Variant report

Variant	rs11789583
Chromosome Location	chr9:2644954-2644955
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11788728	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11790283	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11791537	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793899	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11793901	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13283954	1.00[ASN][1000 genomes]
rs1567712	1.00[ASN][1000 genomes]
rs17656379	1.00[ASN][1000 genomes]
rs17712698	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869593	1.00[ASN][1000 genomes]
rs1947447	1.00[ASN][1000 genomes]
rs2889261	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33955077	1.00[ASN][1000 genomes]
rs33984475	1.00[ASN][1000 genomes]
rs34318472	1.00[ASN][1000 genomes]
rs34562568	1.00[ASN][1000 genomes]
rs35033160	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35043989	1.00[ASN][1000 genomes]
rs35075133	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35456336	1.00[ASN][1000 genomes]
rs35730767	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35769682	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35847091	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36036004	1.00[ASN][1000 genomes]
rs6144	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6145	1.00[ASN][1000 genomes]
rs6148	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475888	0.87[CEU][hapmap];1.00[ASN][1000 genomes]
rs7030221	1.00[ASN][1000 genomes]
rs7040916	1.00[ASN][1000 genomes]
rs7045124	1.00[ASN][1000 genomes]
rs7045363	1.00[ASN][1000 genomes]
rs72692565	1.00[ASN][1000 genomes]
rs72692571	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692574	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72692579	1.00[ASN][1000 genomes]
rs72692580	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72694628	1.00[ASN][1000 genomes]
rs8210	0.86[CEU][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970122	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970123	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[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	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv916750	chr9:2430846-2826706	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv531564	chr9:2452325-2700375	Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1017581	chr9:2494815-3172020	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	nsv539934	chr9:2494815-3172020	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 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	chr9:2627200-2648400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:2633200-2646000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr9:2633600-2656600	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:2634000-2645000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:2634200-2645400	Weak transcription	HSMMtube	muscle
6	chr9:2634400-2648200	Weak transcription	Placenta	Placenta
7	chr9:2635000-2652600	Strong transcription	Dnd41	blood
8	chr9:2635200-2655000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr9:2635200-2656200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:2635400-2656000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:2635400-2656800	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:2635400-2656800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:2635600-2647600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr9:2635600-2655000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr9:2635800-2656000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:2635800-2657800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:2637400-2654400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:2638000-2654400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:2638000-2656400	Strong transcription	Fetal Muscle Trunk	muscle
20	chr9:2638400-2655800	Strong transcription	Fetal Lung	lung
21	chr9:2638400-2656400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:2638600-2653600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:2638600-2655400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:2638600-2655800	Strong transcription	Stomach Smooth Muscle	stomach
25	chr9:2638800-2656000	Strong transcription	Fetal Muscle Leg	muscle
26	chr9:2639000-2650800	Weak transcription	HSMM	muscle
27	chr9:2639000-2655800	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr9:2639200-2655200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr9:2639400-2646600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:2639600-2645000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:2639600-2654800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr9:2639800-2654200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:2639800-2655200	Strong transcription	Brain Cingulate Gyrus	brain
34	chr9:2639800-2656000	Strong transcription	H9 Cell Line	embryonic stem cell
35	chr9:2639800-2656000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr9:2640000-2650800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:2640000-2655000	Strong transcription	Left Ventricle	heart
38	chr9:2640000-2655600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:2640000-2655600	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:2640000-2662200	Weak transcription	Right Atrium	heart
41	chr9:2640200-2645200	Weak transcription	Fetal Intestine Large	intestine
42	chr9:2640200-2653800	Strong transcription	Brain Anterior Caudate	brain
43	chr9:2640200-2654200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr9:2640200-2655400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr9:2640200-2656200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:2640800-2655800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr9:2640800-2655800	Strong transcription	Adipose Nuclei	Adipose
48	chr9:2641000-2653800	Weak transcription	HepG2	liver
49	chr9:2641000-2655600	Strong transcription	Brain Hippocampus Middle	brain
50	chr9:2641200-2654000	Strong transcription	Fetal Kidney	kidney

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