Variant report

Variant	rs4699349
Chromosome Location	chr4:99486957-99486958
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	chr4:99485403..99488335-chr4:99490236..99493906,4	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10002696	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs10006366	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs10018825	0.92[CEU][hapmap]
rs10021296	0.92[CEU][hapmap]
rs10025051	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs11097621	0.81[EUR][1000 genomes]
rs13108940	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs13141997	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs13149070	0.92[CEU][hapmap]
rs1528547	0.81[ASN][1000 genomes]
rs1534554	0.86[ASN][1000 genomes]
rs1534555	0.96[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1573478	0.96[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1893714	0.83[JPT][hapmap]
rs2037832	0.96[CEU][hapmap];0.93[JPT][hapmap]
rs2866016	1.00[JPT][hapmap]
rs2866017	0.91[CEU][hapmap]
rs4699343	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs4699345	0.93[JPT][hapmap]
rs4699348	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4699353	0.81[JPT][hapmap]
rs4699354	1.00[JPT][hapmap]
rs4699639	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs4699640	0.92[CEU][hapmap];0.94[JPT][hapmap]
rs4699644	0.92[CEU][hapmap]
rs6532742	0.92[CEU][hapmap]
rs6532751	1.00[JPT][hapmap]
rs6831643	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6837359	0.88[CEU][hapmap]
rs71600251	0.81[ASN][1000 genomes]
rs7672134	0.92[CEU][hapmap]
rs7678323	1.00[JPT][hapmap]
rs7691465	0.89[CHB][hapmap];0.84[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1004181	chr4:99208152-99529576	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2760882	chr4:99460485-99521345	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99466800-99501600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:99477400-99487600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:99477400-99487600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:99479000-99490200	Weak transcription	HSMMtube	muscle
5	chr4:99479000-99506400	Weak transcription	Aorta	Aorta
6	chr4:99479200-99487000	Weak transcription	NH-A	brain
7	chr4:99479200-99487200	Weak transcription	NHLF	lung
8	chr4:99479800-99487000	Weak transcription	NHDF-Ad	bronchial
9	chr4:99480400-99487200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr4:99483000-99487000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr4:99483200-99487600	Weak transcription	Esophagus	oesophagus
12	chr4:99483200-99495800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr4:99483400-99487000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:99483400-99498800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:99484000-99487600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:99484200-99495400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:99484800-99487200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr4:99484800-99487800	Enhancers	Brain Substantia Nigra	brain
19	chr4:99485000-99490800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:99485000-99501400	Weak transcription	HUVEC	blood vessel
21	chr4:99485200-99487000	Enhancers	Brain Cingulate Gyrus	brain
22	chr4:99485200-99487200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr4:99485200-99487800	Enhancers	Brain Anterior Caudate	brain
24	chr4:99485400-99488000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr4:99485400-99491000	Enhancers	Fetal Brain Male	brain
26	chr4:99485400-99495000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr4:99485600-99487400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr4:99485600-99487600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:99485600-99488000	Enhancers	HUES48 Cell Line	embryonic stem cell
30	chr4:99485600-99488200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr4:99485600-99488400	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr4:99485600-99489200	Enhancers	Fetal Heart	heart
33	chr4:99485800-99488000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:99485800-99488400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr4:99486000-99487000	Enhancers	Brain Hippocampus Middle	brain
36	chr4:99486000-99487000	Enhancers	Colon Smooth Muscle	Colon
37	chr4:99486000-99487800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr4:99486000-99488000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:99486000-99488000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr4:99486000-99488200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:99486000-99488200	Enhancers	Fetal Brain Female	brain
42	chr4:99486000-99488400	Enhancers	H1 Cell Line	embryonic stem cell
43	chr4:99486000-99488400	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr4:99486000-99488400	Enhancers	Rectal Smooth Muscle	rectum
45	chr4:99486000-99488800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr4:99486000-99489000	Enhancers	Ovary	ovary
47	chr4:99486000-99489200	Enhancers	Fetal Thymus	thymus
48	chr4:99486000-99491000	Enhancers	Thymus	Thymus
49	chr4:99486000-99491400	Enhancers	Fetal Muscle Leg	muscle
50	chr4:99486200-99487200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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