Variant report

Variant	rs180431
Chromosome Location	chr12:47179317-47179318
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	chr12:47170591..47173470-chr12:47179230..47182105,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11183610	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs11183618	0.88[CHB][hapmap]
rs11183621	1.00[EUR][1000 genomes]
rs12298652	1.00[EUR][1000 genomes]
rs12301214	0.87[AMR][1000 genomes]
rs12301345	1.00[EUR][1000 genomes]
rs12301396	1.00[EUR][1000 genomes]
rs12304394	1.00[EUR][1000 genomes]
rs12307687	0.84[AMR][1000 genomes]
rs12309262	1.00[EUR][1000 genomes]
rs12316757	1.00[EUR][1000 genomes]
rs12321267	0.88[CHB][hapmap]
rs12581848	1.00[CHB][hapmap]
rs17097246	1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs17097355	1.00[EUR][1000 genomes]
rs1860372	0.88[CHB][hapmap]
rs235621	0.82[MEX][hapmap]
rs3794308	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs3862137	1.00[CHB][hapmap]
rs4768740	0.90[MEX][hapmap]
rs4768758	0.87[AMR][1000 genomes]
rs4768759	0.89[AMR][1000 genomes]
rs6582676	0.82[AMR][1000 genomes]
rs7310614	0.90[MEX][hapmap]
rs977069	0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv826361	chr12:47159545-47200894	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47164200-47187800	Genic enhancers	Liver	Liver
2	chr12:47165200-47187200	Weak transcription	Fetal Kidney	kidney
3	chr12:47165600-47182000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:47168400-47180800	Weak transcription	Pancreas	Pancrea
5	chr12:47169400-47180000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:47169400-47182200	Weak transcription	Psoas Muscle	Psoas
7	chr12:47169400-47185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:47175600-47183000	Weak transcription	Aorta	Aorta
9	chr12:47177200-47180800	Enhancers	Osteobl	bone
10	chr12:47177200-47181000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:47177400-47181200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr12:47177400-47182400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:47177600-47180800	Enhancers	NHLF	lung
14	chr12:47177600-47181200	Enhancers	HSMM	muscle
15	chr12:47177800-47181000	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr12:47177800-47182400	Enhancers	NHDF-Ad	bronchial
17	chr12:47178000-47180800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:47178200-47180000	Weak transcription	Fetal Stomach	stomach
19	chr12:47178200-47181400	Enhancers	Hela-S3	cervix
20	chr12:47178400-47183400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:47178600-47179400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:47178600-47181800	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr12:47178600-47182200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:47178600-47182600	Enhancers	HSMMtube	muscle
25	chr12:47178800-47180000	Weak transcription	HMEC	breast
26	chr12:47179000-47179400	Enhancers	GM12878-XiMat	blood
27	chr12:47179000-47180000	Weak transcription	NH-A	brain
28	chr12:47179000-47180000	Weak transcription	NHEK	skin
29	chr12:47179000-47180800	Weak transcription	A549	lung
30	chr12:47179000-47181400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:47179000-47181600	Weak transcription	HepG2	liver
32	chr12:47179000-47189800	Weak transcription	Fetal Lung	lung
33	chr12:47179200-47179600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr12:47179200-47180200	Weak transcription	HUVEC	blood vessel
35	chr12:47179200-47180600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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