Variant report

Variant	rs11677461
Chromosome Location	chr2:205530404-205530405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:205529750..205532118-chr2:205534862..205537646,2	MCF-7	breast:
2	chr2:205528626..205531544-chr2:205538166..205540869,3	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1016338	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180873	0.83[EUR][1000 genomes]
rs10186433	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10196457	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10196548	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10202248	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10205296	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1030087	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10804144	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11688854	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691772	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11693425	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11893764	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11899398	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12468818	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12613314	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12694008	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12694009	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1477179	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1549012	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1549013	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1549014	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1861763	0.84[EUR][1000 genomes]
rs2052349	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2080601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2098461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2111446	0.84[EUR][1000 genomes]
rs2160689	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2216317	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2335632	0.81[EUR][1000 genomes]
rs2335633	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2335634	0.81[EUR][1000 genomes]
rs2335636	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3856507	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4591325	0.84[EUR][1000 genomes]
rs4675471	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4675472	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57144931	0.80[EUR][1000 genomes]
rs57951921	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58858166	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61043122	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6435249	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6733714	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6742535	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750084	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6751181	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6753683	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73059082	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs73059084	0.86[EUR][1000 genomes]
rs7577059	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7593604	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7594540	0.91[EUR][1000 genomes]
rs9653326	0.84[AMR][1000 genomes];0.87[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	nsv998485	chr2:205407813-206184006	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv536122	chr2:205407813-206184006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv875722	chr2:205462099-205572718	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv875723	chr2:205489653-205612846	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1010210	chr2:205489653-206076013	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:205520800-205542800	Weak transcription	Psoas Muscle	Psoas
2	chr2:205521000-205546200	Weak transcription	Aorta	Aorta
3	chr2:205527800-205531400	Enhancers	HSMM	muscle
4	chr2:205527800-205531800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:205527800-205533200	Enhancers	HSMMtube	muscle
6	chr2:205528000-205546200	Weak transcription	Pancreas	Pancrea
7	chr2:205528400-205532800	Weak transcription	Gastric	stomach
8	chr2:205528600-205531000	Enhancers	NHLF	lung
9	chr2:205528600-205531200	Enhancers	Colon Smooth Muscle	Colon
10	chr2:205528800-205530600	Flanking Active TSS	A549	lung
11	chr2:205528800-205530800	Enhancers	Hela-S3	cervix
12	chr2:205528800-205531000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:205528800-205531000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:205529000-205530600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:205529000-205530800	Enhancers	HUVEC	blood vessel
16	chr2:205529000-205531000	Enhancers	Osteobl	bone
17	chr2:205529000-205531400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr2:205529000-205531400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:205529000-205534400	Weak transcription	Stomach Mucosa	stomach
20	chr2:205529200-205530800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:205529200-205530800	Enhancers	HepG2	liver
22	chr2:205529200-205531000	Enhancers	HMEC	breast
23	chr2:205529200-205531000	Enhancers	NH-A	brain
24	chr2:205529400-205530800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr2:205529400-205530800	Enhancers	Fetal Heart	heart
26	chr2:205529400-205531800	Enhancers	Fetal Kidney	kidney
27	chr2:205529600-205530600	Enhancers	Placenta Amnion	Placenta Amnion
28	chr2:205529800-205530800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr2:205529800-205531000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:205530000-205530600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:205530000-205530600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr2:205530000-205530800	Enhancers	Ovary	ovary
33	chr2:205530000-205530800	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:205530000-205531200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:205530000-205531200	Enhancers	Rectal Smooth Muscle	rectum
36	chr2:205530000-205531600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:205530200-205530600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr2:205530200-205532200	Weak transcription	Liver	Liver
39	chr2:205530200-205532800	Weak transcription	Fetal Intestine Large	intestine
40	chr2:205530200-205535000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr2:205530200-205535000	Weak transcription	Lung	lung
42	chr2:205530200-205535400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr2:205530400-205530800	Enhancers	NHEK	skin
44	chr2:205530400-205531000	Enhancers	Stomach Smooth Muscle	stomach
45	chr2:205530400-205531800	Enhancers	NHDF-Ad	bronchial
46	chr2:205530400-205532200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:205530400-205532200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:205530400-205534200	Weak transcription	Fetal Lung	lung
49	chr2:205530400-205535000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr2:205530400-205535000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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