Variant report

Variant	rs11006990
Chromosome Location	chr10:28581773-28581774
allele	A/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:
4	chr10:28580670..28582435-chr10:28590410..28593368,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10826445	0.95[AMR][1000 genomes]
rs10826446	0.95[AMR][1000 genomes]
rs11006923	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11006927	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11006928	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11006933	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11006937	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11006938	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11006939	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11006947	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006950	0.88[AMR][1000 genomes]
rs11006954	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006958	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006960	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11006964	0.87[EUR][1000 genomes]
rs11006989	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11006992	0.87[AMR][1000 genomes]
rs11006994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006995	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11006997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006998	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11006999	0.90[AMR][1000 genomes]
rs11007000	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11007003	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11007004	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11007005	0.83[ASN][1000 genomes]
rs11007006	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12218294	0.95[AMR][1000 genomes]
rs12570440	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17831816	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1984853	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2368306	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35016093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3842931	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs3847387	0.87[AMR][1000 genomes]
rs4598572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604776	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs57137891	0.86[AFR][1000 genomes]
rs57441879	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs59663023	0.86[AFR][1000 genomes]
rs60648801	0.86[AFR][1000 genomes]
rs7901835	0.95[AMR][1000 genomes]
rs7902785	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7903242	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915405	0.83[AMR][1000 genomes]
rs7916067	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs7916711	0.95[AMR][1000 genomes]
rs7916740	0.95[AMR][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:50 , 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	chr10:28572400-28582200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr10:28573600-28582600	Weak transcription	Primary T cells from cord blood	blood
7	chr10:28573600-28582600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr10:28573800-28587400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr10:28575800-28582000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr10:28576400-28582200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr10:28577800-28585200	Weak transcription	Gastric	stomach
12	chr10:28578400-28583000	Weak transcription	HepG2	liver
13	chr10:28578600-28583800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr10:28578800-28582200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr10:28579000-28588400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr10:28579400-28585000	Weak transcription	Stomach Mucosa	stomach
17	chr10:28580000-28581800	Enhancers	HMEC	breast
18	chr10:28580000-28590400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr10:28580200-28581800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:28580200-28581800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr10:28580200-28581800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:28580200-28581800	Enhancers	NHEK	skin
23	chr10:28580200-28582600	Enhancers	Osteobl	bone
24	chr10:28580200-28582800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr10:28580200-28582800	Enhancers	HSMM	muscle
26	chr10:28580400-28582200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr10:28580400-28583000	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr10:28580600-28582400	Weak transcription	Esophagus	oesophagus
29	chr10:28580600-28583800	Weak transcription	Left Ventricle	heart
30	chr10:28580600-28587800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr10:28580600-28591000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:28581000-28582200	Weak transcription	Placenta	Placenta
33	chr10:28581000-28583800	Weak transcription	Lung	lung
34	chr10:28581000-28583800	Weak transcription	Pancreas	Pancrea
35	chr10:28581200-28582000	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr10:28581200-28582000	Weak transcription	HSMMtube	muscle
37	chr10:28581200-28582200	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr10:28581200-28582400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr10:28581200-28582400	Weak transcription	Aorta	Aorta
40	chr10:28581200-28582400	Weak transcription	Right Atrium	heart
41	chr10:28581200-28584400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:28581200-28584600	Weak transcription	Psoas Muscle	Psoas
43	chr10:28581200-28590200	Weak transcription	Fetal Heart	heart
44	chr10:28581400-28581800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr10:28581400-28582200	Enhancers	Muscle Satellite Cultured Cells	--
46	chr10:28581400-28582800	Weak transcription	Stomach Smooth Muscle	stomach
47	chr10:28581400-28583200	Weak transcription	Colon Smooth Muscle	Colon
48	chr10:28581400-28584000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr10:28581600-28582000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr10:28581600-28583600	Weak transcription	Rectal Smooth Muscle	rectum

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