Variant report

Variant	rs12209200
Chromosome Location	chr6:57217336-57217337
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	chr6:57217129..57218039-chr6:57539079..57539990,3	MCF-7	breast:
2	chr6:57214841..57217586-chr6:57224303..57226247,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12190422	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12197484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12198315	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap]
rs12200910	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12201331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12201359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12204746	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12205722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12205821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12208485	1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs12210456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12210940	0.83[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs12213707	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17658313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2067973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3805793	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6908145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7748620	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2758056	chr6:57184541-57562604	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	esv2759432	chr6:57184541-57562604	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1034139	chr6:57192993-57253423	ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1022055	chr6:57192993-57353692	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1015853	chr6:57205882-57528899	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv538231	chr6:57205882-57528899	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1026876	chr6:57205882-57911812	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538232	chr6:57205882-57911812	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
10	nsv1017144	chr6:57205882-58055059	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
11	nsv538233	chr6:57205882-58055059	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
12	nsv931006	chr6:57205883-58060394	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
13	nsv603191	chr6:57205920-57381883	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
14	nsv970125	chr6:57205998-57285497	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
15	esv2453782	chr6:57206998-57575589	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
16	nsv1024888	chr6:57208043-57541463	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1020263	chr6:57208043-57562028	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
18	nsv538234	chr6:57208043-57562028	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
19	nsv1025413	chr6:57208043-57617947	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
20	nsv538235	chr6:57208043-57617947	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
21	nsv1024375	chr6:57208043-58002217	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 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	chr6:57194600-57226200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:57194600-57244800	Weak transcription	Spleen	Spleen
3	chr6:57195600-57238400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:57199600-57221000	Weak transcription	Hela-S3	cervix
5	chr6:57199600-57229000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:57199800-57251000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:57200000-57218000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:57208800-57231200	Weak transcription	Aorta	Aorta
9	chr6:57209000-57244800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:57211000-57217800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:57211800-57219000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr6:57212000-57217600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:57212000-57217800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr6:57212000-57218200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr6:57212000-57226000	Weak transcription	Primary B cells from cord blood	blood
16	chr6:57212600-57223800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr6:57212800-57217400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr6:57214000-57220600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr6:57214200-57219200	Weak transcription	Primary T cells from cord blood	blood
20	chr6:57214200-57226000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr6:57215000-57220200	Weak transcription	Thymus	Thymus
22	chr6:57215400-57218400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:57215400-57229600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:57215600-57218800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr6:57215600-57219000	Weak transcription	Osteobl	bone
26	chr6:57215600-57219600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr6:57215600-57220400	Weak transcription	Pancreas	Pancrea
28	chr6:57216000-57226000	Weak transcription	NHLF	lung
29	chr6:57216400-57221200	Weak transcription	Dnd41	blood
30	chr6:57216600-57218000	Weak transcription	NHDF-Ad	bronchial
31	chr6:57216600-57225800	Weak transcription	GM12878-XiMat	blood

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