Variant report

Variant	rs7743218
Chromosome Location	chr6:1961778-1961779
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	chr6:1961516..1963757-chr6:1966305..1967942,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-10	chr6:1961744-1961823	NONHSAT106568

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11965992	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2449970	1.00[AMR][1000 genomes]
rs35974385	0.94[AFR][1000 genomes]
rs6596861	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6911723	0.85[AFR][1000 genomes]
rs6919560	1.00[ASW][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7763272	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7769222	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9392339	1.00[GIH][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:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1905000-1970600	Weak transcription	Spleen	Spleen
2	chr6:1905400-1962000	Weak transcription	Pancreas	Pancrea
3	chr6:1910200-1965800	Weak transcription	Small Intestine	intestine
4	chr6:1915800-1972800	Weak transcription	Colonic Mucosa	Colon
5	chr6:1919600-1962400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr6:1935800-1964200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:1940800-1967200	Weak transcription	Primary B cells from cord blood	blood
8	chr6:1940800-1969800	Weak transcription	Lung	lung
9	chr6:1943600-1966000	Weak transcription	GM12878-XiMat	blood
10	chr6:1944400-1964000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr6:1946000-1964000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:1947400-1980000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr6:1950200-1964200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr6:1950200-1966400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr6:1951400-1972000	Weak transcription	Liver	Liver
16	chr6:1953000-1962400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:1953400-1977800	Weak transcription	Fetal Intestine Small	intestine
18	chr6:1953600-1962000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:1953600-1963000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr6:1953600-1967200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:1953800-1962400	Weak transcription	Osteobl	bone
22	chr6:1954800-1964200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:1958800-1961800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:1958800-1963800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:1958800-1969800	Weak transcription	Ovary	ovary
26	chr6:1959000-1963800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:1959400-1965800	Weak transcription	Fetal Kidney	kidney
28	chr6:1959400-1966000	Weak transcription	Fetal Lung	lung
29	chr6:1959400-1969800	Weak transcription	Dnd41	blood
30	chr6:1961000-1965600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:1961200-1962000	Weak transcription	Placenta	Placenta
32	chr6:1961200-1963800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:1961200-1964600	Weak transcription	Fetal Intestine Large	intestine
34	chr6:1961200-1970000	Weak transcription	Thymus	Thymus
35	chr6:1961200-1970400	Weak transcription	Primary T cells from cord blood	blood
36	chr6:1961200-1970600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr6:1961400-1961800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:1961400-1961800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr6:1961400-1962000	Weak transcription	Gastric	stomach
40	chr6:1961400-1965000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:1961600-1965800	Weak transcription	HepG2	liver
42	chr6:1961600-1972200	Weak transcription	Stomach Mucosa	stomach

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