Variant report

Variant	rs73834489
Chromosome Location	chr4:99355557-99355558
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	chr4:99352645..99355637-chr4:99364495..99366451,2	MCF-7	breast:

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10001137	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003061	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10006734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10010260	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013248	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017075	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10017827	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10022073	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10025311	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10026222	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10027925	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029895	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032785	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10034649	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10050289	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212883	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1024127	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10470953	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12331722	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353633	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16996571	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027393	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027526	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027538	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027559	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027596	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027597	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17027617	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28373747	1.00[EUR][1000 genomes]
rs28374939	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28407050	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28438716	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28446845	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28451188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28455818	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28459325	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28464398	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28472340	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28478192	0.91[AMR][1000 genomes]
rs28494643	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28497963	0.82[AMR][1000 genomes]
rs28503871	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28529663	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28558542	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28564255	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28589745	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28647503	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28649922	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28651612	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28664868	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28731135	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28786730	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28806635	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28807427	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28840158	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28882140	1.00[EUR][1000 genomes]
rs28883979	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28893208	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275691	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41275693	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41525749	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56805018	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59725407	0.91[AMR][1000 genomes]
rs60544326	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6831386	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6834495	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6858042	0.91[AMR][1000 genomes]
rs73832149	0.87[EUR][1000 genomes]
rs73832156	0.87[EUR][1000 genomes]
rs73832317	1.00[EUR][1000 genomes]
rs73834403	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834404	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834444	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834475	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73834479	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7655622	0.82[AMR][1000 genomes]
rs7656868	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7658383	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9307226	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9991668	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994467	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9995184	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997337	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997973	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9998801	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9999779	0.84[AFR][1000 genomes];1.00[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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99307000-99366200	Weak transcription	Fetal Brain Male	brain
2	chr4:99308600-99363200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:99325800-99367000	Weak transcription	Right Ventricle	heart
4	chr4:99334200-99355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:99334400-99361800	Weak transcription	Aorta	Aorta
6	chr4:99334400-99364600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:99334400-99366000	Weak transcription	Psoas Muscle	Psoas
8	chr4:99334400-99367400	Weak transcription	Small Intestine	intestine
9	chr4:99334400-99368800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:99336400-99365000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr4:99337200-99356000	Weak transcription	Esophagus	oesophagus
12	chr4:99337200-99363200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr4:99337600-99369800	Weak transcription	Fetal Heart	heart
14	chr4:99338400-99363200	Weak transcription	Spleen	Spleen
15	chr4:99339000-99363200	Weak transcription	Colonic Mucosa	Colon
16	chr4:99339000-99370200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:99340800-99370600	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:99341200-99365000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:99342600-99366600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:99342800-99356000	Weak transcription	Brain Angular Gyrus	brain
21	chr4:99342800-99361000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:99342800-99367400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr4:99342800-99370000	Weak transcription	Placenta	Placenta
24	chr4:99343000-99355600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:99343000-99355600	Weak transcription	Ovary	ovary
26	chr4:99343000-99355600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr4:99343000-99355800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:99343000-99356000	Weak transcription	Brain Substantia Nigra	brain
29	chr4:99343000-99363200	Weak transcription	HUVEC	blood vessel
30	chr4:99343000-99368000	Weak transcription	Gastric	stomach
31	chr4:99344200-99355800	Weak transcription	Fetal Stomach	stomach
32	chr4:99344200-99361800	Weak transcription	Lung	lung
33	chr4:99344200-99366200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:99344400-99356000	Weak transcription	HSMMtube	muscle
35	chr4:99344800-99355600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr4:99345000-99367200	Weak transcription	GM12878-XiMat	blood
37	chr4:99345800-99355600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:99345800-99355600	Weak transcription	Fetal Muscle Trunk	muscle
39	chr4:99345800-99356000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr4:99345800-99356000	Weak transcription	Pancreas	Pancrea
41	chr4:99346000-99355600	Weak transcription	Left Ventricle	heart
42	chr4:99346400-99371200	Weak transcription	Fetal Brain Female	brain
43	chr4:99346600-99365600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr4:99346800-99359000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr4:99346800-99363000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:99347600-99361800	Weak transcription	Fetal Intestine Small	intestine
47	chr4:99351600-99365200	Weak transcription	Stomach Mucosa	stomach
48	chr4:99352000-99358200	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr4:99352200-99355600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:99352200-99365200	Weak transcription	HepG2	liver

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