Variant report

Variant	rs58589975
Chromosome Location	chr9:2657258-2657259
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs2054073	0.84[EUR][1000 genomes]
rs2063570	0.91[EUR][1000 genomes]
rs2063571	0.91[EUR][1000 genomes]
rs2063572	0.91[EUR][1000 genomes]
rs34003761	1.00[EUR][1000 genomes]
rs34067270	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3421	0.91[EUR][1000 genomes]
rs34458671	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34811022	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35774247	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56020844	0.91[EUR][1000 genomes]
rs58045872	1.00[EUR][1000 genomes]
rs59546407	0.91[EUR][1000 genomes]
rs59816438	1.00[EUR][1000 genomes]
rs7034291	0.87[EUR][1000 genomes]
rs7043836	1.00[EUR][1000 genomes]
rs7043949	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73640160	0.87[EUR][1000 genomes]
rs73640161	0.87[EUR][1000 genomes]
rs73640162	0.87[EUR][1000 genomes]
rs73640163	0.87[EUR][1000 genomes]
rs73640164	0.91[EUR][1000 genomes]
rs7870478	0.91[EUR][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:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2635800-2657800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:2640000-2662200	Weak transcription	Right Atrium	heart
3	chr9:2641400-2668400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:2643600-2657600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:2643800-2664000	Weak transcription	Spleen	Spleen
6	chr9:2643800-2666800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:2644000-2667200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:2648400-2658200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:2649200-2664800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:2649600-2657600	Weak transcription	Gastric	stomach
11	chr9:2653000-2666600	Weak transcription	Fetal Stomach	stomach
12	chr9:2653200-2659400	Weak transcription	Aorta	Aorta
13	chr9:2653200-2660200	Weak transcription	Psoas Muscle	Psoas
14	chr9:2653600-2662800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:2653600-2664000	Weak transcription	Esophagus	oesophagus
16	chr9:2653800-2663600	Weak transcription	Brain Angular Gyrus	brain
17	chr9:2653800-2663800	Weak transcription	Right Ventricle	heart
18	chr9:2654000-2662200	Weak transcription	Brain Substantia Nigra	brain
19	chr9:2654200-2657400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:2654200-2660200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr9:2654200-2666800	Weak transcription	Lung	lung
22	chr9:2654400-2663400	Weak transcription	Fetal Brain Male	brain
23	chr9:2654600-2657800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:2654800-2657400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:2654800-2657800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr9:2655000-2660000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:2655200-2657600	Weak transcription	Left Ventricle	heart
28	chr9:2655200-2657800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr9:2655200-2664400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:2655600-2657400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr9:2655600-2657400	Enhancers	Dnd41	blood
32	chr9:2655600-2661600	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr9:2655600-2662000	Weak transcription	Brain Hippocampus Middle	brain
34	chr9:2655600-2662800	Weak transcription	Brain Anterior Caudate	brain
35	chr9:2655600-2664200	Weak transcription	Ovary	ovary
36	chr9:2655600-2664600	Weak transcription	Fetal Brain Female	brain
37	chr9:2655800-2657400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr9:2655800-2657600	Weak transcription	Fetal Lung	lung
39	chr9:2655800-2659200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:2655800-2660600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:2655800-2661200	Weak transcription	HSMMtube	muscle
42	chr9:2655800-2662000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:2655800-2662200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:2655800-2663200	Weak transcription	Adipose Nuclei	Adipose
45	chr9:2655800-2664000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr9:2656000-2657600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:2656000-2659600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr9:2656000-2660200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr9:2656000-2660400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:2656000-2660400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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