Variant report

Variant	rs180435
Chromosome Location	chr12:47180370-47180371
allele	C/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: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10881001	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183616	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11183617	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12306007	0.83[CEU][hapmap]
rs180438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860371	0.89[ASN][1000 genomes]
rs2079787	0.91[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2191162	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2250010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429472	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2429473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2465604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2465608	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2715788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

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:36 , 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	chr12:47169400-47182200	Weak transcription	Psoas Muscle	Psoas
6	chr12:47169400-47185200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:47175600-47183000	Weak transcription	Aorta	Aorta
8	chr12:47177200-47180800	Enhancers	Osteobl	bone
9	chr12:47177200-47181000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr12:47177400-47181200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:47177400-47182400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:47177600-47180800	Enhancers	NHLF	lung
13	chr12:47177600-47181200	Enhancers	HSMM	muscle
14	chr12:47177800-47181000	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr12:47177800-47182400	Enhancers	NHDF-Ad	bronchial
16	chr12:47178000-47180800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr12:47178200-47181400	Enhancers	Hela-S3	cervix
18	chr12:47178400-47183400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:47178600-47181800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr12:47178600-47182200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:47178600-47182600	Enhancers	HSMMtube	muscle
22	chr12:47179000-47180800	Weak transcription	A549	lung
23	chr12:47179000-47181400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:47179000-47181600	Weak transcription	HepG2	liver
25	chr12:47179000-47189800	Weak transcription	Fetal Lung	lung
26	chr12:47179200-47180600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:47179400-47182000	Weak transcription	GM12878-XiMat	blood
28	chr12:47179400-47182400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:47179600-47180600	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr12:47180000-47180400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:47180000-47180400	Enhancers	Fetal Stomach	stomach
32	chr12:47180000-47181800	Enhancers	HMEC	breast
33	chr12:47180000-47182200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:47180000-47182400	Enhancers	NH-A	brain
35	chr12:47180000-47182600	Enhancers	NHEK	skin
36	chr12:47180200-47183000	Enhancers	HUVEC	blood vessel

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