Variant report

Variant	rs3856668
Chromosome Location	chr3:60051227-60051228
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	chr3:60044792..60047333-chr3:60050018..60052719,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17061880	0.82[CHB][hapmap]
rs191926	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs191927	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs212006	0.84[CHB][hapmap];0.95[ASN][1000 genomes]
rs212009	0.97[ASN][1000 genomes]
rs212011	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2630154	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2630164	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs2736812	0.82[CHB][hapmap]
rs3856667	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3856669	1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7638558	1.00[JPT][hapmap]
rs7640460	0.88[ASN][1000 genomes]
rs9879807	1.00[JPT][hapmap]

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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv13593	chr3:60050980-60057155	Flanking Active TSS Enhancers Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60042000-60051600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:60043000-60051400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:60045000-60054200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr3:60045800-60052400	Enhancers	Primary T cells from cord blood	blood
5	chr3:60046800-60051800	Enhancers	Thymus	Thymus
6	chr3:60047400-60052200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:60048200-60054000	Enhancers	Dnd41	blood
8	chr3:60048800-60059400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:60049000-60051800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:60049200-60052000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr3:60049400-60053200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr3:60049800-60052000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:60049800-60052200	Enhancers	Fetal Thymus	thymus
14	chr3:60050000-60051400	Enhancers	NH-A	brain
15	chr3:60050000-60052000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:60050200-60051400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:60050200-60051400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr3:60050200-60051600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:60050200-60051600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:60050200-60051600	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:60050400-60051400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:60050400-60051600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:60050600-60051400	Enhancers	Primary hematopoietic stem cells	blood
24	chr3:60050600-60051600	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr3:60050600-60051800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr3:60050800-60051600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:60050800-60051800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:60050800-60052400	Enhancers	Primary T cells fromperipheralblood	blood
29	chr3:60051000-60051400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:60051000-60051600	Enhancers	Aorta	Aorta
31	chr3:60051200-60052400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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