Variant report

Variant	rs9859004
Chromosome Location	chr3:61232696-61232697
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11130821	0.89[EUR][1000 genomes]
rs11130822	0.90[EUR][1000 genomes]
rs11130826	0.93[EUR][1000 genomes]
rs11130828	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11720254	0.90[EUR][1000 genomes]
rs12492551	0.93[EUR][1000 genomes]
rs13099397	0.98[ASN][1000 genomes]
rs1470035	0.88[EUR][1000 genomes]
rs1524019	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1554599	0.91[EUR][1000 genomes]
rs17064630	0.90[EUR][1000 genomes]
rs1916800	0.90[EUR][1000 genomes]
rs1916801	0.90[EUR][1000 genomes]
rs1916802	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1949772	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1980308	0.91[EUR][1000 genomes]
rs1980309	0.91[EUR][1000 genomes]
rs1980310	0.91[EUR][1000 genomes]
rs1980311	0.90[EUR][1000 genomes]
rs2365389	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34045993	0.97[ASN][1000 genomes]
rs34515056	0.80[EUR][1000 genomes]
rs35198002	0.90[EUR][1000 genomes]
rs4296587	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4535219	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4605537	0.92[EUR][1000 genomes]
rs4688352	0.87[EUR][1000 genomes]
rs4688354	0.89[EUR][1000 genomes]
rs4688355	0.90[EUR][1000 genomes]
rs4688359	0.80[EUR][1000 genomes]
rs4688379	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6445197	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6445198	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6445199	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6445200	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6785875	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6787292	0.90[EUR][1000 genomes]
rs6787313	0.87[EUR][1000 genomes]
rs6809031	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71296711	0.93[EUR][1000 genomes]
rs7647122	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs815709	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs815710	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs815712	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs815715	0.87[EUR][1000 genomes]
rs815717	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs843812	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs863635	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9831249	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9832387	0.87[EUR][1000 genomes]
rs9832404	0.85[EUR][1000 genomes]
rs9843007	0.80[EUR][1000 genomes]
rs9844741	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846073	0.90[EUR][1000 genomes]
rs9850114	0.93[EUR][1000 genomes]
rs9855716	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9856859	0.82[EUR][1000 genomes]
rs9860681	0.86[EUR][1000 genomes]
rs9875827	0.88[EUR][1000 genomes]
rs9882800	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv532626	chr3:61159646-61388418	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1008399	chr3:61176965-61461349	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61222600-61232800	Weak transcription	Brain Angular Gyrus	brain
2	chr3:61224000-61235200	Weak transcription	K562	blood
3	chr3:61224800-61234400	Weak transcription	GM12878-XiMat	blood
4	chr3:61226000-61232800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:61226200-61232800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:61226200-61235600	Weak transcription	Left Ventricle	heart
7	chr3:61226200-61235600	Weak transcription	Right Atrium	heart
8	chr3:61226200-61235800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:61227000-61232800	Weak transcription	Ovary	ovary
10	chr3:61227000-61235600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:61227000-61235600	Weak transcription	Pancreas	Pancrea
12	chr3:61228200-61232800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:61228200-61235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:61228800-61235400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:61228800-61235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr3:61229000-61236000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:61229000-61236000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:61230600-61235400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:61230600-61236800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:61230800-61235400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr3:61230800-61235800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:61231000-61235600	Weak transcription	Fetal Heart	heart
23	chr3:61231800-61235800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr3:61232200-61233200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:61232600-61233000	Enhancers	H1 Cell Line	embryonic stem cell

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