Variant report

Variant	rs11070888
Chromosome Location	chr15:52517953-52517954
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	chr15:52505827..52511235-chr15:52516876..52519875,7	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10152377	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10152383	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11070887	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635028	0.81[MKK][hapmap];0.86[TSI][hapmap]
rs12592927	0.84[TSI][hapmap]
rs12906784	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2001858	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28730328	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751609	0.82[CHB][hapmap]
rs3794553	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405492	1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6493547	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493549	0.86[TSI][hapmap]
rs7183588	1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs8042218	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042385	0.86[TSI][hapmap]
rs8043150	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats 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	27 gene(s)	inside rSNPs	diseases
3	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv904220	chr15:52485024-52526507	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv1851383	chr15:52501831-52534344	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv1537	chr15:52502246-52537067	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
2	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:52495600-52519000	Strong transcription	HepG2	liver
5	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:52500000-52519000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr15:52501600-52519000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
11	chr15:52502000-52519200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:52502000-52523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:52502400-52520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:52502600-52519000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:52503200-52519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:52505400-52526800	Weak transcription	Right Ventricle	heart
17	chr15:52505600-52525600	Weak transcription	Brain Hippocampus Middle	brain
18	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
20	chr15:52508600-52518800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr15:52508600-52519000	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr15:52509000-52519000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:52509000-52519000	Strong transcription	Duodenum Mucosa	Duodenum
24	chr15:52509000-52519200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:52509400-52537200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr15:52509800-52521800	Weak transcription	Psoas Muscle	Psoas
27	chr15:52509800-52526800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:52510600-52519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:52510600-52521000	Weak transcription	Stomach Mucosa	stomach
30	chr15:52510600-52525600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:52511200-52518400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:52512600-52524800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:52512800-52534000	Weak transcription	Colonic Mucosa	Colon
34	chr15:52513600-52518000	Strong transcription	Adipose Nuclei	Adipose
35	chr15:52513600-52519000	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr15:52513600-52519000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr15:52514000-52539400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr15:52514200-52518000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:52514200-52518600	Strong transcription	Gastric	stomach
40	chr15:52514400-52518800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr15:52514400-52525600	Weak transcription	Thymus	Thymus
42	chr15:52514600-52524600	Enhancers	Primary B cells from cord blood	blood
43	chr15:52514600-52524600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr15:52514800-52521200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:52514800-52523800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr15:52514800-52524600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr15:52515000-52520400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:52515000-52521400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:52515000-52524000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr15:52515000-52524000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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