Variant report

Variant	rs4706460
Chromosome Location	chr6:71415405-71415406
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	chr6:71275330..71278071-chr6:71414560..71416337,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154079	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12215915	0.86[YRI][hapmap]
rs2273566	0.94[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap]
rs2274972	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3734369	0.85[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs4282370	0.82[YRI][hapmap]
rs4706462	0.86[YRI][hapmap]
rs4707842	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4707844	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.82[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61001507	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6902786	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6919104	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6940971	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6941789	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7747310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7748778	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes]
rs7754217	1.00[ASW][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs7764445	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9342795	1.00[ASW][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.84[MEX][hapmap];0.96[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs9342796	0.83[ASW][hapmap];0.85[GIH][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9346403	0.92[EUR][1000 genomes]
rs9351793	0.96[AFR][1000 genomes]
rs9354937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9354938	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9360426	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9364102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9364103	0.96[AFR][1000 genomes]
rs9364106	0.88[LWK][hapmap];0.93[YRI][hapmap]
rs9364109	0.92[EUR][1000 genomes]
rs9364111	0.85[EUR][1000 genomes]

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	nsv932111	chr6:70736835-71633094	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1027049	chr6:70961610-71561488	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv524328	chr6:70961833-71558805	Flanking Bivalent TSS/Enh Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv917312	chr6:70961903-71601688	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv886147	chr6:71273253-71471863	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:71395800-71417400	Weak transcription	Small Intestine	intestine
2	chr6:71404400-71417600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:71404600-71417400	Weak transcription	GM12878-XiMat	blood
4	chr6:71405600-71417600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:71405800-71417400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr6:71407400-71419200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:71407400-71419400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:71407800-71419000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr6:71407800-71419600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr6:71408000-71417600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:71408200-71420200	Weak transcription	Primary B cells from cord blood	blood
12	chr6:71408400-71418000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:71408800-71417600	Weak transcription	Stomach Mucosa	stomach
14	chr6:71409000-71416000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:71409600-71419400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:71409800-71421600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:71409800-71422600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:71410000-71417800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr6:71410800-71417600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:71411200-71417600	Weak transcription	Primary T cells from cord blood	blood
21	chr6:71411200-71417800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr6:71411200-71421400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:71411400-71415800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr6:71411400-71419000	Weak transcription	Esophagus	oesophagus
25	chr6:71411400-71419000	Weak transcription	Gastric	stomach
26	chr6:71411400-71423200	Weak transcription	Psoas Muscle	Psoas
27	chr6:71411600-71416000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr6:71411600-71417600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr6:71411600-71417600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr6:71411600-71417600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr6:71411800-71417600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:71412000-71417600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:71412800-71417600	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr6:71414800-71419200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:71414800-71419600	Weak transcription	NHDF-Ad	bronchial
36	chr6:71415000-71417600	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr6:71415200-71416600	Enhancers	Liver	Liver
38	chr6:71415400-71418200	Weak transcription	Rectal Mucosa Donor 29	rectum

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