Variant report

Variant	rs456000
Chromosome Location	chr4:187598456-187598457
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	chr4:187589219..187591473-chr4:187596376..187599328,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs162063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs162182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs167854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs192997	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28532777	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs327077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs327078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs327111	0.84[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3733409	0.81[CHB][hapmap]
rs462509	0.91[CEU][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][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	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	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
6	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
7	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
8	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
9	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
10	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:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:187573000-187605400	Weak transcription	Gastric	stomach
2	chr4:187583000-187614400	Weak transcription	Colonic Mucosa	Colon
3	chr4:187587600-187610200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:187588400-187604400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:187591200-187604000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:187591200-187607000	Weak transcription	Adipose Nuclei	Adipose
7	chr4:187591200-187614400	Weak transcription	Ovary	ovary
8	chr4:187591400-187603800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr4:187591400-187604400	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:187592200-187604000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr4:187592200-187605400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr4:187594000-187605800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr4:187594200-187603800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr4:187595000-187599000	Enhancers	Colon Smooth Muscle	Colon
15	chr4:187595200-187599400	Enhancers	Rectal Smooth Muscle	rectum
16	chr4:187595600-187598600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr4:187595800-187603800	Weak transcription	Left Ventricle	heart
18	chr4:187596000-187599000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:187596000-187603800	Weak transcription	Fetal Intestine Large	intestine
20	chr4:187596000-187604000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:187596400-187598600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr4:187596400-187599000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:187596600-187598600	Enhancers	HSMMtube	muscle
24	chr4:187596800-187598600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:187596800-187598600	Enhancers	HMEC	breast
26	chr4:187596800-187598800	Enhancers	Stomach Smooth Muscle	stomach
27	chr4:187596800-187598800	Enhancers	NHLF	lung
28	chr4:187596800-187599200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:187596800-187599200	Enhancers	Fetal Heart	heart
30	chr4:187596800-187602800	Weak transcription	Fetal Intestine Small	intestine
31	chr4:187597000-187598600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:187597000-187599000	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr4:187597000-187599000	Enhancers	NH-A	brain
34	chr4:187597000-187599000	Enhancers	NHDF-Ad	bronchial
35	chr4:187597000-187599200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:187597000-187599200	Enhancers	Fetal Kidney	kidney
37	chr4:187597000-187599400	Enhancers	Osteobl	bone
38	chr4:187597000-187603200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr4:187597000-187603800	Weak transcription	Pancreas	Pancrea
40	chr4:187597200-187599000	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr4:187597200-187599400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr4:187597600-187598600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:187597600-187598600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:187597600-187598600	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr4:187597600-187598600	Enhancers	Fetal Lung	lung
46	chr4:187597600-187598800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:187597600-187599200	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr4:187597600-187599200	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr4:187597800-187598600	Enhancers	Stomach Mucosa	stomach
50	chr4:187597800-187599000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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