Variant report

Variant	rs12340179
Chromosome Location	chr9:2228078-2228079
allele	A/C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2226247..2228750-chr9:2234155..2236078,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10081685	0.85[AMR][1000 genomes]
rs10081729	0.85[AMR][1000 genomes]
rs10118435	0.85[AMR][1000 genomes]
rs10118773	0.85[AMR][1000 genomes]
rs10965299	1.00[AMR][1000 genomes]
rs9657574	0.85[AMR][1000 genomes]
rs9657611	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv892057	chr9:2144687-2241994	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv892059	chr9:2198627-2255397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1033628	chr9:2215179-2303623	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv539927	chr9:2215179-2303623	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892060	chr9:2218129-2261944	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2223200-2228400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr9:2223600-2240800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:2224600-2229400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:2225600-2228400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:2226800-2229000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr9:2227200-2229200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr9:2227400-2234400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:2227600-2229400	Enhancers	Pancreas	Pancrea
9	chr9:2227800-2229400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:2227800-2230200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:2227800-2231400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:2227800-2231600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr9:2227800-2231600	Weak transcription	Ovary	ovary
14	chr9:2227800-2234400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:2228000-2228400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr9:2228000-2229000	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr9:2228000-2229800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr9:2228000-2231000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr9:2228000-2231200	Weak transcription	Osteobl	bone
20	chr9:2228000-2231400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:2228000-2234600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links