Variant report

Variant	rs72950533
Chromosome Location	chr4:106345910-106345911
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	chr4:106340779..106343973-chr4:106344387..106347372,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11097889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11737582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12108480	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12108594	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035483	1.00[AMR][1000 genomes]
rs17035566	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035569	0.89[AFR][1000 genomes]
rs17035594	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035595	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035605	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17035618	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28417349	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35695427	1.00[AMR][1000 genomes]
rs41485844	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41505250	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57620916	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57624740	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60734979	1.00[AMR][1000 genomes]
rs72950516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950537	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950550	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950565	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950590	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950594	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72950598	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952274	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952276	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952281	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952296	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952301	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72952362	1.00[AMR][1000 genomes]
rs72952393	1.00[AMR][1000 genomes]
rs72962224	1.00[AMR][1000 genomes]
rs72962234	1.00[AMR][1000 genomes]
rs72962246	1.00[AMR][1000 genomes]
rs72962257	1.00[AMR][1000 genomes]
rs72962270	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72962273	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72963011	1.00[AMR][1000 genomes]
rs72963039	1.00[AMR][1000 genomes]
rs72964211	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964213	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964224	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964228	0.87[AFR][1000 genomes]
rs72964242	0.89[AFR][1000 genomes]
rs72964244	0.89[AFR][1000 genomes]
rs72964262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72964271	0.89[AFR][1000 genomes]
rs72964288	0.89[AFR][1000 genomes]
rs7695564	1.00[AMR][1000 genomes]
rs9968337	0.89[AFR][1000 genomes]
rs9968402	0.89[AFR][1000 genomes]
rs9968408	1.00[AMR][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	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv830027	chr4:106222010-106406738	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106279000-106347400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:106287600-106357000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr4:106287800-106347600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:106290000-106347400	Weak transcription	Fetal Kidney	kidney
5	chr4:106309400-106351000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr4:106321000-106346000	Weak transcription	Hela-S3	cervix
7	chr4:106321400-106367200	Weak transcription	HUVEC	blood vessel
8	chr4:106321600-106356200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:106321800-106353600	Weak transcription	HMEC	breast
10	chr4:106323600-106372800	Weak transcription	Stomach Mucosa	stomach
11	chr4:106324200-106347000	Weak transcription	Fetal Lung	lung
12	chr4:106326000-106356400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:106326000-106356600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:106326000-106363200	Weak transcription	Colon Smooth Muscle	Colon
15	chr4:106326200-106347600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:106327200-106346200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:106327200-106346800	Weak transcription	NHDF-Ad	bronchial
18	chr4:106327200-106365200	Weak transcription	Osteobl	bone
19	chr4:106327200-106389200	Weak transcription	Small Intestine	intestine
20	chr4:106327200-106390600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr4:106330400-106347200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:106330600-106356400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr4:106331400-106346000	Weak transcription	Brain Substantia Nigra	brain
24	chr4:106334000-106346000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:106334800-106347600	Weak transcription	A549	lung
26	chr4:106336400-106347600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr4:106336400-106347600	Weak transcription	NHEK	skin
28	chr4:106336600-106346200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr4:106336600-106347000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:106336600-106356400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:106336800-106346000	Weak transcription	Ovary	ovary
32	chr4:106336800-106346800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:106336800-106346800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:106336800-106347000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr4:106336800-106347400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr4:106336800-106347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:106336800-106347400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:106336800-106347400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr4:106336800-106347400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:106336800-106347400	Weak transcription	Colonic Mucosa	Colon
41	chr4:106336800-106347400	Weak transcription	Lung	lung
42	chr4:106336800-106347400	Weak transcription	Pancreas	Pancrea
43	chr4:106336800-106347400	Weak transcription	Spleen	Spleen
44	chr4:106336800-106347600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr4:106336800-106376400	Weak transcription	Right Ventricle	heart
46	chr4:106336800-106387800	Weak transcription	NHLF	lung
47	chr4:106337000-106346800	Weak transcription	Fetal Stomach	stomach
48	chr4:106337000-106347000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr4:106337000-106347000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:106337000-106347400	Weak transcription	Aorta	Aorta

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