Variant report

Variant	rs58343222
Chromosome Location	chr6:2174767-2174768
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	chr6:1606456..1608668-chr6:2173309..2175661,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1006019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1033533	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs13206375	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs17134714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2038223	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2038224	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2483054	0.83[AMR][1000 genomes]
rs28515035	0.83[AMR][1000 genomes]
rs55847540	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs55937718	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56913552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58405376	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs59370688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59520004	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs60593022	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60813424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61070654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61096641	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs628510	0.83[AMR][1000 genomes]
rs6596871	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6900870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6904830	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6909588	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6920255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6921705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73418780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73420706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73420724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7757356	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9328083	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9501806	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9501807	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9501808	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9501809	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503101	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9503102	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9503103	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9503104	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503108	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9503112	0.83[AMR][1000 genomes]
rs9503118	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9503120	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv931941	chr6:1768439-2246781	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
4	nsv522608	chr6:2032259-2203888	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS 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	46 gene(s)	inside rSNPs	diseases
6	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv883387	chr6:2086679-2176239	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
11	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
12	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2163600-2176800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:2166400-2185400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:2168600-2175000	Weak transcription	Gastric	stomach
4	chr6:2168600-2176200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:2168600-2176600	Weak transcription	Stomach Mucosa	stomach
6	chr6:2168600-2176800	Weak transcription	Pancreas	Pancrea
7	chr6:2168600-2177000	Weak transcription	Aorta	Aorta
8	chr6:2168800-2177000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:2171600-2177200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr6:2172400-2176600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:2172600-2176800	Weak transcription	HepG2	liver
12	chr6:2173400-2177200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:2174400-2176800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:2174400-2178200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:2174400-2178200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:2174600-2175000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:2174600-2175000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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