transcription	Fetal Kidney	kidney
31	chr20:13092000-13093400	Strong transcription	Lung	lung
32	chr20:13092000-13094600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr20:13092400-13092600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr20:13092400-13092800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr20:13092400-13094200	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr20:13092400-13096200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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