Variant report

Variant	rs20514
Chromosome Location	chr9:8362230-8362231
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10511493	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10976946	0.81[CHB][hapmap]
rs12552493	0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap]
rs12554953	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12555585	0.94[CHB][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs12682697	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12682993	0.93[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs12684395	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1500315	0.85[CHB][hapmap]
rs16927547	0.86[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.93[TSI][hapmap]
rs3739578	0.93[CEU][hapmap];0.81[CHB][hapmap]
rs3780336	0.86[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs3847288	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs3847291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs4742486	0.90[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742487	0.81[CHB][hapmap]
rs60965360	0.82[ASN][1000 genomes]
rs72691027	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72691034	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72691035	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7848626	0.81[CHB][hapmap]
rs7848705	0.93[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs7848818	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7873084	0.86[CEU][hapmap]

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:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:8330200-8364200	Weak transcription	Brain Anterior Caudate	brain
2	chr9:8339600-8364400	Weak transcription	Brain Germinal Matrix	brain
3	chr9:8339600-8397600	Weak transcription	Fetal Muscle Leg	muscle
4	chr9:8340200-8366400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr9:8340400-8364600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr9:8340800-8364400	Weak transcription	Fetal Brain Female	brain
7	chr9:8341800-8372600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:8350000-8363800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr9:8350200-8364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr9:8350200-8372400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr9:8350400-8363200	Weak transcription	Brain Hippocampus Middle	brain
12	chr9:8350400-8364000	Weak transcription	Fetal Heart	heart
13	chr9:8353200-8364200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:8357200-8364200	Weak transcription	Fetal Lung	lung
15	chr9:8357200-8374200	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:8357600-8381800	Weak transcription	Aorta	Aorta
17	chr9:8358600-8366800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:8360800-8362600	Enhancers	Fetal Intestine Small	intestine
19	chr9:8361000-8362600	Enhancers	Fetal Intestine Large	intestine
20	chr9:8361400-8364400	Weak transcription	HUVEC	blood vessel
21	chr9:8361400-8401600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr9:8362200-8366600	Weak transcription	Stomach Mucosa	stomach

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