Variant report

Variant	rs9869999
Chromosome Location	chr3:17717340-17717341
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10510477	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11128837	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11128839	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11128841	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11128844	0.83[ASN][1000 genomes]
rs11128848	1.00[ASN][1000 genomes]
rs11719266	0.83[ASN][1000 genomes]
rs11929111	1.00[ASN][1000 genomes]
rs12487916	0.83[ASN][1000 genomes]
rs12497320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12632570	1.00[ASN][1000 genomes]
rs13061771	1.00[ASN][1000 genomes]
rs13065637	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13071934	1.00[ASN][1000 genomes]
rs13085167	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13085441	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13095571	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13097908	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13321297	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17273111	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2033379	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2337387	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34297417	1.00[ASN][1000 genomes]
rs34487714	1.00[ASN][1000 genomes]
rs35642812	1.00[ASN][1000 genomes]
rs35697509	1.00[ASN][1000 genomes]
rs4128509	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4243835	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4243836	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4243838	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4435674	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4470554	1.00[ASN][1000 genomes]
rs4482690	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4484221	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4513482	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4566567	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4566568	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4568172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4589965	1.00[ASN][1000 genomes]
rs4602424	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4908939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4908940	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4908964	1.00[ASN][1000 genomes]
rs4908966	1.00[ASN][1000 genomes]
rs4908973	1.00[ASN][1000 genomes]
rs4908987	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4909009	1.00[ASN][1000 genomes]
rs4909010	1.00[ASN][1000 genomes]
rs4909012	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5014632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs57309958	1.00[ASN][1000 genomes]
rs61081795	1.00[ASN][1000 genomes]
rs6577597	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6577616	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6577617	1.00[ASN][1000 genomes]
rs6577619	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6577622	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6577643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6577644	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6768637	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6779834	1.00[ASN][1000 genomes]
rs6788763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6792422	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6795189	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6797952	1.00[ASN][1000 genomes]
rs6809062	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6809775	1.00[ASN][1000 genomes]
rs6810235	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7427588	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7630695	1.00[ASN][1000 genomes]
rs7632240	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7633601	1.00[ASN][1000 genomes]
rs7642860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7647914	1.00[ASN][1000 genomes]
rs7647928	1.00[ASN][1000 genomes]
rs7652156	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8179983	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9310523	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9681232	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9812199	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9812906	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9821955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9847461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9853571	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9855515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9857910	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9880456	1.00[ASN][1000 genomes]
rs9881850	1.00[CHB][hapmap]
rs9985472	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999460	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv536510	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv1849856	chr3:17646794-17748688	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1828838	chr3:17646794-17757960	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv999594	chr3:17690416-17982318	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17694400-17721800	Weak transcription	A549	lung
2	chr3:17702200-17718400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:17702200-17719000	Weak transcription	Dnd41	blood
4	chr3:17707000-17734800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr3:17709200-17723200	Weak transcription	Aorta	Aorta
6	chr3:17709200-17732000	Weak transcription	Psoas Muscle	Psoas
7	chr3:17709600-17725800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:17710800-17719800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:17711400-17755000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr3:17712600-17732600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:17712800-17719600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:17712800-17719800	Weak transcription	HUVEC	blood vessel
13	chr3:17713400-17723200	Weak transcription	Primary B cells from cord blood	blood
14	chr3:17714400-17719600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:17714400-17719600	Weak transcription	NHDF-Ad	bronchial
16	chr3:17714400-17719800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:17714400-17725200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:17714600-17724800	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:17715000-17719800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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