Variant report

Variant	rs9829623
Chromosome Location	chr3:60066360-60066361
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10510827	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs13099584	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13321394	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17062206	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs2630173	0.82[JPT][hapmap]
rs2630181	0.82[JPT][hapmap]
rs2630184	0.82[JPT][hapmap]
rs2630196	0.82[JPT][hapmap]
rs2630197	0.82[JPT][hapmap]
rs2630200	0.82[JPT][hapmap]
rs2736812	0.82[JPT][hapmap]
rs34908488	0.82[ASN][1000 genomes]
rs59085701	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6788803	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs6793429	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72880845	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72880854	0.97[ASN][1000 genomes]
rs7634772	1.00[JPT][hapmap]
rs9311747	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs969561	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs9818696	0.97[EUR][1000 genomes]
rs9819602	0.97[EUR][1000 genomes]
rs9820238	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs9823026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9874674	0.82[JPT][hapmap]
rs9876422	0.83[YRI][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	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60061800-60066400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:60061800-60068400	Flanking Active TSS	Dnd41	blood
3	chr3:60062400-60066400	Weak transcription	Brain Anterior Caudate	brain
4	chr3:60062400-60066400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:60063400-60066600	Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr3:60063600-60066800	Active TSS	Primary T cells fromperipheralblood	blood
7	chr3:60063800-60066400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
8	chr3:60063800-60068000	Flanking Active TSS	Primary T cells from cord blood	blood
9	chr3:60064400-60066600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
10	chr3:60064600-60068400	Enhancers	Primary B cells from peripheral blood	blood
11	chr3:60064800-60068000	Enhancers	Primary hematopoietic stem cells	blood
12	chr3:60064800-60068000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:60065000-60067200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:60065400-60066400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr3:60065400-60066400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:60065400-60066400	Active TSS	Thymus	Thymus
17	chr3:60065600-60066600	Active TSS	Fetal Thymus	thymus
18	chr3:60065600-60066800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr3:60066000-60066600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:60066000-60067200	Enhancers	Primary B cells from cord blood	blood
21	chr3:60066000-60067800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr3:60066000-60068200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr3:60066200-60066400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
24	chr3:60066200-60066400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:60066200-60066800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:60066200-60067200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:60066200-60067200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr3:60066200-60067400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:60066200-60067400	Enhancers	Stomach Mucosa	stomach
30	chr3:60066200-60068200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood

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