Variant report

Variant	rs10200389
Chromosome Location	chr2:210290736-210290737
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	chr2:210288971..210290856-chr2:210420793..210422129,13	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10153809	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174291	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185216	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10200539	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201740	0.94[EUR][1000 genomes]
rs10210266	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10932297	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10932301	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678209	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11889366	0.90[ASN][1000 genomes]
rs11900413	0.94[ASN][1000 genomes]
rs11904626	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614926	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12614974	0.95[ASN][1000 genomes]
rs12617330	0.93[ASN][1000 genomes]
rs12621534	0.93[ASN][1000 genomes]
rs12622130	0.93[ASN][1000 genomes]
rs12623404	0.96[ASN][1000 genomes]
rs12623555	0.92[ASN][1000 genomes]
rs12694180	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13005529	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13020975	0.93[EUR][1000 genomes]
rs13023264	0.90[ASN][1000 genomes]
rs13024490	0.93[ASN][1000 genomes]
rs13028173	0.93[ASN][1000 genomes]
rs13028553	0.93[ASN][1000 genomes]
rs13033819	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13034750	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13391766	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13391768	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1374333	0.93[ASN][1000 genomes]
rs1446596	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16842875	0.93[ASN][1000 genomes]
rs16842884	0.93[ASN][1000 genomes]
rs17236116	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028893	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123701	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28556312	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28558587	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28610349	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35424736	0.82[ASN][1000 genomes]
rs60358187	0.96[ASN][1000 genomes]
rs6435528	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6435529	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6733750	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6751612	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761283	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72492734	0.82[ASN][1000 genomes]
rs72995681	1.00[ASN][1000 genomes]
rs73060566	0.82[ASN][1000 genomes]
rs7557610	0.93[ASN][1000 genomes]
rs7563521	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7568431	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7568858	0.93[ASN][1000 genomes]
rs7569773	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7575409	0.93[ASN][1000 genomes]
rs7577392	0.94[ASN][1000 genomes]
rs7580883	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7593008	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7594469	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7594842	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595924	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7602104	0.93[ASN][1000 genomes]
rs7608377	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7608854	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288407	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs992028	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs993784	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9967799	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000214	chr2:209987607-210308626	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv536133	chr2:209987607-210308626	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1003864	chr2:210063871-210308626	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv834518	chr2:210204958-210372744	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv834519	chr2:210271017-210400153	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1005298	chr2:210277791-210318067	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210288000-210292000	Active TSS	Brain Inferior Temporal Lobe	brain
2	chr2:210288200-210290800	Active TSS	Brain Substantia Nigra	brain
3	chr2:210288200-210291200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:210288200-210291200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:210288200-210291400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:210288200-210291400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr2:210288200-210291600	Active TSS	Aorta	Aorta
8	chr2:210288200-210291600	Active TSS	Brain Angular Gyrus	brain
9	chr2:210288200-210291600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:210288200-210292400	Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr2:210288200-210294400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:210288400-210291000	Active TSS	Brain Hippocampus Middle	brain
13	chr2:210288600-210291600	Active TSS	Fetal Brain Male	brain
14	chr2:210289400-210291200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:210289400-210291400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:210289600-210291800	Active TSS	Fetal Brain Female	brain
17	chr2:210289800-210290800	Enhancers	Primary B cells from cord blood	blood
18	chr2:210289800-210290800	Flanking Active TSS	NHEK	skin
19	chr2:210289800-210293000	Active TSS	Brain Germinal Matrix	brain
20	chr2:210290000-210290800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:210290000-210291200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:210290000-210291200	Weak transcription	Ovary	ovary
23	chr2:210290000-210291400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:210290000-210292800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr2:210290000-210300200	Weak transcription	Pancreas	Pancrea
26	chr2:210290200-210290800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr2:210290200-210290800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:210290200-210291400	Enhancers	H1 Cell Line	embryonic stem cell
29	chr2:210290200-210291600	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr2:210290200-210291600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr2:210290200-210296400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:210290200-210296400	Weak transcription	Osteobl	bone
33	chr2:210290200-210300200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:210290400-210290800	Flanking Active TSS	HUVEC	blood vessel
35	chr2:210290400-210291200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:210290400-210291600	Weak transcription	A549	lung
37	chr2:210290600-210290800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr2:210290600-210290800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:210290600-210290800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:210290600-210290800	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr2:210290600-210290800	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr2:210290600-210290800	Enhancers	Fetal Lung	lung
43	chr2:210290600-210290800	Enhancers	Hela-S3	cervix
44	chr2:210290600-210290800	Flanking Active TSS	NHLF	lung
45	chr2:210290600-210291000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr2:210290600-210291000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr2:210290600-210291200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:210290600-210291600	Enhancers	HMEC	breast
49	chr2:210290600-210291800	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr2:210290600-210291800	Enhancers	Muscle Satellite Cultured Cells	--

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