Variant report

Variant	rs11172802
Chromosome Location	chr12:59288965-59288966
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:59288180..59291179-chr12:59304081..59306337,2	MCF-7	breast:
2	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	0.92[EUR][1000 genomes]
rs10877182	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10877183	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10877185	0.92[EUR][1000 genomes]
rs10877187	0.83[EUR][1000 genomes]
rs11172795	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172797	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11172801	0.92[EUR][1000 genomes]
rs11172804	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172805	0.92[EUR][1000 genomes]
rs11172806	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172807	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172808	0.92[EUR][1000 genomes]
rs11172809	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172811	0.92[EUR][1000 genomes]
rs11172812	0.92[EUR][1000 genomes]
rs11172816	0.92[EUR][1000 genomes]
rs11172817	0.92[EUR][1000 genomes]
rs11172818	0.92[EUR][1000 genomes]
rs12146851	0.86[EUR][1000 genomes]
rs12426555	0.83[EUR][1000 genomes]
rs17120227	0.87[EUR][1000 genomes]
rs17617428	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2167030	0.92[EUR][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	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:93 , 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	chr12:59273800-59289000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:59274800-59289000	Weak transcription	Right Ventricle	heart
5	chr12:59275000-59300800	Weak transcription	HSMMtube	muscle
6	chr12:59275200-59297800	Weak transcription	Hela-S3	cervix
7	chr12:59279000-59310800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr12:59279200-59290200	Weak transcription	Fetal Heart	heart
9	chr12:59279200-59309400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:59281000-59289400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:59282400-59290200	Weak transcription	Fetal Brain Female	brain
12	chr12:59282400-59290600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr12:59282400-59297800	Weak transcription	A549	lung
14	chr12:59283400-59298000	Weak transcription	Fetal Brain Male	brain
15	chr12:59283800-59300400	Weak transcription	Placenta	Placenta
16	chr12:59284000-59294800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:59284000-59297800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:59284000-59297800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:59284000-59298000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:59284000-59298000	Weak transcription	HSMM	muscle
21	chr12:59284000-59300800	Weak transcription	Colonic Mucosa	Colon
22	chr12:59284000-59300800	Weak transcription	HepG2	liver
23	chr12:59284200-59289000	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:59284200-59290200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:59284200-59297800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:59284200-59297800	Weak transcription	Liver	Liver
27	chr12:59284200-59304600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:59284600-59298000	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:59285000-59290400	Enhancers	Brain Cingulate Gyrus	brain
30	chr12:59285600-59292400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr12:59286000-59290000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:59286000-59292600	Enhancers	NHEK	skin
33	chr12:59286200-59289400	Strong transcription	Fetal Intestine Large	intestine
34	chr12:59286400-59289000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:59286400-59291000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr12:59286600-59289000	Genic enhancers	HMEC	breast
37	chr12:59286600-59292000	Enhancers	Colon Smooth Muscle	Colon
38	chr12:59286800-59289000	Enhancers	Fetal Lung	lung
39	chr12:59286800-59290800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:59286800-59298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr12:59287000-59289600	Enhancers	Stomach Mucosa	stomach
42	chr12:59287200-59289200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr12:59287200-59289200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:59287200-59290000	Enhancers	Esophagus	oesophagus
45	chr12:59287400-59289200	Genic enhancers	Fetal Intestine Small	intestine
46	chr12:59287600-59289000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:59287600-59289600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:59287600-59297800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr12:59287800-59289000	Weak transcription	Lung	lung
50	chr12:59287800-59290800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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