Variant report

Variant	rs17660571
Chromosome Location	chr9:8781539-8781540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10116829	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1036329	0.90[ASN][1000 genomes]
rs10511509	0.82[EUR][1000 genomes]
rs10759013	1.00[JPT][hapmap]
rs10815942	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10815943	0.83[CEU][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815944	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10977282	0.83[CEU][hapmap]
rs10977287	0.83[CEU][hapmap]
rs10977289	0.90[ASN][1000 genomes]
rs10977295	0.90[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10977296	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10977298	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12337561	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12343337	0.92[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12350351	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1549998	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16928634	1.00[JPT][hapmap]
rs17576912	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17660536	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4606116	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62528808	0.85[ASN][1000 genomes]
rs62528809	0.85[ASN][1000 genomes]
rs62528810	0.90[ASN][1000 genomes]
rs62528832	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62528833	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62528834	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62528835	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62528836	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62528837	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62528838	0.95[ASN][1000 genomes]
rs9299073	0.82[EUR][1000 genomes]
rs9299074	0.92[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	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
2	nsv892235	chr9:8700396-8865925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1025800	chr9:8712487-9030627	Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv539980	chr9:8712487-9030627	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv892236	chr9:8745520-8870553	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv892237	chr9:8752743-8794314	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
7	nsv1015898	chr9:8753534-9011443	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv892238	chr9:8757828-8794314	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
9	nsv892239	chr9:8773599-8805462	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region	1 gene(s)	inside rSNPs	diseases
10	esv2761247	chr9:8775019-8786718	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8764800-8783600	Weak transcription	Fetal Stomach	stomach
2	chr9:8777600-8782000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:8778000-8782000	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr9:8778200-8781600	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr9:8778400-8781800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:8778400-8782000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:8778600-8781600	Weak transcription	Ovary	ovary
8	chr9:8778600-8785600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr9:8778800-8798600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr9:8779000-8781800	Enhancers	Brain Anterior Caudate	brain
11	chr9:8779000-8782000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:8779200-8781800	Enhancers	Brain Hippocampus Middle	brain
13	chr9:8779600-8781800	Enhancers	Brain Angular Gyrus	brain
14	chr9:8779600-8781800	Enhancers	Fetal Lung	lung
15	chr9:8779800-8781600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:8779800-8784000	Weak transcription	Aorta	Aorta
17	chr9:8779800-8784600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:8780000-8782000	Enhancers	Brain Cingulate Gyrus	brain
19	chr9:8780600-8781800	Enhancers	Fetal Kidney	kidney
20	chr9:8780800-8782000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr9:8780800-8782000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr9:8781000-8781600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:8781000-8781600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr9:8781000-8781800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr9:8781000-8782000	Enhancers	Liver	Liver
26	chr9:8781200-8781600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr9:8781200-8781800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:8781200-8782400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:8781200-8784800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr9:8781400-8782400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:8781400-8783600	Weak transcription	Brain Substantia Nigra	brain
32	chr9:8781400-8784200	Weak transcription	Fetal Heart	heart

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