Variant report

Variant	rs7090006
Chromosome Location	chr10:28582526-28582527
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:28551828..28553630-chr10:28580648..28583187,2	MCF-7	breast:
2	chr10:28580079..28588330-chr10:28588541..28593496,9	MCF-7	breast:
3	chr10:28580424..28583414-chr10:28585033..28588040,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11006932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11006935	0.81[CEU][hapmap]
rs11006948	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11006952	1.00[AFR][1000 genomes]
rs11006955	0.90[AMR][1000 genomes]
rs11006971	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11006972	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11006980	0.87[AFR][1000 genomes]
rs11006981	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs11006982	1.00[AFR][1000 genomes]
rs11006996	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11007002	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12355677	1.00[AFR][1000 genomes]
rs12356457	0.87[AFR][1000 genomes]
rs12357385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12358648	0.92[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs2100614	1.00[YRI][hapmap]
rs2607548	1.00[YRI][hapmap]
rs41406248	0.81[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4412666	1.00[CHB][hapmap]
rs61845938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61845939	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61845943	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61845945	1.00[ASN][1000 genomes]
rs7078271	0.81[CEU][hapmap]
rs7100335	0.86[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7100619	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs7916525	0.81[CEU][hapmap]
rs7923023	0.81[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][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:63 , 50 per page) page: 1 2

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	chr10:28573600-28582600	Weak transcription	Primary T cells from cord blood	blood
6	chr10:28573600-28582600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr10:28573800-28587400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr10:28577800-28585200	Weak transcription	Gastric	stomach
9	chr10:28578400-28583000	Weak transcription	HepG2	liver
10	chr10:28578600-28583800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:28579000-28588400	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr10:28579400-28585000	Weak transcription	Stomach Mucosa	stomach
13	chr10:28580000-28590400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr10:28580200-28582600	Enhancers	Osteobl	bone
15	chr10:28580200-28582800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:28580200-28582800	Enhancers	HSMM	muscle
17	chr10:28580400-28583000	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr10:28580600-28583800	Weak transcription	Left Ventricle	heart
19	chr10:28580600-28587800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr10:28580600-28591000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:28581000-28583800	Weak transcription	Lung	lung
22	chr10:28581000-28583800	Weak transcription	Pancreas	Pancrea
23	chr10:28581200-28584400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr10:28581200-28584600	Weak transcription	Psoas Muscle	Psoas
25	chr10:28581200-28590200	Weak transcription	Fetal Heart	heart
26	chr10:28581400-28582800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr10:28581400-28583200	Weak transcription	Colon Smooth Muscle	Colon
28	chr10:28581400-28584000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr10:28581600-28583600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr10:28581800-28584200	Weak transcription	NHEK	skin
31	chr10:28581800-28584600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr10:28581800-28585000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr10:28581800-28590600	Weak transcription	HMEC	breast
34	chr10:28582000-28582600	Enhancers	HSMMtube	muscle
35	chr10:28582000-28582800	Enhancers	Hela-S3	cervix
36	chr10:28582000-28585400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr10:28582000-28586400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr10:28582200-28582600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr10:28582200-28582600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr10:28582200-28582800	Active TSS	H9 Cell Line	embryonic stem cell
41	chr10:28582200-28582800	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr10:28582200-28582800	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr10:28582200-28582800	Enhancers	Placenta	Placenta
44	chr10:28582200-28583000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr10:28582200-28583000	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr10:28582200-28584000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr10:28582200-28584400	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr10:28582200-28584400	Enhancers	Adipose Nuclei	Adipose
49	chr10:28582200-28590800	Enhancers	Primary T helper naive cells from peripheral blood	blood
50	chr10:28582400-28582600	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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