Variant report

Variant	rs62565109
Chromosome Location	chr9:79084215-79084216
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	chr9:79078849..79081929-chr9:79083400..79086374,3	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10116800	0.83[ASN][1000 genomes]
rs10118954	0.83[ASN][1000 genomes]
rs10125012	0.83[ASN][1000 genomes]
rs10125667	0.83[ASN][1000 genomes]
rs10781358	0.83[ASN][1000 genomes]
rs10781360	0.83[ASN][1000 genomes]
rs10869770	0.83[ASN][1000 genomes]
rs10869781	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11144870	0.83[ASN][1000 genomes]
rs11144875	0.83[ASN][1000 genomes]
rs11144878	0.83[ASN][1000 genomes]
rs11144881	0.83[ASN][1000 genomes]
rs11144887	0.83[ASN][1000 genomes]
rs11144905	0.80[ASN][1000 genomes]
rs11144908	0.94[ASN][1000 genomes]
rs11144909	0.94[ASN][1000 genomes]
rs1129399	0.83[ASN][1000 genomes]
rs11791951	0.83[ASN][1000 genomes]
rs11793613	0.83[ASN][1000 genomes]
rs11794019	0.83[ASN][1000 genomes]
rs12156473	0.83[ASN][1000 genomes]
rs12351617	0.94[ASN][1000 genomes]
rs12377856	0.83[ASN][1000 genomes]
rs12377878	0.83[ASN][1000 genomes]
rs12378822	0.85[ASN][1000 genomes]
rs12380332	0.89[ASN][1000 genomes]
rs1324212	0.80[ASN][1000 genomes]
rs1324213	0.83[ASN][1000 genomes]
rs1951910	0.83[ASN][1000 genomes]
rs4571791	0.83[ASN][1000 genomes]
rs55740812	0.88[ASN][1000 genomes]
rs57339182	0.89[ASN][1000 genomes]
rs57429014	0.80[ASN][1000 genomes]
rs57480680	0.83[ASN][1000 genomes]
rs58651349	0.94[ASN][1000 genomes]
rs59322809	0.94[ASN][1000 genomes]
rs62564444	0.80[ASN][1000 genomes]
rs62564446	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62564449	0.94[ASN][1000 genomes]
rs62564454	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs62567918	0.88[ASN][1000 genomes]
rs62568690	0.83[ASN][1000 genomes]
rs62568692	0.83[ASN][1000 genomes]
rs6560516	0.83[ASN][1000 genomes]
rs6560524	0.94[ASN][1000 genomes]
rs7025942	0.83[ASN][1000 genomes]
rs7026067	0.83[ASN][1000 genomes]
rs7029439	0.83[ASN][1000 genomes]
rs7035385	0.83[ASN][1000 genomes]
rs7038009	0.83[ASN][1000 genomes]
rs7040138	0.83[ASN][1000 genomes]
rs7041690	0.83[ASN][1000 genomes]
rs7047489	0.83[ASN][1000 genomes]
rs7049245	0.83[ASN][1000 genomes]
rs7851616	0.83[ASN][1000 genomes]
rs7852884	0.83[ASN][1000 genomes]
rs7853410	0.83[ASN][1000 genomes]
rs7854540	0.89[ASN][1000 genomes]
rs7859327	0.83[ASN][1000 genomes]
rs7875575	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893478	chr9:78933874-79101006	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79075200-79085200	Weak transcription	Esophagus	oesophagus
2	chr9:79075200-79087200	Weak transcription	Spleen	Spleen
3	chr9:79075400-79086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:79075400-79086800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:79075400-79087200	Weak transcription	Colonic Mucosa	Colon
6	chr9:79075400-79089800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:79075400-79090200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:79075400-79101000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:79075600-79117800	Weak transcription	Primary T cells from cord blood	blood
10	chr9:79076000-79087400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:79076000-79088000	Weak transcription	NHDF-Ad	bronchial
12	chr9:79076800-79087200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:79077600-79092800	Weak transcription	Fetal Stomach	stomach
14	chr9:79078600-79092400	Weak transcription	HMEC	breast
15	chr9:79078800-79086800	Weak transcription	Small Intestine	intestine
16	chr9:79078800-79087000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:79080600-79085000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:79080600-79086800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr9:79080800-79117200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:79081000-79085800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:79081000-79086000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:79081000-79087200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr9:79081200-79086800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr9:79081200-79087000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:79081400-79087400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:79081400-79088800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr9:79081600-79086200	Weak transcription	Fetal Thymus	thymus
28	chr9:79081800-79093000	Weak transcription	Lung	lung
29	chr9:79081800-79117200	Weak transcription	Gastric	stomach
30	chr9:79082000-79086200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr9:79082600-79085600	Weak transcription	GM12878-XiMat	blood
32	chr9:79082600-79085800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr9:79082600-79117600	Weak transcription	NHLF	lung
34	chr9:79082800-79087200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:79083000-79084600	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr9:79083000-79088800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:79083200-79085800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr9:79083200-79086000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr9:79083400-79085200	Strong transcription	Fetal Intestine Small	intestine
40	chr9:79083400-79086000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr9:79083600-79085000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr9:79083600-79085200	Weak transcription	Primary B cells from cord blood	blood
43	chr9:79083600-79085200	Weak transcription	Fetal Intestine Large	intestine
44	chr9:79083600-79085800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr9:79083600-79085800	Weak transcription	Duodenum Mucosa	Duodenum
46	chr9:79083600-79090200	Weak transcription	HSMM	muscle
47	chr9:79083600-79090400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr9:79083600-79092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr9:79083800-79085200	Weak transcription	Primary B cells from peripheral blood	blood
50	chr9:79083800-79085600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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