Variant report

Variant	rs2047896
Chromosome Location	chr6:80232768-80232769
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:80227058..80229732-chr6:80232396..80234486,2	MCF-7	breast:
2	chr6:80232386..80237378-chr6:80253283..80257767,7	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10943650	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10943651	0.82[AMR][1000 genomes]
rs13206818	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];0.95[ASN][1000 genomes]
rs1351959	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1354452	0.86[CHB][hapmap]
rs1485374	0.83[JPT][hapmap]
rs1485375	0.82[CHB][hapmap]
rs1485376	0.82[CHB][hapmap]
rs2009837	0.81[AFR][1000 genomes]
rs2655662	0.87[CHB][hapmap]
rs2655700	0.81[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs2803183	0.81[ASN][1000 genomes]
rs2812689	0.82[AFR][1000 genomes]
rs2812692	0.86[CHB][hapmap]
rs3747766	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3747767	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3967183	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4055084	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4706789	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs66572100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6915859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6930436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72624517	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7356969	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7754849	1.00[CEU][hapmap];0.95[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];0.94[ASN][1000 genomes]
rs9294148	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9341781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9341782	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9343918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9343919	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9343920	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9343921	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9352736	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9352737	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9352738	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9352739	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9352743	0.82[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9352744	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9352747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9359379	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9359382	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]
rs9359383	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9359384	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9361537	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9361538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9361539	0.82[AFR][1000 genomes]
rs958114	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv886301	chr6:80111104-80339088	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv886302	chr6:80111104-80355973	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1027388	chr6:80113449-80355973	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv830707	chr6:80134625-80325171	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1029259	chr6:80142754-80340332	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv886303	chr6:80147225-80252423	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	esv1798451	chr6:80222511-80234343	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80179800-80235000	Weak transcription	HSMMtube	muscle
2	chr6:80190200-80234400	Weak transcription	Fetal Intestine Large	intestine
3	chr6:80195400-80235000	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:80198400-80235000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr6:80199000-80235000	Weak transcription	Adipose Nuclei	Adipose
6	chr6:80207600-80246000	Weak transcription	Ovary	ovary
7	chr6:80209000-80235000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:80214400-80235000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr6:80214600-80246000	Weak transcription	Fetal Stomach	stomach
10	chr6:80216000-80236800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:80216400-80235000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:80216400-80235000	Weak transcription	NH-A	brain
13	chr6:80217600-80235000	Weak transcription	Pancreas	Pancrea
14	chr6:80217800-80246000	Weak transcription	Aorta	Aorta
15	chr6:80218200-80244000	Weak transcription	Fetal Brain Female	brain
16	chr6:80218400-80233800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr6:80219000-80235400	Weak transcription	Fetal Heart	heart
18	chr6:80221400-80235600	Weak transcription	Fetal Kidney	kidney
19	chr6:80221800-80234400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:80222400-80235200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:80223000-80233200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr6:80223400-80234800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr6:80223400-80240400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:80223600-80233600	Weak transcription	Fetal Lung	lung
25	chr6:80223600-80234000	Weak transcription	HMEC	breast
26	chr6:80224000-80233400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:80224800-80233600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:80225800-80235000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:80227400-80234800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr6:80228000-80241800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:80229000-80234800	Weak transcription	HSMM	muscle
32	chr6:80229200-80234000	Weak transcription	K562	blood
33	chr6:80232400-80233400	Weak transcription	HepG2	liver
34	chr6:80232600-80236000	Enhancers	HUES48 Cell Line	embryonic stem cell

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