Variant report

Variant	rs12200877
Chromosome Location	chr6:1716354-1716355
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	chr6:1714828..1716630-chr6:1737875..1739669,2	MCF-7	breast:

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12209250	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs960295	0.81[CHB][hapmap];0.85[ASN][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	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv530888	chr6:1605768-1739933	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1015682	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv538092	chr6:1661111-1717786	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv432843	chr6:1694719-1725261	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	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
11	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
12	esv1814339	chr6:1702106-1716710	Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1693600-1718200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:1694200-1724400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:1695400-1729400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:1695800-1731400	Weak transcription	Fetal Intestine Large	intestine
5	chr6:1699800-1716600	Weak transcription	Primary T cells from cord blood	blood
6	chr6:1701200-1749400	Weak transcription	Colonic Mucosa	Colon
7	chr6:1703600-1720800	Weak transcription	Right Atrium	heart
8	chr6:1704000-1721000	Weak transcription	Lung	lung
9	chr6:1704200-1725200	Weak transcription	Primary B cells from cord blood	blood
10	chr6:1704600-1720800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:1705800-1724000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:1706000-1724200	Weak transcription	NHEK	skin
13	chr6:1706800-1726800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr6:1707200-1724600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr6:1707800-1724600	Weak transcription	GM12878-XiMat	blood
16	chr6:1708200-1724600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr6:1708800-1717600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:1709800-1720800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:1709800-1724400	Weak transcription	Spleen	Spleen
20	chr6:1710000-1718400	Weak transcription	Gastric	stomach
21	chr6:1710000-1718400	Weak transcription	Pancreas	Pancrea
22	chr6:1711000-1717200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:1711000-1724200	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr6:1712400-1720800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr6:1713200-1719800	Strong transcription	HepG2	liver
26	chr6:1713400-1724800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:1713400-1726000	Weak transcription	Dnd41	blood
28	chr6:1713800-1722800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:1714600-1719800	Strong transcription	Fetal Intestine Small	intestine
30	chr6:1715200-1716600	Weak transcription	Aorta	Aorta
31	chr6:1715400-1717200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr6:1715800-1720800	Weak transcription	Left Ventricle	heart
33	chr6:1715800-1724400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr6:1716000-1749200	Weak transcription	Rectal Mucosa Donor 29	rectum

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