Variant report

Variant	rs62261495
Chromosome Location	chr3:105483583-105483584
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105481713..105484437-chr7:147483253..147485905,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12054270	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12487349	0.87[ASN][1000 genomes]
rs12493071	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12493771	0.81[ASN][1000 genomes]
rs12632595	0.81[AFR][1000 genomes]
rs1443100	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851512	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851553	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851673	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16851707	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1814078	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867194	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2028598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055558	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2055559	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2120103	0.90[AMR][1000 genomes]
rs2120104	0.88[ASN][1000 genomes]
rs2301028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301034	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301035	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3213928	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34360428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35909361	0.90[ASN][1000 genomes]
rs3772517	0.96[ASN][1000 genomes]
rs3772522	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772525	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821490	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4431143	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4469007	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4894956	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62255570	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255571	0.92[AFR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255572	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255573	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62255575	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256353	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62258160	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62261460	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261487	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261491	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261492	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261496	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261497	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261498	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62261538	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62261539	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263056	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62263057	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62263059	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62263169	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62263170	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264260	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6809776	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7619706	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628896	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7631219	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7641527	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7650046	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs964173	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9657903	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9657924	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs971109	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9849559	0.88[ASN][1000 genomes]
rs9856147	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877310	chr3:105409321-105495841	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591244	chr3:105438320-105495841	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv591246	chr3:105439522-105504129	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv877311	chr3:105449986-105493286	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
2	chr3:105472200-105499000	Weak transcription	NHDF-Ad	bronchial
3	chr3:105472400-105504400	Weak transcription	HUVEC	blood vessel
4	chr3:105475200-105485600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:105476000-105486600	Weak transcription	Psoas Muscle	Psoas
6	chr3:105477800-105486800	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:105478200-105495400	Weak transcription	HSMMtube	muscle
8	chr3:105478600-105486600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:105478800-105489200	Weak transcription	Right Atrium	heart
12	chr3:105478800-105496200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:105479800-105483800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:105480400-105483800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:105480400-105484800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:105480600-105484800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:105481200-105500800	Weak transcription	Small Intestine	intestine
18	chr3:105481400-105491600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:105481600-105485200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr3:105481600-105486600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:105481600-105486600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:105481600-105498000	Weak transcription	NH-A	brain
24	chr3:105481800-105485400	Enhancers	Primary B cells from peripheral blood	blood
25	chr3:105481800-105507400	Weak transcription	HSMM	muscle
26	chr3:105482000-105483600	Weak transcription	Thymus	Thymus
27	chr3:105482000-105484000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:105482000-105484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:105482000-105486600	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr3:105482000-105486600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr3:105482000-105486600	Weak transcription	Liver	Liver
32	chr3:105482000-105486600	Weak transcription	Esophagus	oesophagus
33	chr3:105482000-105492400	Weak transcription	HepG2	liver
34	chr3:105482000-105496200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:105482000-105496200	Weak transcription	Lung	lung
36	chr3:105482000-105503800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:105482000-105509600	Weak transcription	Ovary	ovary
39	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
41	chr3:105482200-105483800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:105482200-105494600	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:105482400-105483600	Weak transcription	Primary hematopoietic stem cells	blood
44	chr3:105482400-105486400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:105482400-105486600	Weak transcription	Left Ventricle	heart
46	chr3:105482400-105486600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:105482400-105489400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:105482400-105489800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr3:105482400-105493600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr3:105482400-105494400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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