Variant report

Variant	rs6785538
Chromosome Location	chr3:47486347-47486348
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	chr3:47479631..47481186-chr3:47484843..47486561,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1024036	1.00[EUR][1000 genomes]
rs1038393	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10865945	1.00[EUR][1000 genomes]
rs10865947	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1091068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11707272	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11922925	1.00[EUR][1000 genomes]
rs12488371	1.00[EUR][1000 genomes]
rs12631697	1.00[EUR][1000 genomes]
rs13077134	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13078181	1.00[EUR][1000 genomes]
rs1531874	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1872165	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1874264	1.00[EUR][1000 genomes]
rs1979736	1.00[EUR][1000 genomes]
rs2170814	1.00[AMR][1000 genomes]
rs2350642	1.00[EUR][1000 genomes]
rs295431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295432	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295434	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295443	1.00[EUR][1000 genomes]
rs295444	1.00[EUR][1000 genomes]
rs295445	1.00[EUR][1000 genomes]
rs295448	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295450	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295451	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295453	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295454	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295457	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs295459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs448018	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858812	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858823	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4858855	1.00[AMR][1000 genomes]
rs4858896	1.00[EUR][1000 genomes]
rs6442062	1.00[EUR][1000 genomes]
rs6442063	1.00[EUR][1000 genomes]
rs6442066	1.00[EUR][1000 genomes]
rs6442068	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6442069	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs648226	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6767868	1.00[EUR][1000 genomes]
rs6772449	1.00[EUR][1000 genomes]
rs6778673	1.00[EUR][1000 genomes]
rs6778687	1.00[EUR][1000 genomes]
rs6783591	1.00[EUR][1000 genomes]
rs6787210	1.00[EUR][1000 genomes]
rs6788978	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6789730	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6808117	1.00[EUR][1000 genomes]
rs6808629	1.00[EUR][1000 genomes]
rs7372780	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831482	1.00[EUR][1000 genomes]
rs7612191	0.87[AMR][1000 genomes]
rs7615774	1.00[EUR][1000 genomes]
rs7621853	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7639121	1.00[EUR][1000 genomes]
rs7643150	1.00[EUR][1000 genomes]
rs7644043	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649413	1.00[EUR][1000 genomes]
rs7652492	1.00[EUR][1000 genomes]
rs807930	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs807933	1.00[EUR][1000 genomes]
rs900688	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900689	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900690	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900691	1.00[EUR][1000 genomes]
rs900692	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs900694	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs924009	1.00[EUR][1000 genomes]
rs9823599	0.85[AMR][1000 genomes]
rs9828124	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9861247	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv511233	chr3:47484797-47494157	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv590212	chr3:47485029-47500662	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47473200-47487200	Weak transcription	HUVEC	blood vessel
2	chr3:47474600-47489600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:47481400-47496000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:47481400-47500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:47481800-47492600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:47482200-47488800	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr3:47482600-47486400	Enhancers	Stomach Mucosa	stomach
9	chr3:47483000-47486400	Enhancers	Fetal Intestine Small	intestine
10	chr3:47483200-47487400	Enhancers	Liver	Liver
11	chr3:47483400-47486600	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:47484000-47507800	Weak transcription	Primary B cells from cord blood	blood
13	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:47484200-47486600	Enhancers	Fetal Muscle Leg	muscle
15	chr3:47484200-47511200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:47484400-47486400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:47484400-47492600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:47484400-47497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:47484600-47486400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:47484600-47486800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:47484600-47487400	Weak transcription	Fetal Brain Female	brain
22	chr3:47484600-47490000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:47484600-47494200	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:47484600-47497400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:47484600-47500600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:47484600-47514000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:47484600-47514200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr3:47484600-47514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:47484600-47514200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr3:47484600-47514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr3:47484800-47487000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr3:47484800-47487400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:47484800-47504400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:47484800-47504600	Weak transcription	Primary T cells from cord blood	blood
35	chr3:47484800-47514800	Weak transcription	Thymus	Thymus
36	chr3:47485000-47487400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:47485000-47487400	Weak transcription	Dnd41	blood
38	chr3:47485000-47514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:47485200-47486600	Enhancers	Duodenum Mucosa	Duodenum
40	chr3:47485200-47502600	Weak transcription	K562	blood
41	chr3:47485400-47486400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr3:47485400-47486600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr3:47485400-47488600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:47485400-47489400	Weak transcription	GM12878-XiMat	blood
45	chr3:47485400-47490800	Weak transcription	Fetal Lung	lung
46	chr3:47485400-47493000	Weak transcription	Spleen	Spleen
47	chr3:47485400-47494200	Weak transcription	Ovary	ovary
48	chr3:47485400-47503200	Weak transcription	Gastric	stomach
49	chr3:47485600-47493200	Weak transcription	Esophagus	oesophagus
50	chr3:47485600-47494000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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