Variant report

Variant	rs10962886
Chromosome Location	chr9:17164433-17164434
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10511633	0.81[EUR][1000 genomes]
rs10810738	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10962897	0.93[EUR][1000 genomes]
rs10962898	0.93[EUR][1000 genomes]
rs10962904	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10962917	0.85[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.87[ASN][1000 genomes]
rs11562136	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12003380	0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1576957	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1576960	0.82[CEU][hapmap]
rs1930594	0.92[EUR][1000 genomes]
rs2183502	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2210539	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2774626	0.81[CEU][hapmap]
rs2779761	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs2779767	0.82[EUR][1000 genomes]
rs2779768	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2779769	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2779772	0.81[CEU][hapmap]
rs2815174	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2815176	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2815179	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2815180	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2815183	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2815184	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3122360	0.81[EUR][1000 genomes]
rs4272490	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4458955	0.85[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4961531	0.95[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs59047675	0.81[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6475113	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs6475121	0.86[ASN][1000 genomes]
rs7028249	0.92[EUR][1000 genomes]
rs7034418	0.93[EUR][1000 genomes]
rs7039814	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7048983	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7854322	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7862706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7862811	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7870682	0.81[JPT][hapmap]
rs9407787	0.81[EUR][1000 genomes]
rs9407788	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv892657	chr9:17008137-17223492	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv1023525	chr9:17121773-17236072	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv892659	chr9:17130360-17236376	Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
9	nsv428537	chr9:17146369-17308494	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17146200-17167200	Weak transcription	Gastric	stomach
2	chr9:17148800-17167400	Weak transcription	Dnd41	blood
3	chr9:17149400-17167400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:17155400-17169400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr9:17155600-17169200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr9:17155800-17167400	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr9:17156000-17169000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr9:17156000-17171400	Weak transcription	Liver	Liver
9	chr9:17156200-17165600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr9:17156200-17165800	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:17156200-17166200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:17156200-17167400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:17156200-17168800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:17156200-17168800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:17156200-17169000	Weak transcription	Left Ventricle	heart
16	chr9:17156200-17171400	Weak transcription	Ovary	ovary
17	chr9:17156200-17171400	Weak transcription	Pancreas	Pancrea
18	chr9:17156200-17171600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:17156200-17177400	Weak transcription	Fetal Stomach	stomach
20	chr9:17156200-17178200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:17156200-17178800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:17156400-17169000	Weak transcription	Fetal Lung	lung
23	chr9:17157800-17169000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr9:17158000-17167400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:17159800-17195600	Weak transcription	Aorta	Aorta
26	chr9:17163600-17167000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:17164200-17165600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr9:17164400-17165400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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