Variant report

Variant	rs10976999
Chromosome Location	chr9:8366231-8366232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10115782	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10125894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10758962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815824	0.84[ASN][1000 genomes]
rs10815825	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10815835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10976971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10976972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10976973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs10976977	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs10976979	0.84[ASN][1000 genomes]
rs10976982	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs10976984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10976994	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10976995	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976996	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes]
rs10976997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10976998	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977012	1.00[ASN][1000 genomes]
rs10977013	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10977015	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11999568	0.83[YRI][hapmap]
rs12004779	0.83[YRI][hapmap]
rs12057000	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12236853	0.81[ASN][1000 genomes]
rs12349797	1.00[CEU][hapmap]
rs16924677	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs2202012	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736380	0.84[ASN][1000 genomes]
rs3847286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs73643611	0.84[ASN][1000 genomes]
rs7859123	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7868317	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7874090	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7875563	0.90[CEU][hapmap];0.92[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	nsv8414	chr9:7827373-8511613	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1031472	chr9:8250901-8712547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv892225	chr9:8345072-8379313	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv1022796	chr9:8360729-9110046	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
2	chr9:8340200-8366400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:8341800-8372600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:8350200-8372400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr9:8357200-8374200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:8357600-8381800	Weak transcription	Aorta	Aorta
7	chr9:8358600-8366800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:8362200-8366600	Weak transcription	Stomach Mucosa	stomach
10	chr9:8364400-8366400	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr9:8364400-8366600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:8364400-8366800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:8364400-8366800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr9:8364400-8367200	Enhancers	Dnd41	blood
15	chr9:8364600-8366800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:8364600-8367000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:8364600-8367000	Enhancers	NH-A	brain
18	chr9:8364600-8367200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:8364600-8370400	Weak transcription	Fetal Lung	lung
20	chr9:8364600-8382200	Weak transcription	Ovary	ovary
21	chr9:8364800-8367000	Enhancers	HSMM	muscle
22	chr9:8364800-8367200	Enhancers	Osteobl	bone
23	chr9:8364800-8368200	Weak transcription	Lung	lung
24	chr9:8364800-8376000	Weak transcription	Fetal Brain Male	brain
25	chr9:8364800-8377200	Weak transcription	Fetal Brain Female	brain
26	chr9:8364800-8401600	Weak transcription	Brain Germinal Matrix	brain
27	chr9:8365000-8366800	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:8365000-8367200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:8365000-8395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:8365200-8367000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr9:8365200-8367000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr9:8365200-8386800	Weak transcription	Brain Anterior Caudate	brain
33	chr9:8365600-8366400	Enhancers	Fetal Thymus	thymus
34	chr9:8365600-8366800	Enhancers	NHLF	lung
35	chr9:8365600-8367600	Enhancers	HUVEC	blood vessel
36	chr9:8365600-8376600	Weak transcription	Brain Substantia Nigra	brain
37	chr9:8365600-8386200	Weak transcription	Brain Angular Gyrus	brain
38	chr9:8365600-8386200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr9:8365800-8375800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:8366000-8367000	Enhancers	Fetal Heart	heart
41	chr9:8366000-8367600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr9:8366200-8366600	Weak transcription	Brain Cingulate Gyrus	brain

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