Variant report

Variant	rs11724817
Chromosome Location	chr4:187589798-187589799
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:187589219..187591473-chr4:187596376..187599328,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10002129	0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11723473	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11939575	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs13123522	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1877731	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs327070	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs327109	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs327110	0.95[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs327113	0.88[ASN][1000 genomes]
rs455935	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs466535	0.82[CHB][hapmap]
rs4862723	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57663778	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6850371	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs950113	0.86[CHB][hapmap]
rs997696	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025088	chr4:187407683-187674585	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1025244	chr4:187419770-188284813	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1034212	chr4:187437895-188030805	Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Strong transcription 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	20 gene(s)	inside rSNPs	diseases
4	nsv537438	chr4:187437895-188030805	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv1015619	chr4:187442453-187595058	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1023800	chr4:187444255-187593799	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv532745	chr4:187471692-188205443	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv1022262	chr4:187475862-187848284	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
9	nsv1024705	chr4:187534005-187849091	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1026970	chr4:187537418-187913351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv596440	chr4:187538133-187848075	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv881509	chr4:187574398-187614434	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187573000-187605400	Weak transcription	Gastric	stomach
2	chr4:187573200-187590200	Weak transcription	Left Ventricle	heart
3	chr4:187573200-187590200	Weak transcription	Pancreas	Pancrea
4	chr4:187573200-187596600	Weak transcription	Esophagus	oesophagus
5	chr4:187573400-187590400	Weak transcription	Ovary	ovary
6	chr4:187573400-187590600	Weak transcription	Right Atrium	heart
7	chr4:187574400-187591600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:187575200-187590200	Weak transcription	Fetal Heart	heart
9	chr4:187575400-187590400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:187575800-187590200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:187576200-187590400	Weak transcription	Placenta	Placenta
12	chr4:187579400-187590200	Weak transcription	Brain Anterior Caudate	brain
13	chr4:187579600-187590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:187579600-187590600	Weak transcription	Brain Hippocampus Middle	brain
15	chr4:187579600-187595400	Weak transcription	Brain Substantia Nigra	brain
16	chr4:187580400-187590200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:187580400-187590400	Weak transcription	Lung	lung
18	chr4:187580400-187590600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr4:187582800-187590600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr4:187583000-187590000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr4:187583000-187590200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:187583000-187590200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr4:187583000-187590400	Weak transcription	Aorta	Aorta
24	chr4:187583000-187590400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:187583000-187590400	Weak transcription	Right Ventricle	heart
26	chr4:187583000-187614400	Weak transcription	Colonic Mucosa	Colon
27	chr4:187583200-187590600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:187583200-187591000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:187583400-187591000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:187583800-187590400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:187584800-187590400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:187585000-187589800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:187585000-187589800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:187585000-187590200	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr4:187585400-187590200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:187586000-187590400	Weak transcription	Adipose Nuclei	Adipose
37	chr4:187587400-187591600	Genic enhancers	HSMM	muscle
38	chr4:187587400-187591600	Enhancers	HSMMtube	muscle
39	chr4:187587600-187589800	Strong transcription	NHDF-Ad	bronchial
40	chr4:187587600-187590000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:187587600-187591000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:187587600-187610200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr4:187587800-187589800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr4:187587800-187597000	Weak transcription	Fetal Kidney	kidney
45	chr4:187588000-187590400	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr4:187588000-187590400	Strong transcription	NHEK	skin
47	chr4:187588000-187590800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr4:187588000-187594200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:187588200-187590200	Weak transcription	Colon Smooth Muscle	Colon
50	chr4:187588200-187590400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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