Variant report

Variant	rs894541
Chromosome Location	chr3:105508651-105508652
allele	C/G
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: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11919893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12486371	0.83[CEU][hapmap]
rs12496588	0.84[CEU][hapmap]
rs12497428	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];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12632980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13326550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13433776	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1503923	0.81[ASN][1000 genomes]
rs16851596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851705	0.84[ASN][1000 genomes]
rs16851706	0.83[ASN][1000 genomes]
rs2120103	0.90[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2120104	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2399056	0.92[CEU][hapmap]
rs3772512	0.80[CEU][hapmap]
rs6437616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6766168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776593	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6778745	0.83[CEU][hapmap]
rs6780432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791765	0.83[CEU][hapmap]
rs7634195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7638504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639888	0.83[CEU][hapmap]
rs9811776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9814582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9838755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9846445	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9849559	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9872895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9876110	0.83[CEU][hapmap]
rs9880744	0.84[CEU][hapmap]

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	chr3:105489600-105509600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:105493000-105511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:105493000-105511200	Weak transcription	Right Atrium	heart
16	chr3:105493200-105509000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:105494400-105509400	Weak transcription	Primary B cells from cord blood	blood
18	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:105495000-105509600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:105495400-105517200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:105495600-105509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:105496400-105510800	Weak transcription	Right Ventricle	heart
23	chr3:105496400-105514000	Weak transcription	Lung	lung
24	chr3:105501200-105509400	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:105501200-105509600	Weak transcription	Small Intestine	intestine
26	chr3:105501800-105509400	Weak transcription	Left Ventricle	heart
27	chr3:105501800-105516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:105505000-105509600	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
30	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr3:105505200-105511000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:105505400-105509400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:105505400-105509600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:105505600-105517400	Weak transcription	Brain Substantia Nigra	brain
35	chr3:105506000-105510800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr3:105506200-105509200	Weak transcription	Osteobl	bone
37	chr3:105506200-105516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:105506400-105509200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:105506400-105509400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr3:105506600-105518200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:105507000-105509200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:105507000-105509200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:105507000-105509400	Weak transcription	A549	lung
44	chr3:105507000-105511000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:105507000-105511800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr3:105507200-105509200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:105507200-105509400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:105507200-105510000	Weak transcription	Primary T cells from cord blood	blood
49	chr3:105507200-105511000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr3:105507200-105511000	Weak transcription	Liver	Liver

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