Variant report

Variant	rs12340211
Chromosome Location	chr9:8531036-8531037
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10117042	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10120190	0.86[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs10123125	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10123138	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10124867	0.85[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs10511499	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10758978	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10758979	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10758980	0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10815883	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs10815896	0.86[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs10815898	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10815900	0.86[CHB][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10815905	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10815906	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10815907	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10815908	1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10977146	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs10977169	0.81[ASN][1000 genomes]
rs10977170	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs10977181	0.86[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10977189	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10977192	0.85[CHB][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10977196	0.85[AMR][1000 genomes]
rs12341045	0.82[ASN][1000 genomes]
rs12341078	0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs12344975	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12683581	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs12686431	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs17650044	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs1998513	0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs1998515	0.92[CHB][hapmap];0.83[ASN][1000 genomes]
rs2273998	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3763653	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6477313	0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][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	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
2	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
3	nsv892228	chr9:8482778-8703733	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv831504	chr9:8496277-8665773	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8420600-8557600	Weak transcription	Aorta	Aorta
2	chr9:8486200-8531600	Weak transcription	Fetal Kidney	kidney
3	chr9:8493200-8531200	Weak transcription	Fetal Brain Female	brain
4	chr9:8494200-8531200	Weak transcription	Fetal Brain Male	brain
5	chr9:8509800-8532800	Weak transcription	Brain Angular Gyrus	brain
6	chr9:8518400-8533800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr9:8518400-8534000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:8518400-8555200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:8519800-8531600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:8520000-8531200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:8522200-8531400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:8522400-8531600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:8524200-8531600	Weak transcription	Brain Substantia Nigra	brain
14	chr9:8525000-8531600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:8525000-8533200	Weak transcription	Fetal Lung	lung
16	chr9:8526200-8531800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr9:8529000-8531600	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:8529200-8531400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:8529200-8532800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr9:8530000-8534000	Enhancers	Brain Germinal Matrix	brain
21	chr9:8531000-8532600	Enhancers	Brain Anterior Caudate	brain

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