Variant report

Variant	rs4894950
Chromosome Location	chr3:105507929-105507930
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	chr3:105504771..105508747-chr3:105511531..105514547,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10804442	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10933830	0.82[CHB][hapmap]
rs10933833	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11711088	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11924742	0.81[CEU][hapmap]
rs12636287	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13060223	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085563	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13100446	0.93[AMR][1000 genomes]
rs1443102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1470283	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1550711	0.83[YRI][hapmap]
rs1550712	0.82[CHB][hapmap]
rs1867191	0.86[YRI][hapmap]
rs1867195	0.94[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2055557	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2099892	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2399056	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427229	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28533328	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821489	0.86[CHB][hapmap]
rs3996189	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4243427	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4447799	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894953	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4894957	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894960	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4894962	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6437624	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6782206	0.82[CHB][hapmap]
rs6788366	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6795961	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6807382	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71627856	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7432372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7637327	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7645021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7647955	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7651784	0.87[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs769315	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971110	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9841500	0.87[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105467600-105509400	Weak transcription	Stomach Mucosa	stomach
2	chr3:105478600-105509400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:105478600-105511200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:105481400-105509600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:105482000-105509600	Weak transcription	Ovary	ovary
7	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
9	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
10	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
11	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
12	chr3:105487000-105508400	Weak transcription	Fetal Lung	lung
13	chr3:105487200-105508400	Weak transcription	Fetal Kidney	kidney
14	chr3:105489600-105509600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
16	chr3:105493000-105511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:105493000-105511200	Weak transcription	Right Atrium	heart
18	chr3:105493200-105509000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:105494400-105509400	Weak transcription	Primary B cells from cord blood	blood
20	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:105495000-105509600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:105495400-105517200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:105495600-105509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:105496400-105510800	Weak transcription	Right Ventricle	heart
25	chr3:105496400-105514000	Weak transcription	Lung	lung
26	chr3:105501200-105508400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:105501200-105509400	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:105501200-105509600	Weak transcription	Small Intestine	intestine
29	chr3:105501800-105509400	Weak transcription	Left Ventricle	heart
30	chr3:105501800-105516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr3:105504000-105508000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:105505000-105508200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:105505000-105509600	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
35	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:105505200-105511000	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:105505400-105509400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:105505400-105509600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr3:105505600-105517400	Weak transcription	Brain Substantia Nigra	brain
40	chr3:105506000-105510800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:105506200-105509200	Weak transcription	Osteobl	bone
42	chr3:105506200-105516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr3:105506400-105508400	Weak transcription	Fetal Heart	heart
44	chr3:105506400-105509200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:105506400-105509400	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:105506600-105518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr3:105507000-105509200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:105507000-105509200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:105507000-105509400	Weak transcription	A549	lung
50	chr3:105507000-105511000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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