Variant report

Variant	rs10477889
Chromosome Location	chr5:107682386-107682387
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	chr5:107674221..107676262-chr5:107681301..107685297,3	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10055785	0.94[JPT][hapmap];0.91[YRI][hapmap]
rs10056658	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10057274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10057905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10070565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10072616	0.83[ASN][1000 genomes]
rs10464048	0.82[CEU][hapmap]
rs10477894	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11240960	0.87[JPT][hapmap]
rs11747188	0.90[YRI][hapmap]
rs12519091	0.87[JPT][hapmap]
rs12521975	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13174270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13174635	0.81[CEU][hapmap]
rs1421971	0.94[JPT][hapmap]
rs169592	1.00[YRI][hapmap]
rs1839224	0.91[EUR][1000 genomes]
rs2044711	0.90[EUR][1000 genomes]
rs2122157	0.91[EUR][1000 genomes]
rs286760	1.00[YRI][hapmap]
rs286762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs286765	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs286766	0.93[CHB][hapmap];0.84[JPT][hapmap];0.90[YRI][hapmap];0.87[EUR][1000 genomes]
rs286772	1.00[YRI][hapmap]
rs28868900	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2922409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2922410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2922411	0.91[EUR][1000 genomes]
rs2922413	0.91[EUR][1000 genomes]
rs2922414	0.90[EUR][1000 genomes]
rs2922415	0.90[EUR][1000 genomes]
rs2922416	0.90[EUR][1000 genomes]
rs2922419	0.91[EUR][1000 genomes]
rs2922434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2966794	0.91[EUR][1000 genomes]
rs2966805	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[EUR][1000 genomes]
rs2966806	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs2966807	0.82[EUR][1000 genomes]
rs2966808	1.00[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs2966809	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs2966810	0.91[EUR][1000 genomes]
rs2966812	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.91[EUR][1000 genomes]
rs2966815	0.90[EUR][1000 genomes]
rs2966817	0.90[EUR][1000 genomes]
rs2966819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs34019963	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34088844	0.81[AFR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35053804	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35624833	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35959276	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs399438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs4276393	0.91[EUR][1000 genomes]
rs4385196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4957750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4957757	0.93[JPT][hapmap]
rs66855775	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6860212	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs715638	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv882684	chr5:107521677-107695558	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830442	chr5:107539150-107697020	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv882685	chr5:107564746-107695558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv882686	chr5:107564746-107769095	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv882687	chr5:107595383-107695558	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv882688	chr5:107595383-107715746	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv882689	chr5:107595383-108299744	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	esv2755544	chr5:107614101-107748101	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1018396	chr5:107634887-107684450	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107615000-107705600	Weak transcription	Left Ventricle	heart
2	chr5:107639800-107697200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:107648000-107704800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:107654600-107709400	Weak transcription	Pancreas	Pancrea
5	chr5:107656000-107686400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr5:107658600-107709200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr5:107659400-107700000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr5:107661600-107687600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:107661800-107696400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr5:107662800-107682800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr5:107663800-107709400	Weak transcription	Primary T cells from cord blood	blood
12	chr5:107667600-107709200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr5:107668600-107706800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:107668800-107699600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:107669200-107685400	Weak transcription	Adipose Nuclei	Adipose
16	chr5:107669200-107708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr5:107669400-107700400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr5:107670000-107686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:107670000-107702400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr5:107675000-107709200	Weak transcription	Fetal Thymus	thymus
21	chr5:107675800-107700000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:107676000-107696200	Weak transcription	Fetal Lung	lung
23	chr5:107676800-107702400	Weak transcription	Fetal Kidney	kidney
24	chr5:107677400-107700800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:107677800-107684800	Weak transcription	Osteobl	bone
26	chr5:107677800-107687200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr5:107677800-107700400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:107677800-107709200	Weak transcription	Ovary	ovary
29	chr5:107678000-107684000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:107678400-107699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:107679200-107684000	Weak transcription	Brain Substantia Nigra	brain
32	chr5:107679200-107688600	Weak transcription	Primary B cells from cord blood	blood
33	chr5:107679200-107706800	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr5:107679600-107699800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr5:107679800-107682400	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:107679800-107683000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr5:107679800-107696800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr5:107679800-107705600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr5:107680000-107683800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr5:107680000-107706800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:107680400-107682400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr5:107680400-107707600	Weak transcription	Fetal Intestine Large	intestine
43	chr5:107680600-107687400	Weak transcription	Liver	Liver
44	chr5:107680600-107690000	Weak transcription	Fetal Intestine Small	intestine
45	chr5:107680800-107697400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr5:107681000-107683400	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr5:107681200-107686000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:107681400-107693600	Weak transcription	GM12878-XiMat	blood
49	chr5:107681600-107699800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:107682000-107703600	Weak transcription	Dnd41	blood

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