Variant report

Variant	rs12204264
Chromosome Location	chr6:45540607-45540608
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	chr6:45540470..45542325-chr6:45555218..45557403,2	MCF-7	breast:
2	chr6:45521600..45524007-chr6:45539938..45542034,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RUNX2-1	chr6:45540498-45543034	XLOC_005302

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10807322	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10948242	0.81[ASN][1000 genomes]
rs11751172	0.81[ASN][1000 genomes]
rs11751184	0.81[ASN][1000 genomes]
rs12201995	0.90[ASN][1000 genomes]
rs12202314	0.84[EUR][1000 genomes]
rs12664797	0.87[ASN][1000 genomes]
rs13200687	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13205082	0.81[ASN][1000 genomes]
rs2280225	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280226	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280227	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280228	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2280229	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280230	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34528484	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35611098	0.90[ASN][1000 genomes]
rs3763191	0.87[ASN][1000 genomes]
rs68057028	0.90[ASN][1000 genomes]
rs6913882	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914235	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6937759	0.89[ASN][1000 genomes]
rs6938170	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6938214	0.90[ASN][1000 genomes]
rs6938450	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6938843	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6938991	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7752324	0.85[ASN][1000 genomes]
rs7758107	0.85[ASN][1000 genomes]
rs7758317	0.83[ASN][1000 genomes]
rs9463102	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9463103	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9472507	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9472508	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv603009	chr6:45530471-45543530	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv462940	chr6:45532214-45545975	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv603010	chr6:45532214-45545975	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45537200-45542000	Weak transcription	Fetal Thymus	thymus
2	chr6:45537400-45544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:45537400-45559000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:45537600-45542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:45537600-45544400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:45537600-45544600	Weak transcription	Left Ventricle	heart
7	chr6:45537600-45544600	Weak transcription	Lung	lung
8	chr6:45537600-45545200	Weak transcription	NH-A	brain
9	chr6:45537600-45546000	Weak transcription	Right Atrium	heart
10	chr6:45537800-45544600	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:45538000-45542000	Weak transcription	Dnd41	blood
12	chr6:45538000-45542200	Weak transcription	HMEC	breast
13	chr6:45538000-45542600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:45538800-45544800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr6:45539000-45541600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:45539400-45541600	Enhancers	Primary T cells fromperipheralblood	blood
17	chr6:45539400-45544400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:45540000-45541400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:45540000-45541400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr6:45540200-45541200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr6:45540200-45541400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:45540200-45541400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:45540200-45542000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:45540400-45540800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr6:45540400-45541000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr6:45540400-45541000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:45540400-45541000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr6:45540400-45541200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr6:45540600-45540800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:45540600-45541000	Enhancers	Primary T cells from cord blood	blood
31	chr6:45540600-45542800	Enhancers	HepG2	liver
32	chr6:45540600-45543000	Enhancers	Esophagus	oesophagus

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