Variant report

Variant	rs28407050
Chromosome Location	chr4:99389617-99389618
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	chr4:99388707..99389636-chr4:99749659..99750550,4	MCF-7	breast:

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10001137	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003496	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10022073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353633	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027393	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027597	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027617	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464398	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	1.00[AMR][1000 genomes]
rs28494643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28497963	0.91[AMR][1000 genomes]
rs28503871	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28649922	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28664868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28705201	0.80[AMR][1000 genomes]
rs28731135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28883979	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56805018	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	1.00[AMR][1000 genomes]
rs60544326	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6831386	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	1.00[AMR][1000 genomes]
rs73832317	1.00[EUR][1000 genomes]
rs73834403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834489	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655622	0.91[AMR][1000 genomes]
rs7656868	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998801	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	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
4	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	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

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99388000-99390200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:99388600-99389800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:99388600-99390200	Enhancers	Stomach Mucosa	stomach
4	chr4:99388800-99389800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:99388800-99390400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr4:99389200-99389800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr4:99389200-99389800	Weak transcription	Psoas Muscle	Psoas
8	chr4:99389200-99389800	Weak transcription	Right Atrium	heart
9	chr4:99389200-99390000	Bivalent Enhancer	Fetal Intestine Small	intestine
10	chr4:99389200-99390000	Enhancers	Fetal Stomach	stomach
11	chr4:99389200-99390000	Weak transcription	Right Ventricle	heart
12	chr4:99389200-99390000	Enhancers	Skeletal Muscle Female	skeletal muscle
13	chr4:99389200-99390000	Enhancers	Small Intestine	intestine
14	chr4:99389200-99390200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:99389200-99390200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr4:99389200-99390200	Enhancers	Left Ventricle	heart
17	chr4:99389200-99390400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr4:99389200-99390400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:99389200-99390400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:99389200-99390400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr4:99389200-99390400	Enhancers	Fetal Lung	lung
22	chr4:99389200-99390400	Enhancers	HMEC	breast
23	chr4:99389200-99390600	Enhancers	Fetal Muscle Leg	muscle
24	chr4:99389200-99390800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:99389200-99391200	Weak transcription	Thymus	Thymus
26	chr4:99389200-99391400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr4:99389200-99391400	Weak transcription	Brain Germinal Matrix	brain
28	chr4:99389200-99391400	Enhancers	Fetal Heart	heart
29	chr4:99389200-99392000	Enhancers	Brain Substantia Nigra	brain
30	chr4:99389200-99392400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:99389200-99394400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr4:99389200-99395200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr4:99389200-99397400	Weak transcription	Fetal Brain Male	brain
34	chr4:99389200-99398200	Weak transcription	Aorta	Aorta
35	chr4:99389200-99403600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:99389200-99404000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr4:99389200-99404000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr4:99389200-99404000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr4:99389200-99404200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr4:99389200-99407000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:99389200-99413000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:99389400-99389800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:99389400-99389800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:99389400-99389800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:99389400-99389800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:99389400-99389800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr4:99389400-99389800	Weak transcription	Esophagus	oesophagus
48	chr4:99389400-99389800	Weak transcription	HSMM	muscle
49	chr4:99389400-99390000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr4:99389400-99390000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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