Variant report

Variant	rs4713822
Chromosome Location	chr6:11688305-11688306
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	chr6:11675436..11677701-chr6:11686415..11688887,2	MCF-7	breast:

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs10485418	0.94[EUR][1000 genomes]
rs10807142	0.93[EUR][1000 genomes]
rs10947504	0.94[EUR][1000 genomes]
rs10947511	0.96[EUR][1000 genomes]
rs10947513	0.96[EUR][1000 genomes]
rs10947514	0.96[EUR][1000 genomes]
rs10947515	0.96[EUR][1000 genomes]
rs10947516	0.96[EUR][1000 genomes]
rs10947517	0.94[EUR][1000 genomes]
rs10947518	0.96[EUR][1000 genomes]
rs10947519	0.94[EUR][1000 genomes]
rs10947520	0.94[EUR][1000 genomes]
rs10947522	0.94[EUR][1000 genomes]
rs10947523	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10947529	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150586	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150588	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1150589	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1150592	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752668	0.94[EUR][1000 genomes]
rs11752767	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11752868	0.96[EUR][1000 genomes]
rs11753959	0.94[EUR][1000 genomes]
rs11754457	0.94[EUR][1000 genomes]
rs11755543	0.94[EUR][1000 genomes]
rs11758121	0.96[EUR][1000 genomes]
rs11758138	0.96[EUR][1000 genomes]
rs11759654	0.94[EUR][1000 genomes]
rs11964548	0.93[EUR][1000 genomes]
rs1206001	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1206002	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1206007	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1206008	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12173585	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12175829	0.96[EUR][1000 genomes]
rs12175836	0.96[EUR][1000 genomes]
rs12191630	0.94[EUR][1000 genomes]
rs12191903	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes]
rs12191906	0.94[EUR][1000 genomes]
rs12193984	0.94[EUR][1000 genomes]
rs12200077	0.93[EUR][1000 genomes]
rs12201911	0.94[EUR][1000 genomes]
rs12202334	0.95[EUR][1000 genomes]
rs12204642	0.93[EUR][1000 genomes]
rs12214396	0.94[EUR][1000 genomes]
rs12216511	0.94[EUR][1000 genomes]
rs12663442	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs1413347	0.95[EUR][1000 genomes]
rs1416451	0.96[EUR][1000 genomes]
rs1416452	0.95[EUR][1000 genomes]
rs1546863	0.94[EUR][1000 genomes]
rs2021340	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2022016	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs210922	0.89[EUR][1000 genomes]
rs2142892	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2142893	0.94[EUR][1000 genomes]
rs2142894	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142895	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179268	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2209259	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2224855	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2860114	0.95[EUR][1000 genomes]
rs3857564	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs4711397	0.96[EUR][1000 genomes]
rs4711398	0.96[EUR][1000 genomes]
rs4713818	0.95[EUR][1000 genomes]
rs4713819	0.96[EUR][1000 genomes]
rs4713821	0.96[EUR][1000 genomes]
rs4713826	0.94[EUR][1000 genomes]
rs62395208	0.93[EUR][1000 genomes]
rs6902790	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6907010	0.96[EUR][1000 genomes]
rs6907423	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6914246	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917101	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917670	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6934072	0.96[EUR][1000 genomes]
rs6936345	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7449935	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7749947	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7750635	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs7760877	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7763722	0.93[EUR][1000 genomes]
rs7764199	0.93[EUR][1000 genomes]
rs7772346	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7774946	0.93[EUR][1000 genomes]
rs9296117	0.95[EUR][1000 genomes]
rs9348946	0.94[EUR][1000 genomes]
rs9348948	0.96[EUR][1000 genomes]
rs9348951	0.94[EUR][1000 genomes]
rs9357183	0.94[EUR][1000 genomes]
rs9357184	0.82[EUR][1000 genomes]
rs9366859	0.94[EUR][1000 genomes]
rs9366861	0.94[EUR][1000 genomes]
rs9366868	1.00[CEU][hapmap];0.92[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs9366869	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9366872	0.92[CEU][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9366874	0.90[TSI][hapmap]
rs9368818	0.95[EUR][1000 genomes]
rs9368822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368823	0.95[EUR][1000 genomes]
rs9368824	0.96[EUR][1000 genomes]
rs9368833	0.94[EUR][1000 genomes]
rs9380431	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380444	0.95[EUR][1000 genomes]
rs9380446	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9380464	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9394211	0.95[EUR][1000 genomes]
rs9394234	0.95[EUR][1000 genomes]
rs9394236	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394237	0.96[EUR][1000 genomes]
rs9394239	0.94[EUR][1000 genomes]
rs9394242	0.94[EUR][1000 genomes]
rs9394243	0.94[EUR][1000 genomes]
rs9394244	0.94[EUR][1000 genomes]
rs9461985	1.00[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9469793	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9469816	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469826	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9637952	0.94[EUR][1000 genomes]
rs9637968	0.94[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	esv2758036	chr6:11679753-11822351	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2759407	chr6:11679753-11822351	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv428470	chr6:11686198-11747850	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11684800-11688600	Enhancers	Placenta Amnion	Placenta Amnion
2	chr6:11685000-11688600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:11685000-11689400	Enhancers	Fetal Intestine Large	intestine
4	chr6:11685200-11688400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:11685200-11693000	Weak transcription	Spleen	Spleen
6	chr6:11685400-11688800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr6:11686600-11689000	Weak transcription	HSMM	muscle
8	chr6:11686600-11701400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:11686600-11702400	Weak transcription	HSMMtube	muscle
10	chr6:11687000-11688600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:11687200-11688800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:11687200-11689200	Enhancers	Fetal Heart	heart
13	chr6:11687200-11689200	Enhancers	Fetal Stomach	stomach
14	chr6:11687200-11689400	Enhancers	Brain Germinal Matrix	brain
15	chr6:11687400-11689000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:11687600-11688600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:11687600-11688800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:11687600-11688800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:11687600-11688800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr6:11687600-11688800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr6:11687800-11688400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:11687800-11688400	Enhancers	Fetal Brain Male	brain
23	chr6:11687800-11688600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr6:11687800-11688600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr6:11687800-11688600	Flanking Active TSS	Fetal Lung	lung
26	chr6:11688000-11688400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr6:11688000-11688600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr6:11688200-11688400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr6:11688200-11688600	Flanking Active TSS	Fetal Intestine Small	intestine
30	chr6:11688200-11688600	Active TSS	Fetal Kidney	kidney
31	chr6:11688200-11688600	Active TSS	Ovary	ovary

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