Variant report

Variant	rs652067
Chromosome Location	chr11:121360169-121360170
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	chr11:121358992..121360735-chr11:121362875..121365300,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs12798073	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1784927	0.85[CEU][hapmap]
rs1784934	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs523917	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs550469	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs560573	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593769	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs596437	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs599161	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs624310	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs633197	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs641120	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs645275	0.82[JPT][hapmap]
rs656338	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs662821	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs668387	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs676759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs681970	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs687228	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs689021	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs693855	0.90[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs923892	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898427	chr11:121299288-121411041	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv522474	chr11:121356968-121436270	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv975233	chr11:121359656-121574786	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:121349800-121365000	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr11:121349800-121393000	Weak transcription	Colonic Mucosa	Colon
3	chr11:121350000-121401400	Weak transcription	Fetal Brain Male	brain
4	chr11:121350200-121367800	Weak transcription	Fetal Kidney	kidney
5	chr11:121350400-121393200	Weak transcription	Gastric	stomach
6	chr11:121350800-121368400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:121351200-121366600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:121351400-121384600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:121352800-121377600	Strong transcription	HepG2	liver
10	chr11:121353600-121364400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:121353600-121367200	Weak transcription	Fetal Lung	lung
12	chr11:121353600-121377000	Weak transcription	Pancreas	Pancrea
13	chr11:121353800-121365000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:121353800-121365000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:121353800-121374200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:121354200-121365000	Weak transcription	HMEC	breast
17	chr11:121354400-121364000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr11:121354400-121364600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr11:121354400-121365000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr11:121354600-121363000	Strong transcription	Liver	Liver
21	chr11:121354600-121365000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr11:121354800-121360600	Strong transcription	GM12878-XiMat	blood
23	chr11:121355000-121364200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr11:121355200-121362600	Strong transcription	Fetal Thymus	thymus
25	chr11:121355200-121363000	Strong transcription	Dnd41	blood
26	chr11:121355200-121364400	Strong transcription	Primary T cells from cord blood	blood
27	chr11:121355400-121364600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:121355600-121360800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr11:121355600-121362000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr11:121355600-121363400	Strong transcription	Fetal Intestine Large	intestine
31	chr11:121355600-121365000	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr11:121355800-121361000	Strong transcription	Primary B cells from cord blood	blood
33	chr11:121355800-121362000	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr11:121355800-121362600	Strong transcription	Primary hematopoietic stem cells	blood
35	chr11:121355800-121364000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr11:121356000-121362800	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr11:121356000-121363000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:121356000-121364000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:121356000-121365000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr11:121356400-121360800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr11:121356600-121362800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr11:121356600-121363200	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr11:121357600-121361000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr11:121357600-121361000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr11:121357600-121362200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:121357600-121362400	Strong transcription	Fetal Brain Female	brain
47	chr11:121357600-121362400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr11:121357600-121363000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr11:121357800-121363000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr11:121357800-121363800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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