Variant report

Variant	rs16851587
Chromosome Location	chr3:105506419-105506420
allele	A/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: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10460808	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs10511246	0.81[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1075739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11921710	0.81[ASN][1000 genomes]
rs12633654	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635232	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12637560	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12637809	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639271	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1561922	0.82[CEU][hapmap];0.87[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16844736	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs16851523	0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851539	0.85[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16851563	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851570	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16851630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1867192	0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs1947000	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1992521	0.82[EUR][1000 genomes]
rs2089091	0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2197208	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197209	0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301036	0.82[EUR][1000 genomes]
rs3772540	0.82[CEU][hapmap]
rs57520912	0.81[ASN][1000 genomes]
rs58340800	0.81[ASN][1000 genomes]
rs59534462	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59611997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60295307	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60619938	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6437620	0.81[ASN][1000 genomes]
rs6437621	0.81[ASN][1000 genomes]
rs73854891	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73854894	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73857222	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7624400	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629357	0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7648842	0.81[ASN][1000 genomes]
rs9631436	0.81[ASN][1000 genomes]
rs9789988	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826886	0.81[ASN][1000 genomes]
rs9846534	0.88[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9874600	0.87[CHB][hapmap];0.82[JPT][hapmap];0.81[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:62 , 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	chr3:105481800-105507400	Weak transcription	HSMM	muscle
6	chr3:105482000-105509200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:105482000-105509600	Weak transcription	Ovary	ovary
8	chr3:105482000-105510800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:105482000-105511200	Weak transcription	Aorta	Aorta
10	chr3:105482800-105517400	Weak transcription	Fetal Intestine Large	intestine
11	chr3:105483200-105555200	Weak transcription	Placenta	Placenta
12	chr3:105486800-105519000	Weak transcription	Esophagus	oesophagus
13	chr3:105487000-105508400	Weak transcription	Fetal Lung	lung
14	chr3:105487200-105508400	Weak transcription	Fetal Kidney	kidney
15	chr3:105489600-105509600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:105489600-105525400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:105493000-105511200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:105493000-105511200	Weak transcription	Right Atrium	heart
19	chr3:105493200-105509000	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:105494400-105509400	Weak transcription	Primary B cells from cord blood	blood
21	chr3:105494400-105516200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:105495000-105509600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:105495400-105517200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:105495600-105509400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:105496400-105510800	Weak transcription	Right Ventricle	heart
26	chr3:105496400-105514000	Weak transcription	Lung	lung
27	chr3:105500600-105507400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr3:105500800-105506800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:105500800-105507600	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:105501200-105508400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr3:105501200-105509400	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:105501200-105509600	Weak transcription	Small Intestine	intestine
33	chr3:105501800-105509400	Weak transcription	Left Ventricle	heart
34	chr3:105501800-105516600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr3:105503200-105507000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:105504000-105506600	Weak transcription	Primary T cells from cord blood	blood
37	chr3:105504000-105508000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:105504200-105507200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr3:105504400-105507000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:105504400-105507200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr3:105505000-105507600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr3:105505000-105508200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:105505000-105509600	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:105505000-105527800	Weak transcription	Pancreas	Pancrea
45	chr3:105505000-105548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr3:105505200-105511000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr3:105505400-105509400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:105505400-105509600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:105505600-105507200	Weak transcription	Psoas Muscle	Psoas
50	chr3:105505600-105517400	Weak transcription	Brain Substantia Nigra	brain

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