Variant report

Variant	rs12344941
Chromosome Location	chr9:79081454-79081455
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: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10119532	0.85[CHB][hapmap]
rs10781363	0.80[ASN][1000 genomes]
rs2490573	0.80[EUR][1000 genomes]
rs2501925	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2501933	0.80[EUR][1000 genomes]
rs2501935	0.80[EUR][1000 genomes]
rs3739516	0.83[CHB][hapmap]
rs4526423	0.83[CHB][hapmap]
rs4745551	0.81[CHB][hapmap]
rs4745552	0.86[CHB][hapmap]
rs509326	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs638410	0.91[JPT][hapmap]
rs7858497	0.83[CHB][hapmap]
rs785933	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs785936	0.86[CHB][hapmap]
rs7871849	0.86[CHB][hapmap]

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:55 , 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	chr9:79075600-79083800	Enhancers	Primary B cells from peripheral blood	blood
10	chr9:79075600-79117800	Weak transcription	Primary T cells from cord blood	blood
11	chr9:79076000-79083600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:79076000-79084000	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr9:79076000-79087400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:79076000-79088000	Weak transcription	NHDF-Ad	bronchial
15	chr9:79076200-79083000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:79076200-79083000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:79076800-79087200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:79077400-79083200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:79077600-79082600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:79077600-79083000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:79077600-79083400	Genic enhancers	Fetal Intestine Small	intestine
22	chr9:79077600-79092800	Weak transcription	Fetal Stomach	stomach
23	chr9:79078400-79083000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:79078600-79092400	Weak transcription	HMEC	breast
25	chr9:79078800-79082600	Enhancers	GM12878-XiMat	blood
26	chr9:79078800-79086800	Weak transcription	Small Intestine	intestine
27	chr9:79078800-79087000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:79080000-79082200	Enhancers	Fetal Intestine Large	intestine
29	chr9:79080400-79081600	Genic enhancers	Duodenum Mucosa	Duodenum
30	chr9:79080400-79081600	Enhancers	Fetal Thymus	thymus
31	chr9:79080400-79081800	Enhancers	Gastric	stomach
32	chr9:79080400-79082000	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr9:79080400-79083200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:79080400-79083600	Enhancers	Primary B cells from cord blood	blood
35	chr9:79080600-79081800	Enhancers	Primary hematopoietic stem cells	blood
36	chr9:79080600-79082000	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr9:79080600-79082600	Strong transcription	NHLF	lung
38	chr9:79080600-79083600	Strong transcription	HSMM	muscle
39	chr9:79080600-79085000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:79080600-79086800	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr9:79080800-79083200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:79080800-79083200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:79080800-79117200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:79081000-79082400	Weak transcription	Stomach Mucosa	stomach
45	chr9:79081000-79083600	Strong transcription	Muscle Satellite Cultured Cells	--
46	chr9:79081000-79084000	Strong transcription	Osteobl	bone
47	chr9:79081000-79085800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr9:79081000-79086000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:79081000-79087200	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr9:79081200-79084200	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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