Variant report

Variant	rs9348658
Chromosome Location	chr6:25028230-25028231
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25027553..25029661-chr6:25041949..25043586,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272053	Chromatin interaction
ENSG00000229313	Chromatin interaction
ENSG00000111913	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs441342	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6906443	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6907293	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6929342	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6929348	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6929749	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6934141	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9295644	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9348655	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9348656	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9348657	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9348659	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9356953	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9356954	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356955	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9356956	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9356957	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9356958	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9358823	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9358824	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9358825	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9358826	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366595	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366596	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366597	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9366598	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9366599	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9379706	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9379707	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9393607	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9393608	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467378	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv883482	chr6:24926730-25035920	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv1030634	chr6:24938277-25040161	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 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	chr6:25011200-25035600	Weak transcription	Spleen	Spleen
2	chr6:25024800-25028400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:25025000-25028600	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr6:25025200-25028600	Enhancers	Fetal Thymus	thymus
5	chr6:25025400-25028400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr6:25026400-25033600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:25027000-25028400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr6:25027000-25028600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr6:25027000-25028600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:25027400-25028400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr6:25027400-25028400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:25027400-25028400	Enhancers	Lung	lung
13	chr6:25027600-25028400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:25027800-25028800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:25027800-25029200	Enhancers	Primary hematopoietic stem cells	blood
16	chr6:25028000-25028400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr6:25028000-25028400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr6:25028000-25028600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr6:25028000-25028600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:25028000-25030600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:25028200-25028400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:25028200-25028400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr6:25028200-25028400	Enhancers	GM12878-XiMat	blood
24	chr6:25028200-25028600	Enhancers	Primary B cells from peripheral blood	blood
25	chr6:25028200-25028600	Enhancers	Primary T cells fromperipheralblood	blood
26	chr6:25028200-25028600	Enhancers	Dnd41	blood
27	chr6:25028200-25030600	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:25028200-25032200	Weak transcription	Thymus	Thymus
29	chr6:25028200-25032400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:25028200-25033600	Weak transcription	Primary B cells from cord blood	blood
31	chr6:25028200-25033600	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr6:25028200-25034600	Weak transcription	Primary T cells from cord blood	blood
33	chr6:25028200-25035600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:25028200-25037600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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