Variant report

Variant	rs11790230
Chromosome Location	chr9:104336721-104336722
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	chr9:104332562..104334673-chr9:104335549..104338409,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10512282	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11788114	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11789610	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11790317	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11790832	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11791337	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11793752	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11793946	0.81[AFR][1000 genomes]
rs1323432	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16920443	0.85[CEU][hapmap];0.93[EUR][1000 genomes]
rs16920462	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17188758	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35681249	0.86[EUR][1000 genomes]
rs57596144	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59782949	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61051202	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61396182	0.93[EUR][1000 genomes]
rs61685305	0.93[EUR][1000 genomes]
rs62575808	0.87[EUR][1000 genomes]
rs62575815	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575836	0.81[AFR][1000 genomes]
rs62575837	0.81[AFR][1000 genomes]
rs62575839	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62575842	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62575844	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575845	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62575846	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575847	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575848	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62575849	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62575850	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62575851	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62575852	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62577397	0.87[EUR][1000 genomes]
rs66786600	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs67248872	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7045287	1.00[CEU][hapmap]
rs72745305	0.81[AFR][1000 genomes]
rs7859863	0.91[AFR][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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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 target site	15 gene(s)	inside rSNPs	diseases
2	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking 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 target site	14 gene(s)	inside rSNPs	diseases
3	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104296800-104337400	Weak transcription	Stomach Mucosa	stomach
2	chr9:104325200-104344400	Weak transcription	NHLF	lung
3	chr9:104325200-104350000	Weak transcription	HSMMtube	muscle
4	chr9:104326800-104337000	Weak transcription	Esophagus	oesophagus
5	chr9:104327000-104338400	Weak transcription	Gastric	stomach
6	chr9:104327000-104344600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:104327400-104339600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:104327400-104348400	Weak transcription	Aorta	Aorta
9	chr9:104327600-104337000	Weak transcription	Pancreas	Pancrea
10	chr9:104327600-104337600	Weak transcription	HepG2	liver
11	chr9:104327600-104344400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:104327800-104338400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:104327800-104344400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr9:104328000-104342200	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:104328400-104340600	Weak transcription	GM12878-XiMat	blood
16	chr9:104329000-104338800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr9:104329400-104337400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr9:104329400-104337800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr9:104329400-104338200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr9:104330200-104338600	Weak transcription	Colonic Mucosa	Colon
21	chr9:104330400-104337400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:104331800-104337000	Weak transcription	Left Ventricle	heart
23	chr9:104331800-104337200	Weak transcription	Brain Angular Gyrus	brain
24	chr9:104331800-104337400	Enhancers	Primary T cells fromperipheralblood	blood
25	chr9:104331800-104344600	Weak transcription	HSMM	muscle
26	chr9:104332400-104338800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr9:104332400-104344600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:104332800-104340600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr9:104333000-104337200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr9:104333000-104340600	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr9:104333000-104342200	Weak transcription	Spleen	Spleen
32	chr9:104333000-104342400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr9:104333000-104344400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr9:104333000-104344400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:104333000-104344800	Weak transcription	A549	lung
36	chr9:104333200-104337000	Weak transcription	Liver	Liver
37	chr9:104333200-104337200	Weak transcription	Adipose Nuclei	Adipose
38	chr9:104333400-104337000	Weak transcription	Lung	lung
39	chr9:104333400-104337200	Weak transcription	Right Atrium	heart
40	chr9:104333400-104337400	Enhancers	Primary T cells from cord blood	blood
41	chr9:104333400-104340000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr9:104333400-104340600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr9:104333400-104340800	Weak transcription	Primary B cells from cord blood	blood
44	chr9:104333400-104342400	Weak transcription	Fetal Stomach	stomach
45	chr9:104335200-104340600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:104335200-104344600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr9:104335400-104340600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:104335400-104344600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr9:104335400-104344800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr9:104335600-104340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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