Variant report

Variant	rs230509
Chromosome Location	chr4:103478265-103478266
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	chr4:103420331..103423503-chr4:103475320..103478755,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109320	Chromatin interaction
ENSG00000260651	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs11723120	0.83[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs118882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12509517	0.80[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs12648696	0.89[CHB][hapmap]
rs1585213	1.00[JPT][hapmap]
rs1585215	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1598859	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1599961	1.00[JPT][hapmap]
rs17032683	1.00[YRI][hapmap]
rs17032705	1.00[JPT][hapmap]
rs170731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1801	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2085549	1.00[YRI][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230491	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230493	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230504	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230505	1.00[JPT][hapmap]
rs230511	1.00[CEU][hapmap]
rs230514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230526	1.00[JPT][hapmap]
rs230528	1.00[JPT][hapmap]
rs230529	1.00[JPT][hapmap]
rs230531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230533	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs230535	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230539	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs230540	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs230541	0.91[JPT][hapmap]
rs230542	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs2903281	1.00[YRI][hapmap]
rs3755867	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	1.00[JPT][hapmap]
rs3774936	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3774963	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3774964	0.90[JPT][hapmap]
rs3817685	0.95[JPT][hapmap]
rs3821958	0.91[JPT][hapmap]
rs4235404	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4456957	1.00[YRI][hapmap]
rs4648011	1.00[JPT][hapmap]
rs4648055	0.88[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs4648058	0.91[JPT][hapmap]
rs4648068	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4648085	1.00[YRI][hapmap]
rs4648133	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs4698858	0.89[JPT][hapmap]
rs4698861	0.82[CEU][hapmap]
rs4699030	0.91[JPT][hapmap]
rs747559	1.00[JPT][hapmap]
rs9790601	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs980455	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830020	chr4:103387343-103581284	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1003490	chr4:103391483-103521772	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv1004030	chr4:103419352-103504042	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv537203	chr4:103419352-103504042	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:103440200-103478600	Weak transcription	Right Ventricle	heart
3	chr4:103440200-103488200	Weak transcription	Gastric	stomach
4	chr4:103441400-103482000	Weak transcription	Spleen	Spleen
5	chr4:103443200-103496000	Weak transcription	A549	lung
6	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:103461200-103487800	Weak transcription	Colonic Mucosa	Colon
8	chr4:103461200-103490400	Weak transcription	Dnd41	blood
9	chr4:103461600-103485400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:103461600-103496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:103463200-103481800	Weak transcription	Fetal Thymus	thymus
12	chr4:103464600-103488200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:103466600-103481200	Weak transcription	Fetal Intestine Small	intestine
14	chr4:103466800-103498600	Weak transcription	Placenta	Placenta
15	chr4:103467000-103495600	Weak transcription	HepG2	liver
16	chr4:103467200-103485400	Weak transcription	HMEC	breast
17	chr4:103468800-103490400	Weak transcription	Stomach Mucosa	stomach
18	chr4:103469600-103498000	Weak transcription	Esophagus	oesophagus
19	chr4:103469800-103481200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:103470000-103480800	Weak transcription	Lung	lung
21	chr4:103470000-103482600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr4:103470000-103483000	Weak transcription	Pancreas	Pancrea
23	chr4:103470000-103485400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:103470000-103485400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr4:103470000-103485400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:103470000-103498000	Weak transcription	Fetal Stomach	stomach
27	chr4:103470200-103478600	Weak transcription	Left Ventricle	heart
28	chr4:103470400-103482000	Weak transcription	Ovary	ovary
29	chr4:103470800-103484000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr4:103472600-103480600	Weak transcription	Right Atrium	heart
31	chr4:103473400-103481000	Weak transcription	Liver	Liver
32	chr4:103473400-103481000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:103473400-103481600	Weak transcription	Fetal Intestine Large	intestine
34	chr4:103473400-103482000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
36	chr4:103473600-103481600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:103473600-103481800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:103473600-103482400	Weak transcription	Psoas Muscle	Psoas
39	chr4:103473600-103488200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr4:103473600-103498000	Weak transcription	Aorta	Aorta
41	chr4:103474000-103481400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr4:103474200-103478600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr4:103474200-103480800	Weak transcription	Small Intestine	intestine
44	chr4:103474200-103485400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:103474400-103480800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr4:103474400-103481200	Weak transcription	Fetal Lung	lung
47	chr4:103474400-103483000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr4:103474400-103485400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr4:103474600-103481200	Genic enhancers	Primary T helper cells PMA-I stimulated	--
50	chr4:103474800-103480400	Strong transcription	Monocytes-CD14+_RO01746	blood

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