Variant report

Variant	rs11006995
Chromosome Location	chr10:28585496-28585497
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	chr10:28580424..28583414-chr10:28585033..28588040,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150054	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10763655	0.82[JPT][hapmap]
rs10763656	0.87[ASN][1000 genomes]
rs10763657	0.93[ASN][1000 genomes]
rs10826445	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10826446	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006913	0.84[MEX][hapmap]
rs11006923	0.90[AMR][1000 genomes]
rs11006927	0.86[AMR][1000 genomes]
rs11006928	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs11006933	0.90[AMR][1000 genomes]
rs11006937	0.91[MEX][hapmap]
rs11006939	0.86[AMR][1000 genomes]
rs11006947	0.86[AMR][1000 genomes]
rs11006950	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11006954	0.93[AMR][1000 genomes]
rs11006958	1.00[MEX][hapmap];0.90[AMR][1000 genomes]
rs11006960	0.93[AMR][1000 genomes]
rs11006989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006990	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11006992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006993	0.83[CHB][hapmap];0.94[YRI][hapmap]
rs11006994	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11006997	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11006998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11006999	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11007000	0.98[AMR][1000 genomes]
rs11007003	0.87[CHB][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes]
rs11007004	0.81[AMR][1000 genomes]
rs11007006	0.83[AMR][1000 genomes]
rs11007010	0.85[ASN][1000 genomes]
rs1148175	0.87[JPT][hapmap]
rs12218186	0.82[ASN][1000 genomes]
rs12218294	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12570440	0.95[AMR][1000 genomes]
rs1984853	0.83[AMR][1000 genomes]
rs2368306	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs35016093	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs3842931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3843586	0.86[ASN][1000 genomes]
rs3847386	0.91[ASN][1000 genomes]
rs3847387	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4317882	0.84[MEX][hapmap]
rs4506531	0.84[MEX][hapmap]
rs4598572	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs4604776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57441879	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7901835	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7902785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7903242	0.83[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7915405	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7916067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916711	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7916740	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:28571800-28587800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr10:28573800-28587400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr10:28579000-28588400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr10:28580000-28590400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr10:28580600-28587800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr10:28580600-28591000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr10:28581200-28590200	Weak transcription	Fetal Heart	heart
8	chr10:28581800-28590600	Weak transcription	HMEC	breast
9	chr10:28582000-28586400	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr10:28582200-28590800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr10:28582400-28590600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr10:28582600-28586200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr10:28582600-28586400	Enhancers	Primary T cells from cord blood	blood
14	chr10:28583000-28585600	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr10:28583000-28585800	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr10:28583000-28586200	Enhancers	HepG2	liver
17	chr10:28583000-28589000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr10:28583000-28590600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr10:28583200-28586200	Enhancers	Colon Smooth Muscle	Colon
20	chr10:28583200-28590800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr10:28583400-28585600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr10:28583400-28585600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr10:28583600-28586200	Enhancers	Rectal Smooth Muscle	rectum
24	chr10:28583800-28585600	Enhancers	Fetal Stomach	stomach
25	chr10:28583800-28585600	Enhancers	Ovary	ovary
26	chr10:28583800-28585600	Enhancers	HSMMtube	muscle
27	chr10:28584000-28585600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr10:28584000-28588000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr10:28584200-28585600	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr10:28584200-28586000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr10:28584200-28587600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr10:28584200-28589400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr10:28584400-28585600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr10:28584400-28585600	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr10:28584400-28590600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr10:28584600-28585600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:28584600-28585600	Enhancers	Fetal Intestine Small	intestine
38	chr10:28584800-28591000	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr10:28585000-28585600	Bivalent/Poised TSS	Fetal Brain Male	brain
40	chr10:28585000-28585600	Enhancers	Stomach Mucosa	stomach
41	chr10:28585000-28586200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr10:28585000-28590600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr10:28585200-28585600	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr10:28585200-28587600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr10:28585200-28590200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr10:28585200-28590400	Weak transcription	Aorta	Aorta
47	chr10:28585400-28585600	Enhancers	Fetal Intestine Large	intestine
48	chr10:28585400-28585600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr10:28585400-28586000	Weak transcription	Gastric	stomach
50	chr10:28585400-28587800	Weak transcription	Small Intestine	intestine

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