Variant report

Variant	rs11172805
Chromosome Location	chr12:59290279-59290280
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:59288180..59291179-chr12:59304081..59306337,2	MCF-7	breast:
2	chr12:59288987..59291985-chr12:59299185..59301925,2	MCF-7	breast:
3	chr12:59288053..59290390-chr12:59292489..59294032,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1020031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877182	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10877183	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10877185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172790	0.83[TSI][hapmap]
rs11172795	0.81[EUR][1000 genomes]
rs11172797	0.86[EUR][1000 genomes]
rs11172801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172802	0.92[EUR][1000 genomes]
rs11172804	0.92[EUR][1000 genomes]
rs11172806	0.89[EUR][1000 genomes]
rs11172807	0.92[EUR][1000 genomes]
rs11172808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172809	0.92[EUR][1000 genomes]
rs11172811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172812	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172816	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11172817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172818	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12146851	0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs17120227	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17617428	0.81[EUR][1000 genomes]
rs2167030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279718	0.83[TSI][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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1067596	chr12:59167152-59764208	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv492251	chr12:59167152-59764208	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59262600-59295000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:59266000-59311000	Weak transcription	Fetal Thymus	thymus
3	chr12:59275000-59300800	Weak transcription	HSMMtube	muscle
4	chr12:59275200-59297800	Weak transcription	Hela-S3	cervix
5	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:59282400-59290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:59282400-59297800	Weak transcription	A549	lung
9	chr12:59283400-59298000	Weak transcription	Fetal Brain Male	brain
10	chr12:59283800-59300400	Weak transcription	Placenta	Placenta
11	chr12:59284000-59294800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr12:59284000-59297800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:59284000-59297800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:59284000-59298000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:59284000-59298000	Weak transcription	HSMM	muscle
16	chr12:59284000-59300800	Weak transcription	Colonic Mucosa	Colon
17	chr12:59284000-59300800	Weak transcription	HepG2	liver
18	chr12:59284200-59297800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr12:59284200-59297800	Weak transcription	Liver	Liver
20	chr12:59284200-59304600	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr12:59284600-59298000	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:59285000-59290400	Enhancers	Brain Cingulate Gyrus	brain
23	chr12:59285600-59292400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr12:59286000-59292600	Enhancers	NHEK	skin
25	chr12:59286400-59291000	Enhancers	Duodenum Smooth Muscle	Duodenum
26	chr12:59286600-59292000	Enhancers	Colon Smooth Muscle	Colon
27	chr12:59286800-59290800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:59286800-59298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:59287600-59297800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:59287800-59290800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:59287800-59291600	Weak transcription	Small Intestine	intestine
32	chr12:59287800-59297800	Weak transcription	NH-A	brain
33	chr12:59287800-59298000	Weak transcription	Brain Angular Gyrus	brain
34	chr12:59287800-59301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr12:59288000-59290600	Enhancers	Brain Anterior Caudate	brain
36	chr12:59288000-59290600	Enhancers	Brain Substantia Nigra	brain
37	chr12:59288000-59293400	Weak transcription	NHDF-Ad	bronchial
38	chr12:59288000-59297800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:59288000-59297800	Weak transcription	Osteobl	bone
40	chr12:59288200-59290600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr12:59288200-59290600	Enhancers	Brain Hippocampus Middle	brain
42	chr12:59288200-59298000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:59288200-59298600	Weak transcription	NHLF	lung
44	chr12:59288600-59290400	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr12:59288600-59293000	Enhancers	Ovary	ovary
46	chr12:59288600-59295200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:59288800-59291800	Enhancers	Psoas Muscle	Psoas
48	chr12:59288800-59292200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:59288800-59297800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:59289000-59290400	Enhancers	Pancreatic Islets	Pancreatic Islet

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