Variant report

Variant	rs10115879
Chromosome Location	chr9:108100179-108100180
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108100023..108102655-chr9:108105720..108107994,2	MCF-7	breast:
2	chr9:108098361..108100329-chr9:108109945..108112298,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10081709	1.00[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10115833	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10116656	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11506819	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12339205	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12348983	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12350341	0.81[YRI][hapmap]
rs13289885	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13297419	1.00[EUR][1000 genomes]
rs13298325	1.00[EUR][1000 genomes]
rs13299711	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16924487	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16924552	0.83[YRI][hapmap]
rs28545469	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34253461	1.00[EUR][1000 genomes]
rs34350840	1.00[EUR][1000 genomes]
rs35111325	1.00[EUR][1000 genomes]
rs35275407	1.00[EUR][1000 genomes]
rs35322610	1.00[EUR][1000 genomes]
rs35533765	1.00[EUR][1000 genomes]
rs60502553	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479309	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67844420	1.00[EUR][1000 genomes]
rs7034136	1.00[CEU][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7034666	0.81[YRI][hapmap]
rs7040751	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7048586	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71494522	0.88[EUR][1000 genomes]
rs71494524	1.00[EUR][1000 genomes]
rs71494526	1.00[EUR][1000 genomes]
rs71494527	1.00[EUR][1000 genomes]
rs7856033	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7856524	1.00[CEU][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7860321	1.00[CEU][hapmap];0.83[YRI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7870687	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7871855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299385	1.00[CEU][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299386	1.00[CEU][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9299387	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9632901	1.00[CEU][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108055600-108151200	Weak transcription	Esophagus	oesophagus
2	chr9:108062400-108104600	Weak transcription	Right Ventricle	heart
3	chr9:108069000-108104000	Weak transcription	Fetal Heart	heart
4	chr9:108078400-108101800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:108081000-108123000	Weak transcription	Primary B cells from cord blood	blood
6	chr9:108090800-108108600	Weak transcription	Brain Germinal Matrix	brain
7	chr9:108091600-108103800	Weak transcription	Thymus	Thymus
8	chr9:108091600-108150400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:108091800-108101400	Weak transcription	NHEK	skin
10	chr9:108092000-108101000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr9:108092000-108124000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:108092000-108148000	Weak transcription	Psoas Muscle	Psoas
13	chr9:108092200-108104200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:108093200-108108400	Weak transcription	Fetal Brain Female	brain
15	chr9:108093200-108123200	Weak transcription	Colonic Mucosa	Colon
16	chr9:108093200-108149800	Weak transcription	HUVEC	blood vessel
17	chr9:108093600-108102000	Weak transcription	A549	lung
18	chr9:108095000-108102000	Weak transcription	GM12878-XiMat	blood
19	chr9:108095400-108104200	Weak transcription	NHLF	lung
20	chr9:108095600-108122200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:108096400-108102000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr9:108096400-108102600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:108096400-108131800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr9:108096600-108104600	Weak transcription	Gastric	stomach
26	chr9:108097000-108103800	Weak transcription	Fetal Intestine Small	intestine
27	chr9:108097000-108103800	Weak transcription	Stomach Mucosa	stomach
28	chr9:108097000-108103800	Weak transcription	NHDF-Ad	bronchial
29	chr9:108097000-108104000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr9:108097000-108104400	Weak transcription	Small Intestine	intestine
31	chr9:108097000-108122800	Weak transcription	Fetal Kidney	kidney
32	chr9:108097200-108104200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr9:108097200-108124600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:108097400-108133600	Weak transcription	Placenta	Placenta
35	chr9:108097600-108101000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr9:108097600-108102200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:108097600-108147000	Weak transcription	HMEC	breast
38	chr9:108097800-108100200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:108097800-108100200	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr9:108097800-108100600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr9:108097800-108100600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr9:108097800-108101000	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:108097800-108101000	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr9:108097800-108101400	Strong transcription	Liver	Liver
45	chr9:108097800-108102000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr9:108097800-108108400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:108098400-108100200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr9:108098400-108101800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:108098400-108102000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:108098600-108100200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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