Variant report

Variant	rs4957553
Chromosome Location	chr5:107679879-107679880
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107678990..107681640-chr5:107716469..107719656,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145743	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10036343	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10041907	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10063449	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10063866	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs10071595	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10072270	0.96[CEU][hapmap];0.95[EUR][1000 genomes]
rs10075907	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs10455007	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11743651	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11744374	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13178456	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1849011	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2029104	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2044709	0.85[EUR][1000 genomes]
rs2044710	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2112306	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2122158	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2167001	0.91[EUR][1000 genomes]
rs2416188	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28497144	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs286764	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs286767	0.81[EUR][1000 genomes]
rs2922423	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2922424	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2922426	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs2922427	0.90[EUR][1000 genomes]
rs2922428	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2922429	0.91[EUR][1000 genomes]
rs2922430	0.82[EUR][1000 genomes]
rs2922433	0.88[EUR][1000 genomes]
rs2966795	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2966797	0.91[EUR][1000 genomes]
rs2966799	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2966812	0.83[YRI][hapmap]
rs34298471	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35053804	0.80[AFR][1000 genomes]
rs3756573	0.85[YRI][hapmap]
rs4541643	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4957554	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4957751	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4957753	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55896795	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57222565	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6596770	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6596771	0.81[EUR][1000 genomes]
rs6596777	0.89[EUR][1000 genomes]
rs6875297	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs6883082	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7708996	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7713705	0.81[CEU][hapmap]
rs7717747	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7726298	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9326725	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs962680	0.90[EUR][1000 genomes]
rs989001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv1030202	chr5:107634887-107680335	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	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
12	nsv1033956	chr5:107640933-107680335	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1029462	chr5:107645821-107680335	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

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	chr5:107662200-107681400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr5:107662800-107682800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:107663800-107709400	Weak transcription	Primary T cells from cord blood	blood
13	chr5:107667600-107709200	Weak transcription	Duodenum Mucosa	Duodenum
14	chr5:107668600-107706800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:107668800-107699600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:107669200-107685400	Weak transcription	Adipose Nuclei	Adipose
17	chr5:107669200-107708400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr5:107669400-107700400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:107670000-107686400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:107670000-107702400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:107675000-107709200	Weak transcription	Fetal Thymus	thymus
22	chr5:107675800-107700000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr5:107676000-107696200	Weak transcription	Fetal Lung	lung
24	chr5:107676800-107702400	Weak transcription	Fetal Kidney	kidney
25	chr5:107677400-107680800	Enhancers	Fetal Heart	heart
26	chr5:107677400-107700800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:107677600-107680800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr5:107677800-107684800	Weak transcription	Osteobl	bone
29	chr5:107677800-107687200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:107677800-107700400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:107677800-107709200	Weak transcription	Ovary	ovary
32	chr5:107678000-107680200	Weak transcription	Placenta	Placenta
33	chr5:107678000-107684000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:107678200-107680000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr5:107678200-107680400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr5:107678400-107699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr5:107678600-107680000	Strong transcription	Primary hematopoietic stem cells	blood
38	chr5:107679000-107680000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr5:107679200-107680600	Enhancers	Fetal Intestine Small	intestine
40	chr5:107679200-107684000	Weak transcription	Brain Substantia Nigra	brain
41	chr5:107679200-107688600	Weak transcription	Primary B cells from cord blood	blood
42	chr5:107679200-107706800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr5:107679400-107680400	Enhancers	Fetal Intestine Large	intestine
44	chr5:107679400-107680600	Enhancers	Liver	Liver
45	chr5:107679400-107680800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr5:107679600-107699800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:107679800-107680000	Enhancers	Psoas Muscle	Psoas
48	chr5:107679800-107680200	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr5:107679800-107682400	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr5:107679800-107683000	Weak transcription	Primary T helper cells fromperipheralblood	blood

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