Variant report

Variant	rs459796
Chromosome Location	chr4:187601359-187601360
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	chr4:187600208..187602040-chr4:187645390..187648035,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000083857	Chromatin interaction

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

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

rs_ID	r²[population]
rs10002129	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs162181	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327107	1.00[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs327109	0.85[EUR][1000 genomes]
rs327110	0.93[CEU][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs327113	0.85[EUR][1000 genomes]
rs455600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs455935	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs461232	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818490	0.85[AFR][1000 genomes];0.91[AMR][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:70 , 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	chr4:187595800-187603800	Weak transcription	Left Ventricle	heart
15	chr4:187596000-187603800	Weak transcription	Fetal Intestine Large	intestine
16	chr4:187596000-187604000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr4:187596800-187602800	Weak transcription	Fetal Intestine Small	intestine
18	chr4:187597000-187603200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:187597000-187603800	Weak transcription	Pancreas	Pancrea
20	chr4:187598200-187603800	Weak transcription	Fetal Stomach	stomach
21	chr4:187598200-187604000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr4:187598200-187604000	Weak transcription	Right Atrium	heart
23	chr4:187598200-187604000	Weak transcription	Right Ventricle	heart
24	chr4:187598200-187606000	Weak transcription	Small Intestine	intestine
25	chr4:187598200-187614400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr4:187598400-187609400	Weak transcription	Aorta	Aorta
27	chr4:187598600-187601400	Weak transcription	HSMM	muscle
28	chr4:187598600-187601600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:187598600-187601600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:187598600-187602600	Weak transcription	HMEC	breast
31	chr4:187598600-187603800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:187598600-187603800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr4:187598600-187604400	Weak transcription	Fetal Lung	lung
34	chr4:187598600-187605400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr4:187598600-187605400	Weak transcription	Stomach Mucosa	stomach
36	chr4:187598600-187605800	Weak transcription	HSMMtube	muscle
37	chr4:187598600-187606000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr4:187598600-187606400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:187598800-187604000	Weak transcription	NHLF	lung
40	chr4:187598800-187604400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr4:187598800-187606000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:187599000-187601400	Weak transcription	NHEK	skin
43	chr4:187599000-187601600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:187599000-187601600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr4:187599000-187602400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:187599000-187602600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr4:187599000-187603800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:187599000-187605800	Weak transcription	NH-A	brain
49	chr4:187599000-187606000	Weak transcription	NHDF-Ad	bronchial
50	chr4:187599200-187603000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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