Variant report

Variant	rs2970800
Chromosome Location	chr12:22219230-22219231
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	chr12:22199280..22201713-chr12:22218617..22220760,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10841928	0.81[AMR][1000 genomes]
rs10841929	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]
rs10841931	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10841934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10841935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10841936	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11046275	0.91[CEU][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11046276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11046281	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11046289	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046290	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046291	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046292	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11046297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2058849	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2111352	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2216296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418037	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2418038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2955515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809204	0.90[ASN][1000 genomes]
rs61921546	0.82[ASN][1000 genomes]
rs6487268	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6487272	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487273	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6487275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487276	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135019	1.00[CEU][hapmap];0.89[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs731355	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7316741	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7316854	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs759582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	nsv1051073	chr12:21910875-22271209	Flanking Bivalent TSS/Enh Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2758298	chr12:22140834-22339299	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2759883	chr12:22140834-22736907	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv438196	chr12:22195202-22234058	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv1850259	chr12:22198865-22244741	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:22200000-22220200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:22200000-22220200	Weak transcription	Lung	lung
3	chr12:22200200-22219600	Weak transcription	Aorta	Aorta
4	chr12:22200400-22220400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr12:22200800-22220800	Weak transcription	Fetal Heart	heart
6	chr12:22201400-22220400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:22202000-22219600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:22202000-22220200	Weak transcription	Fetal Brain Male	brain
9	chr12:22202200-22223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr12:22203800-22220200	Weak transcription	Esophagus	oesophagus
11	chr12:22203800-22220200	Weak transcription	Small Intestine	intestine
12	chr12:22203800-22235200	Weak transcription	Gastric	stomach
13	chr12:22204600-22219400	Weak transcription	Stomach Mucosa	stomach
14	chr12:22204600-22223400	Weak transcription	Pancreas	Pancrea
15	chr12:22205200-22222200	Weak transcription	Fetal Intestine Small	intestine
16	chr12:22207000-22220200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:22207600-22219400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr12:22208000-22219600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr12:22208000-22219800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:22208000-22219800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:22208400-22219600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr12:22208400-22219800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:22208400-22220800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:22208600-22219800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:22208800-22220400	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr12:22209800-22222000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:22209800-22223200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr12:22209800-22229200	Weak transcription	Thymus	Thymus
29	chr12:22210000-22219400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:22210000-22219800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr12:22210000-22221200	Strong transcription	Liver	Liver
32	chr12:22210200-22220200	Weak transcription	Spleen	Spleen
33	chr12:22210400-22221200	Weak transcription	Right Ventricle	heart
34	chr12:22211200-22219600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:22211400-22219600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:22211600-22221000	Weak transcription	Fetal Stomach	stomach
37	chr12:22212000-22220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr12:22212200-22219600	Weak transcription	Brain Substantia Nigra	brain
39	chr12:22212200-22220600	Weak transcription	Hela-S3	cervix
40	chr12:22213000-22221200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:22213200-22219800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:22213200-22219800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:22213400-22219800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:22213400-22220200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr12:22213400-22220600	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr12:22213600-22219400	Strong transcription	HMEC	breast
47	chr12:22213800-22219800	Strong transcription	Fetal Intestine Large	intestine
48	chr12:22214000-22219800	Strong transcription	Adipose Nuclei	Adipose
49	chr12:22214000-22220600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr12:22214400-22220800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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