Variant report

Variant	rs230491
Chromosome Location	chr4:103484615-103484616
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	chr4:103480320..103483101-chr4:103483579..103486269,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1005819	0.91[JPT][hapmap]
rs1020760	0.91[JPT][hapmap]
rs11722146	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11723120	0.92[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs118882	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12509517	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs12648696	0.89[CHB][hapmap]
rs1585213	1.00[JPT][hapmap]
rs1585215	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1598859	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1599961	1.00[JPT][hapmap]
rs17032705	1.00[JPT][hapmap]
rs170731	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1801	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs2168805	0.95[JPT][hapmap]
rs230492	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs230495	1.00[JPT][hapmap]
rs230496	1.00[JPT][hapmap]
rs230498	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230500	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap]
rs230505	1.00[JPT][hapmap]
rs230509	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230511	0.92[CEU][hapmap]
rs230514	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230515	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230516	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230519	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230520	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230521	1.00[JPT][hapmap]
rs230525	0.88[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	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230532	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230533	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230534	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230535	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs230539	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs230540	0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs230541	0.91[JPT][hapmap]
rs230542	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs3755867	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs3774933	1.00[JPT][hapmap]
rs3774936	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774937	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3774938	1.00[JPT][hapmap]
rs3774956	0.95[JPT][hapmap]
rs3774959	0.96[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	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs4648011	1.00[JPT][hapmap]
rs4648055	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4648058	0.91[JPT][hapmap]
rs4648068	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs4648133	0.81[CEU][hapmap];0.81[CHB][hapmap]
rs4698858	0.89[JPT][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:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103440000-103484800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:103440200-103488200	Weak transcription	Gastric	stomach
3	chr4:103443200-103496000	Weak transcription	A549	lung
4	chr4:103445000-103496600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:103461200-103487800	Weak transcription	Colonic Mucosa	Colon
6	chr4:103461200-103490400	Weak transcription	Dnd41	blood
7	chr4:103461600-103485400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:103461600-103496400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:103464600-103488200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:103466800-103498600	Weak transcription	Placenta	Placenta
11	chr4:103467000-103495600	Weak transcription	HepG2	liver
12	chr4:103467200-103485400	Weak transcription	HMEC	breast
13	chr4:103468800-103490400	Weak transcription	Stomach Mucosa	stomach
14	chr4:103469600-103498000	Weak transcription	Esophagus	oesophagus
15	chr4:103470000-103485400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr4:103470000-103485400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:103470000-103485400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:103470000-103498000	Weak transcription	Fetal Stomach	stomach
19	chr4:103473400-103524600	Weak transcription	Fetal Brain Male	brain
20	chr4:103473600-103488200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:103473600-103498000	Weak transcription	Aorta	Aorta
22	chr4:103474200-103485400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:103474400-103485400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:103475000-103496600	Weak transcription	HUVEC	blood vessel
25	chr4:103475200-103485200	Weak transcription	NHEK	skin
26	chr4:103475200-103496400	Weak transcription	Hela-S3	cervix
27	chr4:103476000-103498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:103476200-103485200	Weak transcription	NH-A	brain
29	chr4:103476200-103491200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr4:103476400-103498000	Weak transcription	Fetal Muscle Leg	muscle
31	chr4:103476400-103498200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:103478200-103511800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr4:103478600-103498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:103479200-103497800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr4:103480400-103488000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr4:103481000-103484800	Weak transcription	Primary B cells from peripheral blood	blood
37	chr4:103481000-103487600	Weak transcription	Lung	lung
38	chr4:103481200-103487600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr4:103481600-103489000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr4:103481800-103485400	Weak transcription	NHLF	lung
41	chr4:103481800-103486400	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr4:103481800-103488200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:103482000-103485400	Weak transcription	Primary hematopoietic stem cells	blood
44	chr4:103482000-103488600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:103482200-103485800	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:103482200-103487800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:103482200-103488000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr4:103482200-103495400	Weak transcription	Fetal Thymus	thymus
49	chr4:103482200-103498000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr4:103482200-103498800	Weak transcription	Brain Cingulate Gyrus	brain

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