Variant report

Variant	rs12192948
Chromosome Location	chr6:1842762-1842763
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	chr6:1841908..1843510-chr6:1844738..1846986,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10484694	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs13209589	0.87[CEU][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13218267	0.92[CEU][hapmap]
rs1570534	0.88[CEU][hapmap]
rs1977262	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1980713	0.92[CEU][hapmap]
rs3778544	0.84[CEU][hapmap]
rs3800110	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs3800116	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3800117	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs3800119	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4959159	0.92[CEU][hapmap]
rs4959616	0.83[EUR][1000 genomes]
rs6930647	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7776397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	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	nsv491607	chr6:1580681-1951526	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1020603	chr6:1697548-1921374	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv538093	chr6:1697548-1921374	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv869043	chr6:1744238-2006788	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv538094	chr6:1757776-1907505	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv883383	chr6:1775436-1918572	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv883384	chr6:1787862-1942538	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1019895	chr6:1832936-1882435	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1829800-1856600	Weak transcription	Primary T cells from cord blood	blood
2	chr6:1833400-1843800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr6:1833400-1845800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:1833400-1856600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:1833600-1843000	Weak transcription	Fetal Intestine Small	intestine
6	chr6:1833600-1845800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr6:1833600-1846000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:1833600-1849600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr6:1834000-1848000	Weak transcription	HepG2	liver
10	chr6:1835600-1845800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:1838200-1862200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:1838400-1843200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:1838400-1845000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:1838400-1845800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:1838800-1846000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:1839600-1844200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:1841200-1845800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr6:1841800-1845200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:1842000-1842800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:1842000-1842800	Enhancers	Left Ventricle	heart
21	chr6:1842200-1842800	Enhancers	Pancreas	Pancrea
22	chr6:1842200-1852200	Weak transcription	Thymus	Thymus
23	chr6:1842400-1842800	Enhancers	Gastric	stomach
24	chr6:1842400-1850200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:1842600-1844400	Weak transcription	Aorta	Aorta

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