Variant report

Variant	rs12219880
Chromosome Location	chr10:28580332-28580333
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	chr10:28580079..28588330-chr10:28588541..28593496,9	MCF-7	breast:
2	chr10:28564267..28567183-chr10:28578724..28581652,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10826441	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10826442	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11006983	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11006986	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11006987	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11006988	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12570446	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3936496	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3936497	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3936499	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3939436	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7089787	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7895813	0.97[AMR][1000 genomes];0.84[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	nsv917149	chr10:28018919-28688694	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1041555	chr10:28419399-29304934	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1037863	chr10:28419399-29378871	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	nsv540521	chr10:28419399-29378871	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv437663	chr10:28562647-28585496	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28550400-28582600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr10:28571400-28584600	Weak transcription	Fetal Intestine Small	intestine
3	chr10:28571600-28583800	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:28571800-28587800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr10:28572000-28580400	Weak transcription	Aorta	Aorta
6	chr10:28572400-28582200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:28573600-28581000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:28573600-28582600	Weak transcription	Primary T cells from cord blood	blood
9	chr10:28573600-28582600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr10:28573800-28581000	Weak transcription	Fetal Heart	heart
11	chr10:28573800-28587400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr10:28575800-28581000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr10:28575800-28582000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:28576400-28581000	Weak transcription	Colon Smooth Muscle	Colon
15	chr10:28576400-28582200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr10:28577800-28585200	Weak transcription	Gastric	stomach
17	chr10:28578400-28583000	Weak transcription	HepG2	liver
18	chr10:28578600-28583800	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr10:28578800-28582200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr10:28579000-28588400	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr10:28579400-28585000	Weak transcription	Stomach Mucosa	stomach
22	chr10:28579600-28580400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr10:28580000-28581000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr10:28580000-28581000	Enhancers	NH-A	brain
25	chr10:28580000-28581200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr10:28580000-28581800	Enhancers	HMEC	breast
27	chr10:28580000-28590400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr10:28580200-28580400	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr10:28580200-28580600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr10:28580200-28580600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr10:28580200-28580600	Enhancers	Esophagus	oesophagus
32	chr10:28580200-28580600	Enhancers	Left Ventricle	heart
33	chr10:28580200-28581000	Enhancers	Lung	lung
34	chr10:28580200-28581000	Enhancers	Pancreas	Pancrea
35	chr10:28580200-28581200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr10:28580200-28581200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr10:28580200-28581200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr10:28580200-28581200	Enhancers	Psoas Muscle	Psoas
39	chr10:28580200-28581200	Enhancers	HSMMtube	muscle
40	chr10:28580200-28581400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr10:28580200-28581600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr10:28580200-28581800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:28580200-28581800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr10:28580200-28581800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr10:28580200-28581800	Enhancers	NHEK	skin
46	chr10:28580200-28582600	Enhancers	Osteobl	bone
47	chr10:28580200-28582800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr10:28580200-28582800	Enhancers	HSMM	muscle

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