Variant report

Variant	rs406292
Chromosome Location	chr5:80961822-80961823
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	chr5:80961632..80964415-chr5:80970591..80972149,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1023747	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1095605	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11957810	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347597	0.89[CEU][hapmap]
rs1436498	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436499	1.00[CHB][hapmap]
rs2043646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2917542	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs365147	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs374479	0.82[CEU][hapmap]
rs380946	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs382297	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs384433	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385332	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385716	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs389860	0.82[CEU][hapmap]
rs390171	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs396231	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs399104	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs402352	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs403777	0.82[CEU][hapmap]
rs411520	0.89[EUR][1000 genomes]
rs413472	1.00[CHB][hapmap]
rs418033	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs419017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420202	0.82[CEU][hapmap]
rs420412	0.82[CEU][hapmap]
rs421348	0.96[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs432617	0.90[EUR][1000 genomes]
rs435901	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs437417	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs438128	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs445253	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs446064	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs446565	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs447574	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs452314	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs453068	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs454487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs585558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682481	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898782	0.85[CHB][hapmap]
rs724913	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs827065	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs863772	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882233	chr5:80849084-81049187	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv882234	chr5:80853708-80966666	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv525437	chr5:80876359-80964452	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv462222	chr5:80900719-80964452	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv598752	chr5:80900719-80964452	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv882235	chr5:80909132-81006061	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv830361	chr5:80909811-81080409	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv882236	chr5:80930992-80999768	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv527374	chr5:80938095-80964452	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv882237	chr5:80938489-81006061	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv519589	chr5:80959001-80964452	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80921200-80983000	Weak transcription	Aorta	Aorta
2	chr5:80924200-80962800	Weak transcription	Ovary	ovary
3	chr5:80924800-80972000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr5:80932400-80963000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:80938800-80965200	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:80939200-80962400	Weak transcription	Fetal Stomach	stomach
7	chr5:80942800-80962800	Weak transcription	Right Atrium	heart
8	chr5:80945600-80985400	Weak transcription	Fetal Kidney	kidney
9	chr5:80946200-80972800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:80948000-80971000	Weak transcription	Primary T cells from cord blood	blood
11	chr5:80950200-80975600	Weak transcription	Thymus	Thymus
12	chr5:80950400-80962600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr5:80951800-80970800	Weak transcription	Primary B cells from cord blood	blood
14	chr5:80953600-80966800	Weak transcription	Fetal Lung	lung
15	chr5:80954400-80962600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:80956800-80970000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:80956800-80971800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:80957200-80966800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr5:80960200-80962000	Strong transcription	Fetal Thymus	thymus
20	chr5:80960400-80963400	Strong transcription	Dnd41	blood
21	chr5:80960600-80962000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:80960800-80962000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:80960800-80965800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:80961600-80962000	Enhancers	Fetal Brain Female	brain
25	chr5:80961600-80962200	Enhancers	Psoas Muscle	Psoas
26	chr5:80961600-80963000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:80961600-80963400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr5:80961800-80962000	Enhancers	Brain Germinal Matrix	brain
29	chr5:80961800-80962400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr5:80961800-80963600	Enhancers	Colon Smooth Muscle	Colon

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