Variant report

Variant	rs12660631
Chromosome Location	chr6:55747433-55747434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:55747110..55749707-chr6:55758918..55761068,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10485079	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10498807	0.91[ASN][1000 genomes]
rs12190955	0.89[ASN][1000 genomes]
rs12193440	0.89[ASN][1000 genomes]
rs12196975	0.91[ASN][1000 genomes]
rs12197097	0.91[ASN][1000 genomes]
rs12202960	0.91[ASN][1000 genomes]
rs12204345	0.89[ASN][1000 genomes]
rs12209008	0.91[ASN][1000 genomes]
rs12209061	0.91[ASN][1000 genomes]
rs12210486	0.91[ASN][1000 genomes]
rs12210591	0.91[ASN][1000 genomes]
rs12210906	0.91[ASN][1000 genomes]
rs12211480	0.82[ASN][1000 genomes]
rs12215767	0.91[ASN][1000 genomes]
rs12215768	0.91[ASN][1000 genomes]
rs12662574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1374542	0.91[ASN][1000 genomes]
rs1374546	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1447130	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16887320	0.85[AMR][1000 genomes]
rs16887333	0.85[AMR][1000 genomes]
rs16887397	0.81[EUR][1000 genomes]
rs16887398	0.81[EUR][1000 genomes]
rs16887399	0.81[EUR][1000 genomes]
rs16887402	0.81[EUR][1000 genomes]
rs17736107	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1868033	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1900526	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1900527	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2084290	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2100105	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2100107	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2197643	0.81[EUR][1000 genomes]
rs2397191	0.91[ASN][1000 genomes]
rs2397194	0.91[ASN][1000 genomes]
rs3798819	0.89[JPT][hapmap]
rs3798821	0.85[AMR][1000 genomes]
rs4623244	0.91[ASN][1000 genomes]
rs5007842	0.85[ASN][1000 genomes]
rs59418534	0.91[ASN][1000 genomes]
rs6908374	0.89[ASN][1000 genomes]
rs6909631	0.91[ASN][1000 genomes]
rs6910852	0.93[ASN][1000 genomes]
rs6915768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6927010	0.91[ASN][1000 genomes]
rs6927212	0.91[ASN][1000 genomes]
rs6927427	0.91[ASN][1000 genomes]
rs6928174	0.89[ASN][1000 genomes]
rs6928604	0.89[ASN][1000 genomes]
rs6928783	0.89[ASN][1000 genomes]
rs6931303	0.81[EUR][1000 genomes]
rs6931309	0.93[ASN][1000 genomes]
rs6931324	0.93[ASN][1000 genomes]
rs6931472	0.93[ASN][1000 genomes]
rs6935710	0.93[ASN][1000 genomes]
rs6935907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7453408	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9382566	0.91[ASN][1000 genomes]
rs9382567	0.91[ASN][1000 genomes]
rs9382568	0.80[ASN][1000 genomes]
rs9396162	0.91[ASN][1000 genomes]
rs9475448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475450	0.93[ASN][1000 genomes]
rs9475451	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9475452	0.91[ASN][1000 genomes]
rs9475453	0.91[ASN][1000 genomes]
rs9968834	0.91[ASN][1000 genomes]
rs9969009	0.91[ASN][1000 genomes]
rs9969010	0.91[ASN][1000 genomes]
rs9969100	0.91[ASN][1000 genomes]
rs9969103	0.91[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	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2752670	chr6:55614978-55781605	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1032684	chr6:55680473-55766876	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024174	chr6:55713889-55829936	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1029301	chr6:55713889-55834480	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55742800-55747600	Weak transcription	Fetal Lung	lung
2	chr6:55745600-55750600	Enhancers	Fetal Heart	heart
3	chr6:55745800-55748600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:55745800-55749200	Enhancers	Hela-S3	cervix
5	chr6:55746600-55748400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:55746800-55749800	Enhancers	HUVEC	blood vessel
7	chr6:55747000-55748200	Enhancers	NHEK	skin
8	chr6:55747000-55748400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:55747000-55748400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:55747000-55748400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr6:55747000-55748600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:55747000-55748600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:55747000-55748600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:55747000-55748600	Enhancers	Osteobl	bone
15	chr6:55747200-55747600	Flanking Active TSS	A549	lung
16	chr6:55747200-55747800	Enhancers	NH-A	brain
17	chr6:55747200-55748000	Enhancers	Adipose Nuclei	Adipose
18	chr6:55747200-55748000	Enhancers	Colon Smooth Muscle	Colon
19	chr6:55747200-55748200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:55747200-55748200	Enhancers	NHDF-Ad	bronchial
21	chr6:55747200-55748200	Enhancers	NHLF	lung
22	chr6:55747200-55748400	Enhancers	HMEC	breast
23	chr6:55747200-55748600	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:55747200-55748600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:55747400-55748000	Enhancers	Rectal Smooth Muscle	rectum
26	chr6:55747400-55749200	Enhancers	Pancreatic Islets	Pancreatic Islet

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