Variant report

Variant	rs12173320
Chromosome Location	chr6:1967397-1967398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:1961516..1963757-chr6:1966305..1967942,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12175531	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1323631	1.00[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1802	1.00[YRI][hapmap]
rs2146920	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3800130	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3800143	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3927456	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6900111	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6939971	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9405154	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9405155	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9405533	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9405545	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	nsv1032149	chr6:1848148-2006021	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032727	chr6:1900622-2064690	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538095	chr6:1900622-2064690	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv883386	chr6:1910108-2122454	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1905000-1970600	Weak transcription	Spleen	Spleen
2	chr6:1915800-1972800	Weak transcription	Colonic Mucosa	Colon
3	chr6:1940800-1969800	Weak transcription	Lung	lung
4	chr6:1947400-1980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr6:1951400-1972000	Weak transcription	Liver	Liver
6	chr6:1953400-1977800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:1958800-1969800	Weak transcription	Ovary	ovary
8	chr6:1959400-1969800	Weak transcription	Dnd41	blood
9	chr6:1961200-1970000	Weak transcription	Thymus	Thymus
10	chr6:1961200-1970400	Weak transcription	Primary T cells from cord blood	blood
11	chr6:1961200-1970600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr6:1961600-1972200	Weak transcription	Stomach Mucosa	stomach
13	chr6:1962600-1969800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:1962600-1970600	Weak transcription	Gastric	stomach
15	chr6:1964600-1969600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:1964600-1969800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:1964800-1969600	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:1964800-1969800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:1965800-1968200	Enhancers	Fetal Kidney	kidney
20	chr6:1966800-1967400	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr6:1967000-1967400	Weak transcription	Fetal Lung	lung
22	chr6:1967200-1967400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:1967200-1967400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr6:1967200-1971800	Weak transcription	HepG2	liver

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