Variant report

Variant	rs1234515
Chromosome Location	chr11:48006060-48006061
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	chr11:48003107..48006285-chr11:48013442..48016525,3	MCF-7	breast:
2	chr11:48005352..48007583-chr11:48007983..48010458,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12275829	1.00[EUR][1000 genomes]
rs1228017	1.00[EUR][1000 genomes]
rs1228028	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs1228031	0.82[ASW][hapmap]
rs1228043	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1228050	1.00[MEX][hapmap]
rs12282774	1.00[MEX][hapmap]
rs12295233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1238706	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs13328902	1.00[MEX][hapmap]
rs1630025	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1681612	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1681625	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs1681626	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1729288	0.82[ASW][hapmap];1.00[MEX][hapmap]
rs2626565	0.85[AMR][1000 genomes]
rs7125276	1.00[MEX][hapmap]
rs7129454	1.00[MEX][hapmap]
rs7130715	1.00[MEX][hapmap]
rs900696	1.00[MEX][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv897326	chr11:47891334-48035474	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1036451	chr11:47902321-48616646	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv541037	chr11:47902321-48616646	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1047490	chr11:47916708-48388686	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1044266	chr11:47929586-48276132	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv541038	chr11:47929586-48276132	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv1053145	chr11:47967902-48086950	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv870381	chr11:47989434-48142648	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
12	esv3396029	chr11:47993857-48241494	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv317	chr11:47995903-48007266	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv528641	chr11:48004369-48043053	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv897327	chr11:48004369-48911660	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:48003800-48006200	Enhancers	Duodenum Smooth Muscle	Duodenum
2	chr11:48003800-48007800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr11:48003800-48008400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr11:48003800-48009000	Weak transcription	Left Ventricle	heart
5	chr11:48003800-48009000	Weak transcription	Right Atrium	heart
6	chr11:48003800-48009000	Weak transcription	Right Ventricle	heart
7	chr11:48003800-48012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr11:48003800-48012800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:48003800-48012800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:48003800-48012800	Weak transcription	Lung	lung
11	chr11:48004000-48006200	Enhancers	Brain Anterior Caudate	brain
12	chr11:48004000-48007400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr11:48004000-48007600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr11:48004000-48007600	Weak transcription	Pancreas	Pancrea
15	chr11:48004000-48007600	Weak transcription	Spleen	Spleen
16	chr11:48004000-48007800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr11:48004000-48008200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:48004000-48008400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr11:48004000-48008600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:48004000-48009200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:48004000-48009200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:48004000-48012600	Weak transcription	Stomach Smooth Muscle	stomach
23	chr11:48004000-48012800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr11:48004000-48013000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:48004000-48013000	Weak transcription	Gastric	stomach
26	chr11:48004000-48013000	Weak transcription	HSMM	muscle
27	chr11:48004000-48014600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr11:48004400-48006200	Flanking Active TSS	GM12878-XiMat	blood
29	chr11:48004600-48006200	Transcr. at gene 5' and 3'	A549	lung
30	chr11:48004600-48009000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr11:48004600-48009000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:48004800-48006200	Enhancers	Primary T cells from cord blood	blood
33	chr11:48004800-48007800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr11:48004800-48007800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:48004800-48009000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr11:48004800-48009000	Enhancers	Stomach Mucosa	stomach
37	chr11:48005000-48011400	Weak transcription	Adipose Nuclei	Adipose
38	chr11:48005200-48007600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr11:48005200-48009000	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr11:48005200-48009200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr11:48005200-48009200	Weak transcription	HSMMtube	muscle
42	chr11:48005200-48009600	Enhancers	Primary T cells fromperipheralblood	blood
43	chr11:48005200-48012600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr11:48005200-48012600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr11:48005400-48006200	Enhancers	Colonic Mucosa	Colon
46	chr11:48005400-48007600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr11:48005400-48007600	Weak transcription	HUVEC	blood vessel
48	chr11:48005400-48009000	Weak transcription	Small Intestine	intestine
49	chr11:48005600-48006200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:48005600-48007000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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